Maldservice Manual

Service Manual
ETTAN Maldi ToF Pro MS
Valid for: Maldi Tof Pro MS
Service Manual Code No. 18-1160-04

Issued March 2004
Mats Källgren, Volker Schnieders
Contents Chapter Service Manual Ettan Maldi Tof Pro MS 18-1160-04, Rev.March2004
contents
General Information Important safety information
The design of Amersham Biosciences instruments is subject to continuous
development and improvement. Consequently, this instrument may incorporate
minor changes in detail from the information contained in this Service Manual.
Suggestions about improving or correcting this manual should be sent to:
Label located at the back of the instrument.
Amersham Biosciences
Instrument Support Department
S-751 82 UPPSALA
SWEDEN
This document is our property and shall not without our written permission be Meaning: The instrument meets the requirement of the EMC Direc-
altered, copied, used for manufacturing or communicated to any other person or tive 89/336/EEC through the harmonized standards EN
company. 50081-1 (emission) and EN 50082-1 (immunity) and
requirements of the Low Voltage Directive (LVD) 73/23/EEC
This document is written for trained Amersham Biosiensces Service personnel. through the harmonized standard EN 61010-1.
Warning: This instrument is designed according to EC regulations. Always use
original spare parts and always assemble the instrument to it's original condition,
or else the regulatory demands may not be fulfilled after servicing.
Trade marks
UNICORNTM Controller, ÄKTATMexplorer are exclusive trade marks of Amersham
Biosciences. In view of the risk of trade mark degeneration, it is respectfully
suggested that authors wishing to use these designations refer to the trade mark
status at least once in each article.
Copyright© 2002 Amersham Biosciences
contents
contents
Chapters
1. Theory of operation
2. Installation
3. Interfacing
4. Troubleshooting
5. Maintenance & Adjustments
6. Dissassembling
7. Spare parts
8. Circuit diagram / Layout
9. Appendix
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Chapter 1
Chapter Contents
1. Theory of operation
Theory of operation 1.1 Maldi Time of flight MS
1.2 The basic principles of Maldi TOF
1.3 Description of Ettan Maldi TOF system
1.3.1 Features
1.3.2 Specifications
1.3.3 The principle of operation
1.3.4 Vacuum system
1.3.5 Mechanics
1.3.6 Glossary Abreviations
Contents Chapter Service Manual Ettan Maldi Tof Pro MS 18-1160-04, Rev March 2004
contents
1. Theory of operation Schematics of a Maldi
1.1 MALDI time of flight MS

Laser
beam
Matrix Assisted Laser Desorption Ionisation
.
Time of Flight
Ion
Mass Spectrometer extraction
Drift tube
A time of flight mass spectrometer works on the principle Ionization Reflectron
chamber
of ion physics.
The instruments consists of the following:
Target
- a vacuum system with sample
- a pulsed laser
Detector
- a sample compartment
- a time of flight tube
- a beam dump
- an ion gate
- a reflectron - ion mirror
- a linear detector
- a micro chanel plate detector for reflectron mode
- a software to control and evaluate
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1.2 The basic principles of Maldi TOF
Linear detector
The Maldi Time of flight mass spectrometer seperates ions

of different masses and monitors electrical signals you´ve
got for ions at each mass.
Quadratic
A pulsed laser ionizes and desorbs the sample which is field reflectron
combined in a matrix.
The ions accelerated by high voltage to a time of flight tube,
each ion with a special velocity, which is related to the mass.
Lighter ions have a higher speed than heavier ions.
Depending on the choosen mode, Linear, to seperate ions
with higher masses, area from 4000 - 130000 m/z,
Reflectron
or Reflectron, area from 500 - 4000 m/z, the ions have to detector
pass different length of travel way.
If working Linear the ions will travel to a ETP, electron
UV Laser
muliplier, detector, in Reflectron they travel by going through High
an ion mirror, quadratric field, to a micro chanel plate Voltage
detector.
The detector signal gives a mass spectrum which is shown
in the software as a diagram where the intensity of the signal
is plotted as single or accumulated shots against
M/Z or time base.
Ions
Sample slide
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1.3 Description of Ettan Maldi Tof system
The Ettan Maldi Tof is the first generation of Mass Spectrom-

eter manufactured by APB,
which can operate in high resolution linear and reflectron
modes.
The Maldi ToF incorporates a patented Harmonic field reflec-

tron from Warwick University, England.
The Harmonic field reflectron facilitates single step

post source decay analysis, which allows identification of a
complete Post Source Decay (PSD) spectrum in one single
scan.
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1.3.1 Features
- Vacuum System as described in the Vacuum Section.
Laser Bench with UV nitrogen laser (337nm. wavelength).
Laser Optics control with beam detection.
Air Outlet - Fans
Pulsed extraction ion optics (time delay).
Low Mass Rejection controller for matrix ion suppression.
Flight Tube vertically mounted.
Timed Ion Gate control and beam deflector.
- Linear and Reflectron Mode of operation
Reflectron (Harmonic field).
Linear Detector (ETP).
Reflectron Detector (MCP).
- Linear mode for high molecular weight peptides and pro
teins 4000 - 130000 M/Z
- Reflectron mode for increased resolution and peptide fin-
gerprinting with PSD capabilities 500 - 4000 M/Z Indicator LED´s
- 1 GHz Transient recorder board
- Optional automatic slide loader, 12 slides per tray
- 24 position sample slide.
- Integrated instrument control and data base search rou-
tines.
- Integrated data analysis software from Proteometrics
- Bench top fingerprint.
Sample Inlet
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1.3.2 Specifications
1.3.2.1 Technical Specification
Mains Voltage 100 - 120 V 50/60 Hz

220 - 240 V 50 Hz
Power consumption 900 VA
Operating temperautre 15 - 27 C
Dimensions 153 x 53 x 66 cm ( H x W x D)
Weight 152 kg 152 cm
Laser pulsed UV Laser (Nitrogen)
337 nm, Class 3A
Laser frequency 1 or 8 Hz
Laser beam diameter 0.2 um
Nitrogen supply max. 0.1 bar (10 kPa)
Sample
entry
door
Shipping info
crate dimensions 193 x 86 x 157 ( H x W x L)
crate weight 320 kg
53 cm 66 cm
Ambient temperature -25 - +60 C
Relative humidity 20 - 95 % , non condensing
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1.3.2.2 System specifications
Resolution: 10000
Sensitivity Refl. mode: 5 fmol(<1 fmol*)
at 4:1 signal to noise

Air intake
Sensitivity Lin. mode: <5 fmol (<1 fmol*)
at 4:1 signal to noise
Mass accuracy: 25 ppm (int. calibr.),
100 ppm (ext. calibr.) Indicators
Ion gate resolution: 100 (m1/m2-m1) Mains

inlet
Low mass rejection: Suppression up to 500 Da panel
Sample
Mass range: 500 Da - 500.000 Da entry
door
Sample
Quadratic field reflectron focus: 18 kV door
switch
(75% of mass range)
Acquisition Rate 1 GHz
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1.3.3 The principle of operation
The Ettan Maldi ToF uses a pulsed UV Nitrogen laser at Ettan Maldi Tof MS design
337nm, which is steered by two mirrors, one of which is
adjustable, and focused by a convex lens onto the sample, to
desorb the target analyte from a solid to gaseous state.
The ions in this state form a cloud or plume in a temporary
field free region of the source between the sample slide and
the extraction lens.
A time delay that is mass specific is applied to the extraction
lens before it is fired. This delay is measured with respect to a
pulse generated by the laser beam detector.
Once the pulsed extraction lens is fired the ions pass into the
flight tube.
All the ions have the same kinetic energy and hence lower
mass ions reach the detector faster than higher mass ions.
Consequently a time to mass conversion can be made which
enables a mass analysis of the whole spectrum to be per-
formed.
The ion’s travel up the flight tube into the low mass reject cell.
This can have a timed deflection voltage applied to reject the
lower mass ions which are generally of no interest and are
formed predominantly from the matrix.
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There are two detectors. An electron multiplier (ETP) .
which is used to detect ions in linear mode, figure 1: Linear Mode
and a Multi Channel Plate assembly (MCP) which is used in

Reflectron mode.
Linear mode is primarily used to detect High Mass ions at
medium resolution, typically from 4000 to 130000 Daltons.
see figure 1 on the page beside
Reflectron mode is primarily used for masses below 5000 figure 2: Reflectron Mode
Daltons and has higher resolution for Peptide fingerprinting.
see figure 2 on the page beside
The ions then pass through the gate region.
The gate is used to control ions in Post Source Decay (PSD)
mode.
see figure 4 on the next page
PSD mode is used to measure the fragments or daughter ions
of a parent mass which are products of post source decay.
Parent and daughter ions of a specific molecule, which frag-
ment after they have left the source region, will reach the gate
at the same time figure 3: diagram intensity gainst mass over charge ( m/z dalton)
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If the time taken by these molecules is known it is then possi-
ble to apply a timed voltage to the gate which only allows the figure 4: PSD
precursor and fragments of the molecule of interest to reach
the detectors.
After the gate region the ions pass into the Harmonic field Post-Source Decay
reflectron.
P a re nt ve lo city is ke pt by fragm e nts after d eca y
In linear mode no voltage is applied to the reflectron lens so
they then travel to the linear detector. M
G ate
In reflectron mode a voltage is applied to the reflectron lens
which creates an electrical field which increases quadratically
re flec tro n
as the ions pass further into the lens. Ion sourc e
At a given point in the lens, the ions are reversed and re-
pelled towards the reflectron detector. Lig hte r frag m ent has
sm alle r en ergy m v 2/2
The reflectron mirror effectively increases the flight path by a an d tu rns ba c k at an
ea rlier tim e
factor of three thus giving greater mass separations T im e se paration of fra gm en t ions in reflectron
at the detector and hence higher resolution.
t U
Z ap th e m olec u le s
in duc e s po st
sour ce dec ay
D etecto r
reflec tro n
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1.3.4 Vacuum system
The function of a vacuum system is easy to understand, but
troubleshooting a vacuum system can be time consuming. Do
not vent the system and start to replace parts without thinking
twice (pump down time is long, days can be lost).
1.3.4.1 List of components in vacuum system

Apart from the vacuum chambers the vacuum system con-
sists of the following items.
a. Two solenoid valves (vent and inlet)
b. Rotary pump (rotary vane pump)
c. Backing valve
d. Vacuum Tubing
e. Turbo pump
f. Turbo pump controller
g. Sample door
h. Sample slide assy.
i. Magnetron Gauge
d b j f e l m
j. Pirani Gauge
k. Air admit valve (fitted on source turbo)
l. Sample probe mechanism
m.Laser
1.3.4.2 The function of vacuum pumps and gauges

The rotary pump function is as follows: The movement of the
gas through the rotary pump can be broken down into three
phases. 1) Air moves through the inlet. 2) The vane rotates Rotary vane pump
and seals the gas between the vanes and the housing wall.
Gases will be compressed in this phase causing the pressure
to increase before the next phase.
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3) The gas is transported through the pump to the outlet by the molecules collide with the wire and cooles it. As gas molecules
rotation of the vanes. The rotation of the vane creates a are pumped away there are less molecules and therefore less
smooth flow of the gas through the pumping chamber. cooling and the wire heats up. As it heats up its electrical re-
sistance increases. A simple circuit utilising the wire detects
The turbo pump is a blade turbine that compresses gases. By the change in resistance and once calibrated it can directly
the momentum transfer from the rapidly rotating rotor blades correlate the relationship between pressure and resistance.
to the gas molecules the non-directed thermal motion of the The Pirani gauge works down to 10e-4 mbar. Other forms of
molecules is changed to a directed motion. Hence, the pump- gauge have to be used to measure pressures lower than this.
ing process in a turbomolecular pump results from the directed
motion of the gas molecules from the inlet flange to the fore- The Magnetron is a so called Cold-Cathode Gauge. All CCGs
vacuum port. To create the directed motion of the gas mol- utilize crossed electric and magnetic fields to trap electrons.
ecules the tips of the rotor blades have to move with super- The electron plasma, responsible for ionization, originates
sonic velocity. Hence, a high rotational speed of the rotor is from the random release of an electron at the cathode. A dis-
required. charge slowly builds inside the ionization volume to the point
where the entry of new electrons into the plasma is limited by
In the molecular flow range - i.e. at pressures below 10-3 mbar space charge repulsion. At pressures below 10-4 mbar, the
(0.75 x 10-3 Torr) - the mean free path of the gas molecules is discharge is practically a pure electron plasma. The electrons
larger than the spacing between rotor and stator blades (some move in cycloidal jumps, circling about the anode, and during
tenths of a millimeter). Consequently, the molecules collide part of each jump they have sufficient energy to ionize gas
primarily with the rotor blades with the result that the pumping molecules through electron impact ionization. The probability
process is highly efficient. of collision is proportional to the gas density. The slow ions
In the laminar flow range - i.e. at pressures higher than 10 -1
generated, are quickly captured by the cathode. The current
mbar (0.75 x 10 Torr) - the situation is completely different.
-1
generated by this ion collection process is measured and used
The action of the rotor is diminished by the frequent collisions as an indirect indication of gas pressure. This ion-induced
between the molecules. Therefore, a turbo pump is not capa- current is not linearly related to the pressure in the chamber. A
ble of pumping gases against atmospheric pressure and has typical range for a magnetron is 10e-2 - 10e-9 mbar.
to be backed by an adequate fore-vacuum pump. See next page for a schematic off the vacuum system and a
The Pirani gauge head is based around a heated wire placed description of its function.
in a vacuum system, the electrical resistance of the wire being
proportional to its temperature. At atmospheric pressure, gas
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1.3.4.3 Basic function of the vacuum system
A rotary pump is connected to the source turbo pump and the
reflectron turbo pump by stainless steel vacuum tubing to back
them up. A Backing valve is fitted between the rotary pump
and the two turbo pumps, this valve is used to isolate the high
vacuum side of the vacuum system from atmosphere pressure
Turbo pump during the sample exchange sequence (see below for a de-
tailed description). A Pirani gauge is fitted on top of the rotary
pump to measure the vacuum on the low vacuum side. A for
line trap is fitted between the rotary pump and the backing
valve to protect the vacuum system from back streaming oil
fumes.
1.3.4.4 Pump down sequence

When the system is powered on the rotary pump and the two
N2 or dry air
turbo pumps start to pump down the system. The backing
valve is open. The door will move to the closed position. The
Turbo vent valve sample probe will move to the exchange sample position. This
isolates the sample insertion lock from the high vacuum cham-
Pump out line ber. The vent valve will be closed.
for probe bearing
Backing valve When the turbo pumps have reached 80% of their maximum
speed a green led is illuminated on the turbo pump controllers
Turbo pump
(TPC) to indicate that the turbo pump speed is OK.
Pirani
The source turbo pump controller provides the 24 V needed
Door Magnetron for the Pirani and Magnetron gauges, The trip point for the
(penning gauge)
Pirani is set to 1e-2 mbar. The Magnetron gauge is not enabled
N2 or until both controllers indicate that the turbo pump speed is OK
dry air Vent valve Inlet valve and the Pirani gauge has reached its trip point. This protects
Rotary pump
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the gauge from poor vacuum. The trip point for the magnetron 1.3.4.5 Sample Analysis
is set to 1e-6 mbar. The trip point is set on the I/O pcb. After a sample spot is selected for analysis (see the software
The readings from the gauges can be checked in the Ettan manual for setting up files, etc.). The sample motor will drive
Maldi Control software. the sample slide to the appropriate position so that the laser
Typically value for these gauges will be between 1e-2 and 1e–3 hits the required sample.
mbar for the Pirani gauge and from 1e–6 to 1.0e–7 mbar for the
Magnetron gauge. 1.3.5 Mechanics
The “OPEN DOOR” command drives the sample probe to the The Ettan Maldi Tof has only three moving parts (pumps and
sample exchange position and seals and isolates the high fans excluded)
vacuum side of the instrument from the door interlock.
- The sample probe mechanism
The vent valve opens for a short time venting the sample ex-
change lock and allowing the sample door to open. The magn- - The sample door.
etron reading normally improves slightly during this sequence. - The filter wheel assembly.
If it gets worse then the seal between the sample holder and All three mechanism are motordriven and their limits of travel
sample lock is leaking. Normally this requires a small adjust- are controlled by micro switches. The motors are controlled by
ment to the micro-switch, which controls the maximum motion the I/O pcb, it`s the second pcb from left in the electronic rack.
of the sample holder into the sample exchange lock. The sample probe- and filter wheel motor are stepper motors
The “CLOSE DOOR” command closes the door. The isolation and the door is operated by a dc motor.
or backing valve to the turbo pumps closes. The inlet valve
opens allowing the sample door interlock to be evacuated to
roughing pressure by the rotary pump. 1.3.5.1 Sample probe mechanism
Once the backing line to the sample door reaches the Pirani The sample probe mechanism moves the sample probe with
trip point the backing valve opens, the inlet valve closes and the sample slides in and out of the Maldi. The movement of
the sample probe moves to its reference position. A dip in the the probe is done by a long drive screw made of peek. The
Magnetron reading will be seen whilst the rough pressure from drive screw is turned by a stepper motor and a gearbox. This
the sample lock is pumped away by the turbo pumps. unit is called Sample probe mechanism. The inner and outer
end positions for the sample probe is detected by two micro-
switches. The outer position is the sample exchange position
and the inner position is the start position. The start position is
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where the sample probe stepper motor starts to count the 1.3.5.3 Laser and optics
number of steps it is moving.
The laser used in the Maldi is a nitrogen laser class 3A whit a
The rotation of the drive screw feedthrough is sealed with two wavelength of 337 nm. There are no parts to be replaced in-
o-rings and lubricated with vacuumgrease. The volume side the laser box, all parts is embedded in to a solid piece of
between the o-rings is pumped out by the rotary pump via the rubber. The laser use 24V from the electronic rack as supply
pump out line (see drawing of the vacuum system). This will voltage. The trigger signal for the laser comes in a coaxial
compensate for leaks in the o-rings when the sample probe cable from the T/R pcb. The pulse frequence is 1 or 8 Hz and
feedthrough is turned by the stepper motor and maintain the is set up in the method. At the exit of the laser is a manual
high vacuum in the system. operated shutter which should be open in normal operation.
The upper micro switch on the sample probe mechanism After the laser comes the filter wheel which is used to set re-
determine the start point. It is used to find the first sample quested laser power.
on the slide by counting the number of steps from the micro
switch to the first sample spot on the sample slide. The lower
switch is for the stop position of the sample probe in the 1.3.5.4 The filter wheel assembly
sample exchange position. In this position the sample probe The min. and max position for the filter wheel is controlled by
acts like a isolation valve between the ion source and the two micro switches. The switches is activated by an arm fitted
sample lock. It is important to find the right position to on the filter wheel. The distance between min. and max is
maintain a good vacuum in the Maldi during the sample approximately 2700 and is set to 850 steps by the stepper
exchange procedure. The movement of the sample probe is motor parameter in the Maldi .def file.
controlled by the I/O pcb.
The filter wheel is fitted in a 450 angel to reflect some light
from the laser to the laser detect sensor. The filter is turned by
1.3.5.2 The sample door assy a 12 V stepper motor via a drive belt and its positioning is
controlled by the I/O pcb. After the filter is a transparent mirror
The sample door is moved up and down by a dc motor. The the directs the laser puls to the entrance lens of the ion
open and closed positions for the door is detected by micro source. Inside in the ion source is a wobbulator that reflects
switches. The lower micro switch for the closed position is the laser beam to the sample.
connected in series with the HV interlocks on the I/O pcb, this
means that the sample door has to be closed before the HV is
turned on.
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1.3.6 Abreviations calculated using the average atomic weights for each
element. An average mass is obtained in MALDI-TOF-MS
when a peak is not isotopically resolved.
10% valley
For defining resolution. Two peaks of equal height in a mass Background subtraction
spectrum at masses m and m-m are separated by a valley The process in which the background (chemical noise and
that at its lowestpoint is just 10% of the height of either peak. detector noise) is subtracted, thus leaving the peaks above
the noise at the base level.
Ablation step
Molecular components of a solid are put into a gas phase and Base peak
ionized. The most intense peak in a mass spectrum. A mass spectrum
is usually normalized so that this peak has an intensity of
Adaptive backgroundcorrection (ABC) 100%. See also parent peak.
ABC filters are usually also applied to low resolution data to
enhance the high-frequency signal and remove the low Calibrant
frequency background: I’j = Ij-d/(2n+1).Ij+k k = -n,...,n, where A compound used for the calibration of an instrument.
0 < d < 1, n is the width of the filter, I j+k is the intensity in
channel j+k before the filter has been applied to the data, and Calibration
I’ j is the intensity in channel j after the filter has been applied A process where well-known masses are assigned to certain
to the data. peaks. The purpose is to improve the mass accuracy of an
By applying an ABC filter in combination with a smoothing MS instrument. For ESI-TOF, the calibrant is introduced into
filter the quality of peaks can be improved. the chamber via a second electrospray needle. For MALDI-
TOF-MS, the calibrant is either mixed with the sample
Adduct peak (internal calibration) or run as a separate sample (external
Results from the photochemical breakdown of the matrix into calibration).
more reactive species, which can add to the polypeptide. Can
also result from salt ions, Na + etc., that are embedded in the Centroided mass peak
matrix. The centroided mass peak is located at the weighted centre of
mass of the profile peak.
Average molecular weight
The mass of a molecule of a given empirical formula
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Collision induced dissociation (CID) created from a flowing liquid sample, the extraction of gas
A process whereby a mass-selected ion is excited and caused phase ions from these droplets under a high electric field, and
to fragment by collision with a target gas. Used in some ESI transportation of the ions into a vacuum suitable for MS.
and MALDI instruments. The fragment ions need to be
charged to be mass separated, so many of the MALDI Electrospray ionization (ESI)
fragments may not be detected since they are neutral. An ionization method that allows production of molecular ions
directly from samples in solution. A sample solution is sprayed
C-terminal through a needle, which is kept at a potential (typically 3.5 to 6
The carboxyl residue at the end of a polypeptide chain. Proper kV). The voltage on the needle causes the formed droplets to
nomenclature for indicating product ions containing a C- be charged. As the solvent evaporates, the droplets disappear
terminal is v, w, x, y, and z. leaving highly charged analyte molecules. The resultant ions
often carry multiple charges, which reduces their mass-to-
Daughter ion charge ratio compared to a singly charged species. It is a
See fragment ion continuous method suitable for interfacing with HPLC or
capillary electrophoresis. It is also a very sensitive
Desorption ionization (DI) method well suited for the analysis of small amounts of large
An ionization method used to ionize non-volatile solid samples biological molecules such as peptides and proteins that are
by impact of energetic particles or photon beams. difficult to vaporize or ionize, especially thermally labile
compounds. Generates ions carrying many charges.
Digestion External calibration

Cleavage by proteolytic enzymes such as trypsin and Calibration where a set of calibration constants that have
chymotrypsin. been measured in a previous experiment is applied. The
calibrant is run as aseparate sample.
Dried droplet method
Sample preparation method. A droplet of a protein-matrix Filters
solution is dried. When the solvent has evaporated, the Filters are commonly applied to time-of-flight mass spectra to
sample can be loaded into the MALDI mass spectrometer. improve the appearance of a spectrum and to extract peaks
from poorly resolved signals. The general form for one type
Electrospray (ES) of filters applied to mass spectra is: I’j = c Ij+k Fk k = -n,...,n,
Comprises the formation of electrically charged droplets where c is a normalization constant (c = 1/(.Fk) k=-n,…,n,), n
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is the width of the filter, Ij+k is the intensity in channel j+k Fragment ion
before the filter has been applied to the data, Fk is A charged dissociation product of ionic fragmentation. The ion
filter factor k, and I’j is the intensity in channel j after the filter is generated by fragmentation of an ion and not generated by
has been applied to the data. The filters that are useful for direct ionization of a neutral molecule. Used to be called
processing mass spectra do not shift the peaks and are daughter ion.
therefore required to be symmetric (Fi = F-i , i = 0, 1,…, n);
and of odd order (n = 1, 3, 5,…). Fragmentation
A physical process of dissociation of molecules into fragments
FASTA format in a mass spectrometer. The mass spectrum of fragments is
A format of sequence databases. A sequence in FASTA format unique for the molecule or ion. The fragments can be either
begins with a single-line description, followed by lines of ionic or neutral. Fragmentation can be used to provide
sequence data. The description line is distinguished from the sequence data for the identification of proteins and peptides.
sequence data by a greater-than (”>”) symbol in the first
column. It is recommended that all lines of text be shorter Fragmentation pattern
than 80 characters in length. An example sequence in FASTA Set of reactions leading from the molecular ion to fragment
format is: >gi|532319|pir|TVFV2E|TVFV2E envelope protein ions. Molecules have distinctive fragmentation patterns that
ELRLRYCAPAGFALLKCNDADYDGFKTNCSNVSV provide structural information to identify structural
VHCTNLMNTTVTTGLLLNGSYSENRT components.
QIWQKHRTSNDSALILLNKHYNLTVTCKRPGNKT
VLPVTIMAGLVFHSQKYNLRLRQAWC Fragmentation process
HFPSNWKGAWKEVKEEIVNLPKERYRGTNDPKR If the excess ionization energy in a molecular ion is greater
IFFQRQWGDPETANLWFNCHGEFFYCK than the energy required to break a chemical bond, the
MDWFLNYLNNLTVDADHNECKNTSGTKSGNKR molecule can fragment. There are typically two types: direct
APGPCVQRTYVACHIRSVIIWLETISKK cleavage (e.g. cleavage of a C-C bond) or rearrangement.
TYAPPREGHLECTSTVTGMTVELNYIPKNRTNVTL
SPQIESIWAAELDRYKLVEITPIGF Full length protein
APTEVRRYTGGHERQKRVPFVXXXXXXXXXXXXXX An intact polypeptide chain, constituting a protein in its native
XXXXXXXXVQSQHLLAGILQQQKNL or denatured state. One of the most common applications of
LAAVEAQQQMLKLTIWGVK mass analysis is where the protein is identified from its full
length using a MALDI-TOF-MS.
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Full width at half height (FWHM) optics (open), or that can deflect the ions out of the way of the
A measure of the peak width at 50% of its maximum intensity. later stages of the mass spectrometer.
High-pass filters Ion source

High-pass filters are usually applied to low resolution data to Device used to generate sample ions by MALDI or ESI, for
enhance the high-frequency signal and remove the low example. In MALDI, the probe and the laser (and the
frequency background. An example of a simple high-pass extraction electrodes) are together referred to as the ion
filter (n=5) is F = {,-1,-1,-1,-2,1,F 0 ,1,-2,-1,-1,-1}. By applying source.
a high-pass filter in combination with a smoothing filter the
quality of peaks can be improved. Ion transmission efficiency
Refers to the fraction of the ions produced in the source
In-gel digestion region that actually reaches the detector. Important measure
The second step in transferring the analyte from a 2D-gel to of the sensitivity of the mass spectrometer.
the MS analysis equipment. The protein in the gel is cleaved
in a controlled way, usually with enzymes, although chemical Ionization
cleavage can also be used. During the process, peptides are The generation of an ion. A compound must be charged or
formed, which can easily be removed from the gel. The ionized to be analysed by a mass spectrometer.
process also includes a number of washing and drying steps.
Isotope
Internal calibration Atoms of the same element having different mass numbers
Calibration where known peaks are used in each spectrum to due to differences in their number of neutrons.
calculate a calibration for that particular data set. The calibrant
is mixed with the sample. More accurate than external Isotope abundance
calibration. The relative amount in nature of certain atomic isotopes. Note
that the atomic weight of an element is a weighted average of
Ion detector the naturally occurring isotopes. A high resolving mass
A detector that amplifies and converts ions to an electrical spectrometer can separate the isotopes.
signal.
Linear time-of-flightmass analyser
Ion gate Consists of a long straight, empty flight tube with an ion
A unit that electrically lets ions through to later stages of ion source at one end and a detector at the other.
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MALDI spectrum Mass spectrometer
A typical MALDI spectrum includes the molecular ion, some An instrument that uses the difference in mass-to-charge ratio
multiply-charged ions (only for heavy ions), and very few (m/z) of ionized atoms or molecules to separate them from
fragments. A MALDI spectrum results from a mass each other. All mass spectrometers consist of three main
spectrometer utilizing a MALDI ion source. parts: an ion source, a mass analyser, and an ion detector.
Used for determining chemical and structural information and
Mass accuracy for quantification of atoms and molecules.
The difference between a measured value and the true mass
of the substance. Mass spectrometry (MS)
A technique for analysing the molecular weight of molecules
Mass analyser based upon the motion of a charged particle in an electric or
magnetic field. mass spectrum A plot of ion abundance (Y-
Separates ions according to their m/z value. The ions enter axis) vs. mass-to-charge ratio (X-axis). It contains information
the analyser either continuously (beam) or pulsed (using an on exact mass (i.e. elemental composition), fragmentation
ion gate or a pulsed ion source such as MALDI). Examples of pattern (i.e. structure and ”fingerprint”) and isotope abundance
mass analysers are: electrostatic-magnetic, quadrupole, time- (i.e. presence and number of certain elements).
of-flight and ion trap.
Mass-to-charge ratio (m/z)
Mass range A quantity formed by dividing the mass of an ion (in Da units)
The difference between the upper limit and the lower limit of a by the number of charges carried by the ion.
measurement. For example, the range of mass-to-charge ratio
(m/z) that a mass analyser can analyse. Can be <2 000 (low) Matrix
to > 500 000 (high). In MALDI, referred to as a light-absorbing compound that
forms crystals that incorporate proteins, eject the proteins
Mass resolution intact, and ionize them in the same process.
The degree of separation between two adjacent peaks in a
mass spectrum. The resolution is a measure that can be used Matrix Assisted Laser Desorption Ionization (MALDI)
to determine if two adjacent peaks will overlap or not. For The analyte is dissolved in a solution with an excess of a
example, FWHM resolution of 5000 means that two peaks matrix containing a chromophore that absorbs at the laser
at mass 5000 and 5001 will just join with no valley in-between. wavelength. The mixture is recrystallized and then vaporized
in vacuum by a short flash of laser light. The ionized
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molecules can then be extracted into a mass spectrometer. Multiple-charged ion
Ion with more than a single charge and having
Matrix Assisted Laser Desorption Ionization Time Of correspondingly reduced mass-to-charge ratio.
Flight Mass Spectrometry (MALDI TOF MS)
Used to determine the molecular weight of peptides, proteins, Normalization
oligonucleotides, and other compounds of biological origin as All peaks are reported with peak heights relative to the highest
well as synthetic polymers. The analysis can be performed in peak height or area in the spectrum.
linear mode (high mass, low resolution) up to a molecular
weight of m/z 300 000 (in rare cases), or reflectron mode N-terminal
(lower mass, higher resolution) up to a molecular weight of The amino residue at the end of a polypeptide chain. Proper
4000. nomenclature for indicating product ions containing an N-
terminal is a, b, c and d.
Metastable ion
An ion that decomposes into a charged product ion and a Parent ion
neutral species, or into two charged fragments, during its See precursor ion.
transmission through the mass spectrometer. Is normally a
short-lived reaction intermediate or a vibrationally highly Parent peak
excited molecule. Refers to the peak of an ion that will be selected for
fragmentation. The result of fragmenting the precursor ion is
Method setup the fragment ions (several fragments from one precursor ion).
A group of methods for collecting and analysing data. It
consists of a method for the instrument followed by analyses Peak
and reports. The portion of a spectrum where a maximum can be found.
Monoisotopic molecular weight Peak area

The mass of a molecule containing only the most abundant The area bounded by the peak and the base line. Can be
isotopes, calculated with exact atomic weights. In MALDI- calculated by integrating the abundances from the peak start
TOF-MS, a monoisotopic mass is obtained in high-resolution to the peak end.
mass measurement when the first isotopic peak of the
distribution can be identified. Peak detection
The process of finding a m/z value from a peak in a mass
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spectrum. Commonly, the centroid method is used. the gas by the resistance change caused by the density-
dependent (thus pressure-dependent) cooling effect of the
Peak extraction vacuum rest gas. Can be an instrument that measures very
The process of finding all peaks in the mass spectrum (filtered low pressures in gases, dependent on the conductivity of the
according to specific parameters such as the threshold level). gas.
Compare with peak detection.
Post source decay (PSD)
Peak height A method for obtaining sequence information about a single
The distance between the peak maximum and the baseline. peptide observed in the mass spectrum. It describes the
fragmentation processes that occurs in TOF in the drift region
Peak resolution of the analyser. The PSD is used to fragment peptides within
The extent to which the peaks of two components overlap or the MALDI-TOF-MS. The peptide is ionized at an increased
are separated. Compare with FWHM. laser power, thus giving it more internal energy. The bonds
are broken apart giving rise to a product ion and a neutral
Peak value fragment. Less fragmentation occurs than in CID.
The local maximum of the signal intensity within a small mass
interval. Post translational modification (PTM)
A common name for several hundred types of modifications
Peak width such as phosphorylation or glycosylation. Practically all
The width of a peak at a given height. Compare with FWHM. It protein modifications are associated with either an increase or
is used to define resolution. a decrease in mass. Identification of a modification requires
the specific detection of one particular modified peptide.
Peptide mass fingerprinting
The use of chemical or enzymatic agents to digest protein Precursor ion
molecules according to the specificity of the agent, thus Any ion (including negatively and multiply charged ions) that
creating a unique set of peptide fragment molecular masses gives fragments. Used to be called parent ion.
that can be detected via MS and used to search modified
protein databases. Probe
A sample slide used to introduce the sample into the mass
Pirani gauge spectrometer.
A thermal conductivity gauge, that measures the pressure of
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Protein characterization traps. An entire mass spectrum is collected from a single
The identification of structural aspects of a protein. Includes pulse of ions.
amino acid sequence, molecular weight, three-dimensional
structure, post-translational modifications and biologic Real time monitoring
activity of a particular protein. A data acquisition method in which raw data are generated
and displayed as the experiment is in progress.
Protein sequencing
The determination of the order of amino acids in a particular Reflectron
protein or peptide. This determination can be achieved via Improves resolution of a mass spectrometer. A series of rings
mass spectrometry or chemical degradation techniques of or grids act as an ion mirror. Compensates for the spread in
either the N-terminal or the C-terminal of the protein or kinetic energies of the ions as they enter the drift region.
peptide.
Relative abundance (RA)
Proteome Normalization of a peak relative to base peak. resolution
The complete profile of proteins expressed in a given tissue, Refers to the separation of two ions where R=m/.m. There are
cell or biological system at a given time. A quantitative protein different definitions of the terms .m, 10% valley, FWHM or
expression pattern of a genome under defined conditions. peak width. For a single peak made up of singly charged ions
at mass m in a mass spectrum, the resolution may be
Proteome analysis expressed as m/.m where .m is the width of the peak at a
A systematic analysis comprising separation, identification, height that is a specified fraction of the maximum peak height.
and quantification of many proteins from a sample at the It is recommended that one of the three values 50%, 5% or
same time. 0.5% be used.
Proteomics Run list

Systematic analysis of the protein expression of healthy and A defined set of parameters that define the operating settings
diseased tissues. for a sequential list of samples. It allows the user to run the list
of samples,. Each run list could contain one or several sample
Protocol positions.
A detailed description of how to prepare and analyse the
sample. Also called procedure.pulsed mass analyser Includes Sample preparation
time-of-flight, ion cyclotron resonance, and quadrupole ion A crucial stage to achieve ionization. In MALDI, the sample is
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incorporated into the crystals of a second material, the matrix. Smoothing filters
There are several sample preparation methods that can be Smoothing filters are usually applied to noisy data to reduce
used for this incorporation, for example, the dried droplet the high-frequency noise associated with the signal, i.e. they
method, thin layer method, slow crystallization method and are a type of low-pass filters. An example of a simple smooth-
seeded microcrystalline film method. ing filter (n = 1) is F = {1,1,1}, c = 1/3. By applying few points
wide smoothing filter the quality of peaks can be improved.
Sample slide However, if the width is increased the resolution deteriorates.
Slide with numbered wells where the samples are put before
they are introduced into the mass Template
spectrometer. Also called probe or target plate. A pre-programmed method with default values. The user may
have to add certain data (for example, sample volume). Tem-
Seeded microcrystallinefilm method plates may be edited and stored as user-defined methods.
A sample preparation method. First, a thin layer of small ma-
trix crystals is formed on the sample slide. Then a droplet Thin layer method
containing the analyte is placed on top of this layer. This is left A sample preparation method. Applying the matrix onto the
to dry. The deposit is washed before the sample slide is substrate creates a very thin layer of matrix. A droplet of the
inserted into the mass spectrometer. Is a direct replacement analyte is then dried onto this layer. Contaminants can now be
of the dried droplet method. washed away before introducing the sample into the mass
spectrometer. A variant of the dried droplet method.
Signal to noise ratio (S/N)
The ratio of the signal height and the noise height. An indica- Threshold fluence
tion of the clarity of the data. The lowest laser fluence at which protein ions start to appear
in MALDI.
Slow crystallization method
A sample preparation method. Here, large matrix crystals are Timed ion gate
grown. The analyte is added to a saturated matrix solution. Enables PSD by ion selection. See also ion gate.
Microcrystals are formed. The supernatant is removed and a
slurry of crystals is made. The slurry is then applied to the Time lag focusing (TLF)
sample slide, allowed to dry and inserted into the mass Improved resolution is obtained for a specified mass range by
spectrometer. Can be used when the dried droplet method applying a controlled delay between ion formation and
has failed. acceleration.
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Time of flight (TOF)
Separates ions in time as they travel down a flight tube. Time-

of-flight mass spectrometry (TOF-MS) Uses the differences in
transit time through a drift region to separate ions of different
masses.
Tuning
The process of optimizing the MALDI instrument’s laser power
and target position to obtain the best possible sensitivity and
signal-to-noise ratio for a specific type of experiment.
Unit resolution
Distinguishes between ions separated by 1 m/z unit.
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Chapter 2
Chapter Contents
2. Installation
Installation
2.1 Hardware Installation
2.2 Acceptance test
2.3 Acceptance test document
2.4 Software Installation
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2.1 Hardware installation 2.1.5 Lifting the instrument
Only lift the instrument if you are four strong people, the weight
2.1.1 Lab preparation is 150 kg. Remove the transportation screw for the rotary
Make shore that the lab is prepared and ready for the installa- pump at this stage, it is fitted from the under side of the Maldi.
tion by checking that the lab manager has filled in and re- This will reduce the vibration in the instrument and make it
turned the site prep check list (see page 14 in Site prep guide easier to replace the rotary pump in the future. Check the oil
18-1144-63.) level in the rotary pump fill up if necessary.
2.1.2 Components check 2.1.6 Measure reflectron resistance and all HV

Crate OK • Yes • No damages: feedthrough
Remove the HV cable on the top of the reflector housing for
Boxes inside OK • Yes • No damages: the reflector HV. Measure the resistance between the center
pin in the feedthrough (M131) and ground with a megger. It
Instrument OK • Yes • No damages: should be between 67,2 MΩ Ω - 68,4 MΩ. If the resistance is not
within this range the fault must be corrected before the instal-
Computer OK • Yes • No damages: lation continue.
Check the resistance in the bnc feedthrough with a DMM for
Panels OK • Yes • No damages: the linear and reflectron detectors. The resistance between HT
(M130) for the linear detector and signal output (M132) should
2.1.3 Shock indicators at the crate. be > 40 MΩ, between HT (M130) and ground >40 MΩ, be-
Check the shock indicators at the outside of the crate, if there tween output (M132) and ground > 40 MΩ.
are any damages and there is an indication, please mark the It should be >40 MΩ between HT (M80) and output (M129), 11
area in the drawing underneath. MΩ between HT (M80) and ground. If the resistance is lower
the fault has to be corrected before the installation continues.
2.1.4 Unpack the instrument
Start with the top lid, then the short sides and finally the long 2.1.7 Connection
sides. Remove all boxes and unpack the PC, printer, Slide Connect the computer, power cable and nitrogen gas. Set the
loader, panels etc. Insert the four handles from your tool kit. gas regulator to 0,1 bar. Check all electrical connections in-
Remove the four metal angels that holds the instrument to the side the Maldi on the back of the electronic box, pulser box,
pallet. gate & kicker box, beam dump are correctly fitted. Check all
vacuum connections, make shore that they are tight. Connect
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the printer and monitor to the computer. Apply voltage in 100V steps, wait 2 minutes. Repeat until the
voltage is 1.0 kV. Wait 2 minutes.
2.1.8 Starting up the system Adjust the voltage in 100V steps, wait 5 minutes. Repeat until
Switch of the electronics on the backside off the electronic the voltage is 1.5 kV. Wait 5 minutes.
crate. Switch on the main power switch, this will start the ro- Adjust the voltage at 50V steps, wait 10 minutes. Repeat until
tary pump and the turbo pumps. When the green LED’s on the the voltage is 2 kV.
turbo pump controller goes on the turbo pumps is OK (has The adjustment of HT is done on the trim pot Vi in on the MCP
reached 80% off their speed). This will take about 15 minutes. HT supply. The voltage is checked at the readback at pin
If this does not happened reset the controller were the LED three in the contact to the MCP HT supply.
does not come on by unplugging the power contact to the To condition the rest of the instrument do as follow:
turbo controller for 10 seconds. After half an hour it is time to Run the following tests for one minute each:
switch on the electronics. Start up the PC and start the Maldi 10 kV linear
software. Monitor the vacuum readings in the software. Open 20 kV linear
and close the door a few times to pump out the vacuum tubing 10 kV reflectron
and the valves. When the yellow sign at the Pirani reading 20 kV reflectron
turn off in the Maldi controller software the sample probe This test is to make sure that there is not any short circuit in
moves to its inner position. Leave the system to pump over the Maldi. If any arcing (short circuit) occur during this test the
night. problem must be corrected before the installation continue.
2.1.9 Conditioning 2.1.10 Calibration

The purpose to do the conditioning is to avoid damage on the The calibration should only be done when the instrument has
MCP (micro channel plates) and to find any problem with feed been running for 24 hours with all panels fitted. Run a calibra-
through and connections inside the Maldi. When the Magnet- tion mixture (position 1-6 on slide A) in reflectron mode 10 and
ron reading is in the –7 mbar range and the Pirani reading is 20kV. Repeat the runs in linear mode. Perform a calibration on
in the low –2 to high –3mbar it is time to start to conditioning each run. Save each run as system calibration.
the instrument. The first thing to conditioning is the MCP. Turn
down the HT to the MCP by turning the trim pot Vi in on the 2.1.10.1 Gate calibration
MCP HT supply fully counter clock wise. Check the readback The gate calibration should be done after the instrument has
on pin 3 in the contact that the voltage is zero. Start a run at been calibrated as described in 2.1.10.
5kV in reflectron mode with a slide in the source. It is not nec- Run a position containing 180 fmol ile7AngIII, 120 fmol hACTH
essary to have a sample on the slide.
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18-39 and 225 fmol Iodoacetamide modified Phosphorylase B flight time for the AngIII and hACTH peak, multiple it with
digest. Add methods for both reflectron and PSD to the posi- 0.261. Type in the calculated flight time value for hACTH in
tion. Use the following methods: Acquisition method reflectron the gate time box. Select gate on in the service sw menu. The
= The default method Protein Digest PRO with number of only visible peak should be hACTH. Fine tune the gate time
spectra changed to 1. and gate with until the peak of interest is well centred in a 4ns
Spectrum processing method reflectron = The default method gate with window. Press apply. Repeat with the AngIII peak.
Protein digest The gate is now calibrated.
Acquisition method PSD = The default method PSD PRO but Make a PSD run on Iodoacetamide modified Phosphorylase B
change the number of spectra to 5. digest. The only visible peak should be the 2007.114 peak.
In “waiting for PSD input” view, set the gate on the following The 1980 and 2040 peak should not be visible. Sometimes a
masses; 2007.114 (true peptide mass), 2040 (noise peak) and small adjustment off the gate calibration value has to be done
1980 (noise peak). Adjust the gate width to 2 for all masses. to get the gate well centred on the 2007.114 peak off Phos-
Adjust laser power and position manually to achieve good phorylase B digest.
resolution and S/N.
With the gate set on 2007, a peak with resolution above 2000 2.2 Acceptance test
FWHM and signal height above 200 should be present at a
2.2.1 Description of verification procedure
mass of 2007 +/- 1 Da.
Introduction to concentration and sample amount calculations
With the gate set to 2040, the resolution of the 2007 peak
should disappear and the signal height should drop more then
2.2.1.1 Different ways to describe the amount of a sub-
tenfold.
stance
With the gate set to 1980, the resolution of the 2007 peak
The most common ways to describe the amount of a sub-
should disappear and the signal height should drop more then
stance are listed in the table below:
tenfold.
If this does not work due to the calibration value in the .SED
file is to far off or the .SED file has been lost. Do as follow to
calibrate the gate: Run a spectra with AngIII and hACTH 18-
38. Change the x-axis scale to time. This can be done by go
to Tools; select x-axis label.
Open the service software for the Maldi (Start/Programs/Ettan
Maldi Software/Ettan Maldi tools/Ettan Instrument Service)
Make a not of the flight time of AngIII and hACTH. Take the
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Molar content Molar or Description
moles/litre (mol/l)
Volume litres (l) Used for liquid
Quantity Unit Description
substances (= in
liquid phase in it's
pure form). For V o l um e p e r c e nt vo l % Vol% = (volume of a liquid
example substance/volume of total
Acetonitrile and solution)*100.
TFA. Often used to describe the
concentration of a liquid
Mass gram (g) Most often used for substance in mixture with other
dry substances. liquid substances. For
For example matrix example the concentration of
powders BSA Acetonitrile in Buffer A (see
powder and dried later).
peptides.
Molar content Moles/mol States the number Weight per volume gram/li- Often used to describe the
of molecules tre (g/l) concentration of a solid
present. 1 mol = substance dissolved in a
6.022*10-23 solvent. For example BSA
molecules. For dissolved in water (see later).
example the
amount of peptides Molar content Molar Often used to describe the
present on a or concentration of a solid
MALDI target. moles/ substance dissolved in a
litre solvent. For example peptides
2.2.1.2 Different ways to describe the concentration of a
(mol/l) dissolved in water or Buffer A
substance
(see later).
The most common ways to describe concentration are listed
in the table below:
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2.2.1.3 Prefixes 2.2.1.4 Examples
The units described above are often used together with pre-
fixes. The prefixes are described in the table below: 2.2.1.4.1 Preparation of a mixture of liquids with a defined
volume percentage
Prefix Symbol Factor
exa E 1 0 18 1. Prepare 25 ml of 10 vol% TFA in water.
Use the formula for vol% and put in the information we
peta P 1 0 15 know (vol% and total volume).
tera T 1 0 12 10/100 = (volume of TFA)/25 à Volume of TFA = 2.5 ml, vol-
ume of water = 25 – 2.5 = 22.5 ml.
gi ga G 109
mega M 106 2. Prepare 50 ml of 50 vol% Acetonitrile and 0.9 vol% TFA
in water (use a 10 vol% TFA solution).
kilo K 103 Use the formula for vol% and together with known information
hecto H 102 and calculate the volume for each substance one at a time.
Acetonitrile: 50/100 = (volume of Acetonitrile)/50 à Volume of
d e ka Da 10 Acetonitrile = 25 ml.
d e ci D 10-1 TFA: Volume of pure TFA à 0.9/100 = (Volume of TFA)/50 à
Volume of TFA = 0.45 ml.
centi C 10-2 Volume of 10 vol% TFA à 10/100 = 0.45/(total volume of solu-
milli m 10-3 tion) à Total volume = 4.5 ml.
micro µ 10-6
2.2.1.4.2 How to prepare a solution of defined concentra-
nano N 10-9
tion from a vial with dried peptide
p i co P 10-12 Prepare a solution with concentration 1000 pmol/ml (equiva-
femto F 10-15 lent to 1*10-3 mol/l) from 1 mg of a dried peptide with molecu-
lar mass 897.531.
atto A 10-18 1. First calculate the molar content of dried peptide.
zepto Z 10-21 Molar content = mass/molecular weight = 1*10-3/897.531 mol
yocto Y 10-24 = 1.114*10-6 mol = 1.114 mmol.
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2. Then calculate the volume needed to get the desired con- Neurotensin and Hexatyrosine shall be prepared once every
centration. year (and in case of problems).
Molar content = concentration*volume à Volume = 1.114*10-6/ · Working solutions (20 pmol/ml) of each peptide shall be pre-
1*10-3 l = 1.114*10-3 l = 1114 ml pared every 6 months. 6 vials shall be prepared for each pep-
tide. 5 vials of each peptide shall be stored in a common box
2.2.2 Sample handling routines in the freezer. This box shall never be brought out of the
freezer (except for exchanging samples). 1 vial of each pep-
2.2.2.1 Buffer tide shall be stored in a second box in the freezer. This box
· New bottles of Acetonitrile (ACN) and TFA shall be bought shall be used for preparing samples for spotting (i.e. can be
once every year (and in case of problems). brought in and out of the freezer).
· A new batch of Buffer A and Buffer B shall be prepared once · The peptides stored in the box used for spotting shall be
every month. The buffer shall be stored in a common box in exchanged once every month.
the freezer.
· Each time buffer is needed, an appropriate number of 2.2.2.4 Protein digests
Eppendorf tubes are drawn from the box. However, the box · A new vial with dried digest should be dissolved to 1 pmol/ml
itself shall stay in the freezer at all times until a new batch is each month. The vial shall then be transferred to the box used
prepared. for spotting and be stored in the freezer.
· Vials containing dried digest shall be stored in the freezer.
2.2.2.2 Matrix This box shall never be brought out of the freezer (except for
· New bottles of matrix (Sinapinic acid and alpha-cyano) shall exchanging samples).
be bought and used with a two-month interval.
· Alpha-cyano matrix shall be stored in an exicator in the 2.2.2.5 BSA.
freezer. · A new vial of BSA powder should be bought once every
· Sinapinic acid matrix shall be wrapped in aluminium foil and year. The powder shall be stored in the fridge.
stored in an exicator. · A new batch (6 vials with 4 mg/ml BSA containing 1 ml each)
· Prepared matrix solutions shall be stored dark and are only of working solution shall be prepared every 6 months. 5 vials
allowed to be used for 12 hours after preparation. shall be stored together with working solutions of peptides and
digests in a common box in the freezer. This box shall never
2.2.2.3 Standard peptides be brought out of the freezer (except for exchanging samples).
· New stock solutions of Ile7-Ang III, hACTH18-39, 1 vial shall be stored in a second box in the freezer. This box
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shall be used for preparing samples for spotting (i.e. can be Acetonitrile, TFA, digests, BSA, pipette tips, eppendorf tubes,
brought in and out of the freezer). slides …and more). 2. Description of the preparation of all
· The BSA vial stored in the box for spotting shall be sample solutions (with references to 1.). 3. Notes describing
exchanged once every month. the exchange of samples for spotting (with references to 2).
4. Notes describing the spotting of samples (with references to
2.2.2.6 Dilution series 1-3). 5. References between prepared slides and MALDI
· Dilution series shall be prepared fresh from the working results/delivery test result protocol.
solutions every time samples are to be spotted.
· A diluted sample must be spotted within an hour after dilution 2.2.3 Sample Handling Protocols
(as quick as possible). If a slide with all samples for the acceptance tests is not
available start the acceptance test by preparing buffers, matrix
2.2.2.7 Slides and samples as described below.
· Unused slides shall be used each time samples are spotted.
Clean the slides, according to instructions in kit, before use. 2.2.3.1 Preparation of buffers and matrix solutions
· Opened sample slide kits shall be stored in a dust free
environment, wrapped in aluminum foil. 2.2.3.1.1 Preparation of 25 ml 10 vol% TFA
2.2.2.8 Lab consumables.

· Eppendorf tubes, pipette tips, falcon tubes and all other lab Water (HPLC grade) 22.5 ml
consumables shall be stored in a clean environment (free from 100 vol% TrifuoroAcetic Acid (TFA) 2.5 ml
from dust, salt and other chemical contaminants) and
Total volume 25 ml
shall only be handled by personnel wearing lab gloves.
Use HPLC grade of all chemicals.
2.2.2.9 Laboratory notebook Mix the above components in a clean glass vial and store it in
· A laboratory notebook must be used for all laboratory work the refrigerator (4°C). This vial can be used for buffer
and all notes shall be dated. preparation during 3 months. Use glass pipettes when
· The information in the notebook must admit full traceability handling TFA with concentrations in the range 5-100 vol%
for each result generated on a MALDI. This means: 1. batch/ (plastic pipettes release softeners that can affect the MALDI
lot number and date for all new material bought (peptides, spectrum).
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2.2.3.1.2 Preparations of 50 ml BUFFER A (50 vol% ACN, Water (HPLC grade) 22.5 ml
0.5 vol% TFA)
The solution should be split into smaller aliquots (1 ml 10 vol% TrifuoroAcetic Acid (TFA) 2.5 ml
Eppendorf tubes), wrapped in “parafilm”, stored at -20°C, and
100 vol% Acetonitrile (ACN) 25 ml
used one at a time. Use glass pipettes when handling TFA ith
concentrations in the range 5-100 vol% (plastic pipettes re- Total volume 50 ml
lease softeners that can affect the MALDI spectrum).
Water (HPLC grade) 22.5 ml
2.2.3.1.4 Preparation of ACHCA matrix
10 vol% TrifuoroAcetic Acid (TFA) 2.5 ml
The alpha-cyano-4-hydroxy cinnamic acid (ACHCA) matrix
100 vol% Acetonitrile (ACN) 25 ml should be prepared fresh everyday it is needed. When pre-
pared it should be stored in an Eppendorf tube wrapped in
Total volume 50 ml aluminum foil at room temperature (it can be stored like this for
12 hours).
2.2.3.1.3 Preparation of 50 ml BUFFER B (50 vol% ACN, AmBio Order #

0.9 vol% TFA) 17-6002-80 ACHCA Powder 20 mg
The solution should be split into smaller aliquots (1 ml
Eppendorf tubes), wrapped in “parafilm”, stored at -20°C, and BUFFER A 1 ml
used one at a time. Use glass pipettes when handling TFA with
concentrations in the range 5-100vol%. Use HPLC grade of all chemicals.
Plastic pipettes release softeners that can affect the MALDI
spectrum. 1. Bring out the matrix from the refrigerator and bring the tem-
perature up above room temperature before opening.
2. Mix as described above.
3. Vortex the tube with BUFFER A and matrix powder for 2
minutes.
4. Let the tube sit on the bench for ten minutes.
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5. Spin down in a centrifuge 10 s at 14000 g. 2.2.3.2. Preparation of peptide standard stock solutions
6. Transfer 600 ml of the supernatant (the fluid portion) to a new
Eppendorf tube.
7. The matrix is ready to use! (Store as described above). AmBio Name Water(HP- Final Termed
Order # LC)* Conc.
2.2.3.1.5 Preparation of Sinapic matrix
17-6000-84 hACTH(18-39) 145.7 l 1000 S1
The Sinapic acid matrix should be prepared fresh everyday it is
µ pmol/ l
needed. When prepared it should be stored in an Eppendorf tube µ
wrapped in aluminum foil at room temperature (it can be stored 17-6002-83 Ile7AngIII 470.7 l 2000 S3
like this for 12 hours). µ pmol/ l
µ
Sigma
AmBio Order # Order #
17-6002-82 Sinapic acid Powder 20 mg N6383 Neurotensin 247.1 l 2000 S4
(1mg) µ pmol/ l
BUFFER B 1 ml
µ
T1780 Hexa-L-Tyrosine 392.4 l 2000 S5
(1mg) µ pmol/ l
1. Mix as described above. µ
2. Heat the mixture to 37°C for 1 minute
3. Vortex the tube with BUFFER B and matrix powder for 30 Mix according to the table above and vortex for 30 seconds.
seconds. Transfer the solutions to eppendorf tubes and wrap with
4. Let the tube sit on the bench for a few minutes. “parafilm”. Store at –20 °C until use.
5. Spin down in a centrifuge shortly (if no one is available, just let *The amount of water (HPLC grade) to add to the delivered
the tube sit longer on the bench until all material has settled at the vial (see order #) to produce the described Final concentra-
bottom). tion.
6. Transfer the supernatant (the fluid portion) to a new Eppendorf
NB! The calculations are based on the following values for
tube.
purity and peptide content:
7. The matrix is ready to use! (Store as described above).
contents
Name Peptide purity Peptide amount of Name From previous Buffer A Final conc. Termed
content peptide in vial dilution
hACTH18-39 0.97 0.74 0.359 mg hACTH(18- 10 l S1 490 µ l 20 pmol/ µ l WS1
ILE7
AngIII 0.97 0.87 0.844 mg 39) (2.11.3.2)
Neurotensin 6 l S4 594 µ l 20 pmol/ µ l WS3
Neurotensin 0.96 0.86 0.826 mg
(2.11.3.2)
Hexa-L-Tyrosine 0.99 0.79 0.782 mg Neurotensin 6 l S4 594 µ l 20 pmol/ µ l WS3
(2.11.3.2)
For each new peptide bought, be sure to check the peptide
purity and peptide content for the corresponding batch (this Hexa-L-Tyr- 6 l S5 594 µ l 20 pmol/ µ l WS4
information should be collected from the supplier). If (peptide osine (2.11.3.2)
purity)*(peptide content) deviates more than 10% from the
values above, the preparation of the stock solution has to be 2.2.3.3.2 Preparation of full length BSA working solution
adjusted accordingly.
AmBio Order # Components Amount Final Conc. Termed
2.2.3.3 Preparation of working solutions 17-6002-86 BSA powder 24 mg
2.2.3.3.1 Preparation of peptide working solutions Water 6 ml 4 mg/ml WS6
Follow the instruction below for each vial of working solution that
should be prepared. Wrap eppendorf tubes with “parafilm”. 1. Weigh the BSA sample according to above and put it into a 15
Store at –20°C until use. ml “falcon tube”.
2. Add water according to above.
3. Vortex until the entire sample is dissolved.
4. Distribute the sample into 1 ml Eppendorf tubes (e.g. 1
ml/tube) and wrap with “parafilm”.
5. Store at –20°C until use.
contents
2.2.3.3.3 Preparation of Phosphorylase B working solution 2.2.3.5 Preparation of test slides
Michrom Components Amount Final conc. Termed 2.2.3.5.1 1.5 pmol Ile7-AngIII and 1.5 pmol hACTH18-
Bioresour- 39Slide A spot1-6 and Slide B spot 1-11
ces order# 1. Add 6 ml WS1 (2.11.3.3), 6 ml WS2 (2.11.3.3) and 12 ml
910-0002-- 1 vial 500 pmol ACHCA matrix solution (prepared according to 2.11.3.1.4) to
29 Phosforylase an Eppendorf tube.
B digest. 2. Mix by pipetting up and down 5 times
3. Add 0.3 ml to each appropriate spot (see 2.11.4).
Buffer A 500 µl 1 pmol/µl WS7 4. A maximum of 12 spots can be spotted before a new prepa-
ration must be made.
1. Mix according to table
2. Vortex for 30 seconds 2.2.3.5.2 5 fmol Neurotensin; Slide A spot 9-10 and Slide
3. Store at –20°C until use. B 16-19
2.2.3.4 Preparation of dilution series 1. Add 10 ml D6 (2.11.3.4) and 10 ml ACHCA matrix solution
(2.11.3.1.4) to an Eppendorf tube.
A diluted sample must be spotted within 1 hour after prepara- 2. Mix by pipetting up and down 5 times.
tion (as quick as possible).
Name Amount Buffer A Final conc. Termed 4. A maximum of 6 spots can be spotted before a new prepa-
from ration must be made.
previus
dilution
2.2.3.5.3 100 fmol Phosforylase B digest with internal
Neurotensin 5 l WS3 145 µl 33 fmol/ µl D6 calibrants; Slide A spot 11-15 and Slide C spot 1-4
Hexa-L-Tyr- 5 l WS4 495 µl 200 fmol/ µl D 16 1. Add 6 ml WS2 (2.11.3.3), 4 ml WS1 (11.3.3) and 90 ml
osine ACHCA matrix solution (2.11.3.1.4) to an Eppendorf tube.
2. Mix by pipetting up and down 5 times.
Phosforyla- 10 l WS7 10 µl 500 fmol/µl D 17 3. Add 6 ml of the solution above and 12 ml of D17 (2.11.3.4)
se B to a new Eppendorf tube.
contents
4. Mix by pipetting up and down 5 times. 2.2.3.5.7 50 fmol fmol Phosforylase B digest with internal
5. Add 0.3 ml to each appropriate spot (see 2.11.4). calibrants; Slide C spot 5-8
6. A maximum of 10 spots can be spotted before a new prepa- 1. Add 10 ml from the100 fmol solution made in step
ration must be made. 2.11.3.5.4 to an Eppendorf tube and 10 ml ACHCA matrix solu-
tion (2.11.3.1.4).
2.2.3.5.4 3 pmol Hexatyrosine; Slide A spot 16-19 2. Mix by pipetting up and down 5 times.
1. Add 6 ml WS4 (2.11.3.3.2) and 6 ml ACHCA matrix solution 3. Add 0.3 ml to each appropriate spot (see 2.11.4).
2. Mix by pipetting up and down 5 times. 2.2.3.5.8 5 fmol Phosforylase B digest with internal
3. Add 0.3 ml to each appropriate spot (see 2.11.4). calibrants; Slide C spot 9-12
4. A maximum of 10 spots can be spotted before a new prepa- 1. Add 10 ml from the 50 fmol solution made in step 11.3.5.8
ration must be made. to an Eppendorf tube and 10 ml ACHCA matrix solution
(11.3.1.4).
2.2.3.5.5 30 fmol Hexatyrosine; Slide A spot 20-24 2. Mix by pipetting up and down 5 times.
1. Add 6 ml D16 (2.11.3.4) and 6 ml ACHCA matrix solution 3. Add 0.3 ml to each appropriate spot (see 2.11.4).
4. A maximum of 5 spots can be spotted before a new prepa-
2.2.3.5.6 5 pmol BSA; Slide B spot 20-24

1. Add 6 ml WS6 (2.11.3.2) and 18 ml Sinapic acid matrix
4. A maximum of 10 spots can be spotted before a new prepa-
contents
2.2.4 Slide layout 2.2.4.2 Slide B
2.2.4.1 Slide A
Slide Pos Sample Amount on Expected mono-
sp o t isotopic m/z [M+H]
Slide Sample Amount on spot Expected mono-
P o s. isotopic m/z 1-11 Ile7-AngIII and 1.5 pmol Ile7-AngIII
[M+H] hACTH18-39 each =897.53117
1-6 Ile7-AngIII and 1.5 pmol each Ile7-AngIII HACTH18-39
hACTH18-39 =897.53117 = 2465.19897
HACTH18-39 12-15 Ile7-AngIII 5 fmol 897.53117
= 2465.19897
16-19 Neurotensin 5 fmol 1672.89
7-10 Neurotensin 5 fmol 1672.89
20-24 BSA 3.6 fmol Monomer = 66423
Dimer = 132846
11-15 Ile7-AngIII,hACTH 180 fmol Ile7- 800<m/z< 2600
trimeer = 199269
18-39 and Iodo- AngIII
acetamide 120 fmol
modified hACTH18-39
Phosforylase 100 fmol 2.2.4.3 Slide C
B digest. Phosforylase B
16-19 Hexatyrosine 3 pmol 997.396 slide pos Sample Amount on Expected
(Adducts: sp o t monoisotopic m/z
(Na+)= 1019.396 1-8 Phosforylase B 100 fmol 800<m/z<2600
(K+)=1035.396)
9-16 Phosforylase B 50 fmol 800<m/z<2600
20-24 Hexatyrosine 3 pmol 997.396
Adducts: 17-24 Phosforylase B 25 fmol 800<m/z<2600
1019.396
Each spot Include AngIII (180 fmol) and hACTH (120 fmol) as
1035.396
internal calibrants.
contents
2.2.5 Default method parameters
2.2.5.1 Protein Digest PRO acquisition method
contents
2.2.5.2 PSD PRO acquisition method
contents
2.2.5.3 Full lenght protein PRO acqusition method
contents
2.2.5.4 Protein Digest spectrum processing method
contents
2.2.5.5 PSD spectrum processing method
contents
2.2.5.6 Full lenght protein spectrum processing method
contents
2.2.5.7 Protein digest identification method
contents
2.2.6 Verification cases 4 Reflectron sensitivity
Insert test slide A. One spectrum out Resolution
Run positions con- of five should ca n b e
taining 5 fmol Neu- contain a peak in sacrificed to
Item Test method Acceptance limits comments rotensin with the the right mass obtain the
Expected resulte following method: range with S/N>3 required S/N.
1 Linear sensitivity Acquisition method or above.
Insert test slide B (if For at least one Resolution = The default met-
not already inserted). out of five spectra ca n b e hod Protein Digest
Run two positions must contain a sacrificed PRO with the num-
containing 5 fmol ile7 peak in the right to obtain ber of spectra chan-
AngIII and two mass range with the ged to 5. Manually
positions containing 5 S/N of 3 or higher. required adjust laser power
fmol Neurotensin with S/N. and target position
the following method: to obtain optimal
Acquisition method = S/N.
Use the default method 5 Reflectron resolution
Protein Digest PRO, Insert test slide A. One of five Same as for
but change detection Run positions spectra must fulfil linear
mode to linear and containing 1.5 pmol all the following resolution.
number of spectra to Ile7-AngIII and 1.5 demands: If the
5. pmol hACTH18-39 (1) A resolution monoisotopic
Manually adjust laser using the following above 10 000 peak is out
power and target methods: FWHM. of mass
position to obtain Acquisition method (2) The signal scale do a
optimal S/N. = The default met- height (see 10.5) mass
hod Protein Digest of the monoisoto- calibration
PRO with the num- pic peak must be and save it
ber of spectra chan- 300 or higher. as a system
ged to 15. (3) The mass of calibration
contents
3 Linear high mass 4 Reflectron sensitivity
testI Insert test slide A. One spectrum out Resolution
nsert test slide B. The monomer Run positions con- of five should ca n b e
Run positions con- (m/z = 66 423), taining 5 fmol Neu- contain a peak in sacrificed to
taining 5 pmol BSA the dimer (m/z = rotensin with the the right mass obtain the
with the following 132 846) and the following method: range with S/N>3 required S/N.
methods: Acquisi- trimer (m/z = 199 Acquisition method or above.
tion method = The 269) should all be = The default met-
default method Full present in one hod Protein Digest
length Protein PRO spectrum with PRO with the num-
with the number of S/N>3. ber of spectra chan-
spectra changed to ged to 5. Manually
5 and the lower adjust laser power
intensity for and target position
selective to obtain optimal
accumulation S/N.
changed to 2. 5 Reflectron resolution
Spectrum Insert test slide A. One of five Same as for
processing method Run positions spectra must fulfil linear
= The default containing 1.5 pmol all the following resolution.
method Full length Ile7-AngIII and 1.5 demands: If the
Protein pmol hACTH18-39 (1) A resolution monoisotopic
Manually change the using the following above 10 000 peak is out
laser power and methods: FWHM. of mass
sample position in Acquisition method (2) The signal scale do a
order to obtain the = The default met- height (see 10.5) mass
best possible S/N hod Protein Digest of the monoisoto- calibration
on the m/z = 66423 PRO with the num- pic peak must be and save it
p e a k. ber of spectra chan- 300 or higher. as a system
ged to 15. (3) The mass of calibration
contents
5 Spectrum Process- the monoisotopic and rerun the tolerance (A0) to resolution on
cont ing method = The peak must be sample. 0.02%. Identification ile7AngIII must be
default method within 2465.19897 method = The above 3000.
Protein Digest. +/- 1 Da. default method
6 Mass accuracy Protein digest but
reflectron mode with add the
internal calibration. The modification
Insert test slide A . Two of five calibration Iodoacetamide in
Run a position spectra must fulfil should be the "all appropriate
containing 180 fmol the following performed residues modified"
ile7AngIII, 120 fmol criteria. automatically field.
hACTH18-39 and 1. The protein on ile7AngIII Manually change the
225 fmol Phosforylase B and laser power and
Iodoacetamide must be identified hACTH18-3- position to get an
modified as the top rank. 9. The mass optimal trade off
Phosforylase B 2. At least 15 errors can be between resolution
digest. Use the masses must be read directly and number of
following methods: assigned to in the clearly visible
Acquisition method Phosforylase B identification p e a ks.
= The default and more than result
7 Mass accuracy The mass
method Protein 40% of the (protein
reflectron mode with errors can be
digest but change masses must details).
external calibration read directly
the number of have a mass error
Use the same Same as in 6 but in the
spectra to 5. below 20 ppm in
results as in item 6. more than 30% of identification
Spectrum the mass range
Select a good the masses must result
processing method m/z 900-2500.
spectrum from the have an mass (protein
= The default 3. The resolution
first position and error less than details).
method Protein on hACTH18-39
save the calibration 100 ppm.
digest but change must be above
on this spectrum as
monoisotopic mass 6000 and the
contents
7 system calibration 8 reflectron = The and the signal
cont (both calibrants cont default method height should drop
must have been Protein Digest PRO more then tenfold.
found and have with number of 3. With the gate
clear monoisotopic spectra changed to set to 1980, the
resolution). 1. Spectrum resolution of the
Then load the processing method 2007 peak should
system calibration reflectron = The disappear and the
on all other spectra default method signal height
on the other 3 Protein digest should drop more
positions and add Acquisition method then tenfold.
the identification PSD = The default
method again. method PSD PRO
but change the num-
8 Ion gate calibration
ber of spectra to 5.
Insert test slide A. 1. With the gate See 10.1
In "waiting for PSD
Run a position con- set on 2007, a page 3 for
input" view, set the
taining 180 fmol peak with ion gate
gate on the follow-
ile7AngIII, 120 fmol resolution above calibration.
ing masses;
hACTH18-39 and 2000 FWHM and
2007.114 (true pep-
225 fmol Iodoace- signal height
tide mass), 2040
tamide modified above 200 should
(noise peak) and
Phosforylase B be present at a
1980 (noise peak).
digest. Add mass of 2007 +/-
Adjust the gate
methods for both 1 D a.
width to 2 for all
reflectron and PSD 2. With the gate
masses. Adjust
to the position. Use set to 2040, the
laser power and
the following resolution of the
position manually to
methods: 2007 peak
achieve good
Acquisition method should disappear
resolution and S/N.
contents
9 PSD performance, 9 with the number of
PSD mass cont spectra changed to
accuracy test 5.
Insert test slide A. Two out of five Spectrum proces-
Run positions with 3 spectra must fulfil sing method PSD =
pmol Hexatyrosine. the following The default method
In the "waiting for demands. PSD with a smoot-
PSD input" view; (1) Peaks with hing filter of width 8
calibrate the S/N>3 added. Manually
reflectron spectrum representing all adjust position and
using the mono- the following laser power to ob-
isotopic masses masses must be tain good resolution
997.396 and present; 816.888, and S/N in reflect-
1019.396. Use the 653.712, 490.536, ron mode and best
following methods 327.360. possible S/N in
for the run: (2) The mean PSD mode.
Acquisition method value of the errors Open the results in
reflectron = The de- (calculated from Evaluation. Use a
fault method Protein the absolute value spectrum on the first
Digest PRO with of measured position to calibrate
the number of spec- mass - true mass) the PSD mode
tra changed to 1. must be lower (save the calibration
Spectrum proces- than 1,0 Da. as system calibra-
sing method tion). Use the exact
reflectron = The average masses
default method Pro- 998.07 and 327.36
tein digest. for this purpose.
Acquisition method Finally, add the
PSD = The default PSD spectrum
method PSD PRO processing method
contents
9 described above 10 Acquisition method
cont and load the system cont PSD = The default
calibration on each method PSD PRO
position. with the number of
spectra changed to
10 PSD sensitivity test
5.
Insert test slide A. Two out of five
Spectrum proces-
Run positions with spectra must fulfil
sing method PSD =
60 fmol Hexatyro- the following
The default method
sine. In the "waiting demands:
PSD with a smoot-
for PSD input" view; 1. Peaks with
hing filter of width 8
calibrate the reflec- S/N>3
added.
tron spectrum using representing all
Manually adjust pos-
the monoisotopic the following
ition and laser pow-
masses 997.396 masses must be
er to obtain good
and 1019.396. Use present; 816.888,
resolution and S/N
the following met- 653.712, 490.536,
in reflectron mode
hods for the run: 327.360.
and best pos-sible
Acquisition method 2. The mean value
S/N in PSD mode.
reflectron = The de- of the errors
Open the results in
fault method Protein (calculated from
Evaluation. Use a
Digest PRO with the absolute value
spectrum on the first
the number of spec- of measured
position to calibrate
tra changed to 1. mass - true mass)
the PSD mode
Spectrum must be lower
(save the calibration
processing method than 1,0 Da
as system calibrat-
reflectron = The
ion). Use the exact
default method
average masses
Protein digest.
998.07 and 327.36
contents
characteristics, MCP´s etc). The method settings therefore
10 for this purpose.
need to be regularly checked. The same is true after service or
cont Finally, add the
transport operations.
PSD spectrum
processing method
described above 2.2.8 Description of laser Characteristics in Ettan MALDI-
and load the system ToF Pro
calibration on each
position. 2.2.8.1 Sample slide dimensions.
2.2.7 Auto tuning setup.
The sample slide consist of 24 different sample positions
An important function in order to perform high-throughput ex-
separated a distance of 2.25 mm (center to center). The diam-
periments with MALDI-TOF MS is automatic data acquisition.
eter of each sample position is 1.55 mm (see Figure 1).
The Ettan MALDI-TOF auto-tuning algorithm is designed to
support this function. Laser power and sample position is
changed, according to the rules of the algorithm, in order to 1.55 mm
obtain peaks with high signal to noise ratio as well as
monoisotopic resolution. However, for the automatic acquisi- 2.25 mm
tion to function properly settings for the auto tuning as well as
the acquisition methods have to be optimized. In this memo
the function of the auto-tuning algorithm is described, followed
by optimization procedures in order to find start settings for Figure 2. Sample slide
Figure 1. Sample slide dimensions.
different instrument modes. It should be noted that these set- movement.
tings most likely need tailored optimization for each individual
instrument on the market (depending on laser characteristics). 2.2.8.2 Spot size and Laser intensity profile
Optimal settings is also influenced by which type of matrix that
In Ettan MALDI-ToF Pro the laser beam is focused at a con-
is used as well as sample preparation, (matrix type, relative
stant position (in the plane of the sample slide) that is aligned
matrix quantity, solvent type, salt content, spotting technique
with the extraction lens of the accelerating system. The laser
etc.).
spot is moved over the sample slide by movement of the sam-
It is important to stress that after a certain period of instrument
usage the characteristics of the instrument will change (laser
contents
ple slide itself. Movement is only performed in one direction
(see Figure 2).
The focused laser spot is shaped like an ellipse with the ap-
proximate dimensions of 0.8x1.6 mm (1.6 mm in the direction
of slide movement). However, the laser intensity varies over
the spot area. The maximum intensity and intensity profile
varies between laser individuals. See Figure 3 for intensity
profiles from 5 different laser individuals (white = highest inten-
sity). The size of the area with intensity between 80-100% of
the maximum is normally between 0.08-0.15x0.25-0.5 mm
(0.25-0.5 mm in the direction of movement).
Figure 3A-E. Different laser profiles.
contents
2.2.8.3 Control of laser power
The amount of laser energy delivered at the sample surface is

controlled with an optical density filter wheel. The filter is linear
in optical density i.e. the transmission of laser intensity follows
a logarithmic function. The function describing the relationship
between the laser power in the software and percentage of
transmitted laser intensity is described in equation 1.
T(%) = 100*10 –1.3*(1-laser power/900)
Equation1
Since the desorption process in MALDI is a threshold phenom-
ena, the size of the active laser spot (area of ionization) will be
different for different laser individuals and applied laser pow-
ers.
2.2.9 Description of the auto tuning algorithm
2.2.9.1 Included parameters
The first auto tuning parameter can be found in the MALDIDEF

program under slide details and is called sample slide subdivi-
sions (see Figure 4). This parameter defines the total number
of incremental changes for each sample position and also the
size of each incremental position change (smallest possible
displacement of the sample slide). If the parameter is set to 64
(default), the incremental position change will be 1.55/64 mm.
contents
total tuning time for the position has reached the time-out limit.
The selective accumulation box set the criteria for accept-
able data for accumulation. For each 1- or 8-shot bundle, the
highest and the lowest intensity value in the defined mass
range (as defined by the low and high values in Figure 5) are
extracted. The difference between the highest and the lowest
value is calculated and divided by the laser frequency (1 or 8).
If the obtained value falls within the defined intensity range,
the signal from the bundle (1 or 8 shots) is accumulated. If not,
the laser power or target position is changed according to the
auto-tuning algorithm (see below). For each change in laser or
position performed during the auto tuning the first shots (the
exact number specified by the parameter ”No. Of initial shots
to ignore”) are neither accumulated nor considered by the
auto-tuning algorithm.
Figure 4. The slide subdivision parameter is defined in the slide details

menu of the MALDIDEF program. This parameter defines the size of an
incremental positional change. (The greyed out boxes are instrument
constants and should never be changed). See text for details.
g
eu
F
ri
Ten of the parameters can be found in the acquisition method
(see Figure 5). The Tuning start box set the initial values for
sample sub position and laser power. The Accumulate until
and duration boxes define the termination criteria for each 5. The parameters of the acquisition method that influence auto tuning.
sample position. The auto tuning/data collection for a spectrum See text for details.
is terminated, as the accumulated number of shots in the
The remaining parameters can be found in the Auto tune set
spectra reaches the specified value (No of shots) or when the
up (MALDIDEF program, see Figure 6).
highest peak in the spectrum reaches the specified intensity
value. Change to a new sample spot occurs when the defined
number of spectra (No. Of spectra) is reached or when the
contents
2.2.9.2 Functions of Auto tuning algoritm Once the algorithm has reached refine mode, it can never go
back to initial or fast scan mode. If several spectra should be
collected, a change to a new spectrum will not affect the algo-
The auto tuning algorithm has three different search modes;
rithm. The auto tuning is terminated when the specified
the fast scan mode, the initial mode and the refine mode (fig-
number of spectra has been acquired, or when the time out
ure 6 and 7).
limit is reached.
2.2.9.2.1 Fast scan mode

A
During fast scan the laser is kept at its initial value while the
whole sample position is searched in the number of steps
specified by the Consecutive Adjustments parameter (figure 6
and 7). If an acceptable shot is found the algorithm continues
to refine mode. If no acceptable shot is found during fast scan,
the algorithm continues to initial mode.
2.2.9.2.2 Initial and refine mode
During initial mode, changes in laser and position are alter-

nated in order to find acceptable data (figure 6). Here each
sample movement is defined as one single subset of the total
number of subdivisions. In other words, if the number of subdi-
visions is 64 and slide consecutive adjustment is set to 4, the
total sample position adjustment in each iteration will be (4/ Figure 6. An example of the auto tune set-up window and the different
64)x1.55 mm. Refine mode is reached when acceptable data parameters that influence the rules of the algorithm. The crossed boxes
has been found. The same rules as for initial mode apply. At are non-active (=have no function).
the same time as the algorithm changes from initial to refine
mode, the laser value is set back to the initial laser value.
contents
Fast scan Initial (or refine) mode
B
Signal
No signal Signal
Figure 8. Examples of the difference in incremental changes between

Figure 7. (B). A general description of the logistics of the different tun- fast scan and initial mode. During Fast Scan the whole target is
ing modes. During automatic data acquisition auto tuning searched in large steps whereas in initial and refine mode each incre-
mental change is smaller. In this example the number of subdivisions is
set to 64 and consecutive adjustments is set to 4 in both cases. This will
2.2.9.2.2.1 Positional changes mean that for fast scan mode the whole sample will be covered in 4
consecutive steps and each step with a distance of 16/64 * 1.55 mm.
However in initial and refinement mode the total change in each iteration
The number of changes in position is specified by the param-
will be (4/64) * 1.55 mm. See text for details.
eter sample position consecutive adjustments. The magnitude
of each change is controlled by the parameter sample slide
subdivisions (figure 4). The rules for each incremental 2.2.9.2.2.2 Laser changes
positional change is different in fast scan mode compared to
initial and refinement mode (figure 8).
The number of laser changes in each iteration is specified by
The following is true for fast scan mode: if the subdivisions
the parameter laser power consecutive adjustments (figure 6
parameter is set to 64 and the Consecutive Adjustments set to
and 7). The magnitude of each change is controlled by four
4 the sample will be moved 4 times and each time a distance
user controllable parameters (start laser power, laser power
of 16 subdivisions (16/64 x 1.55 mm). However, for initial and
maximum adjustments, laser power maximum value and laser
refinement mode the same settings will result in a total sample
power check value) and three laser reference variables; Lower
position adjustment of (4/64) x1.55mm.
laser reference, current laser value and upper laser reference
(see, figure 5,6 and 7). The laser reference values are dy-
namic values influenced by the data generation on both the
previous and the current sample spot. The reference values
are changed in order to direct laser changes to a range were
acceptable data has recently been detected.
contents
1. If the intensity difference of a 1- or 8-shot bundle is lower 2.2.10 Recommended settings of Auto tune parameters
than the specified intensity range (see figure 5) the laser value
is normally increased. The algorithm always ”wants” to change In general, we recommend that settings for each type of sam-
the value to halfway between the current laser value and the ple are optimized according to the guidelines in section 5. The
upper laser reference. However, this value can be modified by most important measurement types are described below.
the constraints set by the parameters described above (laser
power maximum adjustments, laser power maximum value 2.2.10.1 Protein mass fingerprinting analysis with 4-hy-
and laser power check value). The laser power check value droxy-alpha-cyano cinnamic acid as matrix.
function as a control point (checkpoint) in order to lower the
risk that the laser energy will raise to rapidly*. If the value of 2.2.10.1.1 Auto tune set-up
the proposed laser change is larger than the check value, the
laser will be set back to the initial laser value and the upper The greyed out boxes contain default values and should not
laser reference is changed to the check value. The constraints be changed (see 2.2.11). Don’t forget to deactivate the check
set by laser power maximum adjustments and laser power value (insert value zero, see below)
maximum value are straightforward.
2. If the intensity is higher than the specified intensity range,
the laser value will be decreased. The algorithm wants to
change the value to halfway between the current laser value
and the lower laser reference. The change is influenced by the
laser power maximum adjustments parameter. toSet
according
to 2.2.11.1
*The optimization procedure includes deactivation of the laser power check value
(see 2.2.10.1.1) since there are other embedded features of the software correcting
for the same thing. 6 4 4
contents
2.2.10.1.2 Acquisition method
Set to 30 Set Set according to

according to 2.2.11.3
2.2.11.1
contents
2.2.10.2 Post source decay with 4-hydroxy-alpha-cyano cinnamic acid as matrix
Except for the parameters in the acquisition method, the same parameters as in peptide mass fingerprinting can be used.
set according to 2.2.11.1
set according to 2.2.11.3
contents
2.2.10.3 Full length protein analysis with sinapinic acid as
matrix
2.2.10.3.1 Auto tune set-up
The greyed out boxes contain default values and should not
be changed (see 2.2.11.1).
toSet
according
to 2.2.11.1
6 4 4
contents
32
Set according to Set according to Set according to

2.2.11.1 2.2.11.2 2.2.11.3
contents
2.2.10.4 Acquisition method for tuning of initial laser
power
Low Mass rejection and auto tuning is disabled and that the 3
first shots should be ignored.
100
3
contents
2.2.10.5 Acquisition method for tuning of intensity range
for selective accumulation (PMF)
contents
2.2.11 Guidelines for optimization of parameters “auto adjust laser power” as well as “sample position” and
successively increase laser power (in quite large steps) until
Depending on the type of samples analysed, matrix type, laser you reach the point just above threshold where signals are
characteristics of the instrument etc., different parameter set- accumulated.
tings are needed. Guidelines for starting optimizing the param- 4. Decrease laser with 80 units, move the slide 20 subposi-
eters are found below. tions and then successively increase laser power, 20 units in
each step. If an increment of laser power does not results in
any signal accumulation after approximately 5 seconds (or
2.2.11.1 Initial laser power and laser power adjustment less), increase the laser power by 20 units. It is important to
parameters perform the different iterations swiftly in order to avoid unnec-
essary loss of material. Threshold value is reached when (at
Desorption and ionization in MALDI is a threshold phenomena. least) one spectrum (80 shots) is automatically accumulated.
The laser threshold varies largely with the type of matrix used, Then move the slide another 20 subpositions and perform the
the specific laser of the instrument and (to a lesser extent) the described laser adjustment procedure once again. Record
nature of the matrix crystals (not homogeneous matrix layers). each threshold laser value for 10 sample positions.
For good results it is important that the laser is operating in a 5. Remove the laser threshold values those obvious differ
power regime ranging from the lowest threshold value to from the data set and then calculate the average threshold
slightly to moderately above the highest threshold value for a laser power and set the initial laser power to that value. For
certain matrix. To set appropriate values for laser parameters PSD investigations, set the initial laser power to 1.4 x average
we recommend you to start with the following procedure. threshold value.
1. Prepare a matrix solution of the matrix you want to optimize 6. Remove the laser threshold values those obvious differ
the laser settings for. Spot the solution to all 24 positions on a from the data set (as above). Calculate the value 1.2 x (maxi-
sample slide using the same spotting method you are using for mum threshold value – minimum threshold value)/4 and set
real samples. the laser power maximum adjustments value for both initial
2. Investigate the threshold value for the different positions by and refine mode to the closest upper multiple of 10. If the
using the acquisition method described in 2.2.10.4. maximum threshold value is 240 and the minimum threshold
value is 150 this yields a value of 30.
3. Start acquisition. The first step is to approximately find the
range where the threshold value is. In processing view, disable 7. Set the laser power consecutive adjustments to 4 in initial
mode and 2 in refine mode.
contents
2.2.11.2 Mass range for selective accumulation concentration, presence of other molecules, ease of ionization,
The mass range used for selective accumulation should cover incorporation in the matrix, type of matrix and heterogeneity of
the m/z range in which most of the analytes are likely to ap- the sample.
pear. If possible, m/z areas often displaying contaminating
peaks should be avoided. 4-hydroxy-alpha-cyano cinnamic Resolution Signal intensity
acid generates cluster ions in the range of m/z = 190-1000.
Therefore, for PMF, it is recommended to set the lower mass
range value to 1000 when this matrix is used. The recom-
mended upper mass range value for PMF using 4-hydroxy-
alpha-cyano cinnamic acid is 2200 in order to tune on analyte Laser power
signal instead of calibrants.
For PSD, the mass range for selective accumulation should Threshold value
cover as much of the expected fragment ion range without

including the parent mass. For an unknown sample, the rec- Figure 9
ommended mass range is m/z = 200-800. If more is known At best, the instrument should always operate close to the resolution
about the sample, the upper limit can be changed (if it is optimum or somewhat to the right. The intensity range for selective
known that all parent masses will be above a certain value, set accumulation can be viewed as a way to guide the laser power/sample
the upper limit just below this value). position to operate close to this optimum. However, if complex samples
such as digests from 2D-gels are used, the values will be a compromise.
For analysis of full-length proteins, set the mass range as We recommend the following procedure as a starting point for optimiza-
narrow as possible around the expected mass range of the tion of peptide mass fingerprinting and full-length proteins.
analytes.
2.2.11.4 Optimisation procedure for peptide mass finger-
printing
2.2.11.3 Intensity range for selective accumulation
1. Prepare a matrix solution of the matrix you want to optimize
The qualitative dependence of resolution and signal intensity the settings for. Spot the solution to all 24 positions on a sam-
on laser power for a peptide can be described according to ple slide using the same spotting method you are using
Figure 9. The exact shape of the curves will vary heavily for a
for real samples.
certain molecule (and for different molecules) depending on
contents
2. Use the same acquisition method as described in 4.4 but 2. Create a new PSD acquisition method using the default
use a constant laser of 1.2 x average threshold level (closest PSD Pro method but with a start laser power of 1.5*minimum
lower multiple of 10), a low ion reject value of 500, a mass threshold. Acquire PSD data from different positions. Set the
range of 1000-2200 (m/z). Set the lower limit for selective gate to m/z =900, 1500 and 2000 (by selecting a noise peak at
accumulation different values for different positions (from 1 to that mass in “Waiting for PSD input” view). For each gate
10). Acquire data from the different positions and find out the value, try different values of the lower intensity value to find
background noise level (chemical and electrical), i.e. a lower out the background noise level.
limit that just barely yields accumulation.
3. Set the lower intensity limit to a value that avoids accumula-
3. Set the lower intensity limit for selective accumulation to a tion of background noise regardless of gate value.
value that avoids accumulation of background noise.
4. Set the upper range for selective accumulation to 10 x
4. Set the upper limit for selective accumulation to 10 x lower lower limit for selective accumulation.
limit for selective accumulation.
5. Preferentially verify the your settings on a CAF-derivatized
5. Preferentially verify your settings on a digested gel sample sample lacking proteins (a blank). The lower intensity limit
lacking proteins (a blank). The lower intensity limit for selective might need some fine-tuning.
accumulation might need some fine-tuning, due to higher salt
content leading to higher chemical noise (matrix clusters etc). 2.2.12 The test procedure of automatic acquisition
If there are problems with matrix clusters in the mass range >
500 (m/z) the low mass reject can be changed to 750 (m/z)).
2.2.12.1 Introduction
2.2.11.5 Optimisation procedure for PSD analysis One of the most important steps during a installation of a Maldi
Pro is to optimize the auto tuning set up and the start settings
1. Prepare a matrix solution of the matrix you want to optimize for different run modes. The procedures for this are described
the settings for. Spot the solution to all 24 positions on a sam- in chapter 2.2.7-2.2.11.5.
ple slide using the same spotting method you are using for
This section describes a test that is aimed to verify the per-
real samples.
formance of automatic acquisition (after method optimization).
This is a part of the acceptance test for Ettan MALDI ToF Pro.
contents
2.2.12.2 Software methods 2.2.12.4 Spectrum processing method (spm)
The following section describes the software methods that

should be used for the automatic acquisition test. Use the
same method set-up for all of the positions of the test slide.
When the method set-up is finished, “click-off“(deactivate)
position 13-24 of the slide in the spectrum processing view.
2.2.12.3 Acquisition method

Use the optimized method. The empty boxes represent pa-
rameters that have to be optimized for each instrument.
32
contents
2.2.12.5 Identification method clude AngIII (180 fmol) and hACTH (120 fmol) as internal
calibrants for all dilutions.
Table 1. Sample composition of the test slide.
Slide possdition Amount on target (fmol)
1-8 100
9-16 50
17-24 25
2.2.13.1 Test for verification of automatic acquisition and

identification
Assure that a current system calibration has been performed.

Insert slide C and start acquisition. The acquisition should be
performed in automatic mode. Following parameters should be
monitored:
1. Acquisition time. Total acquisition time for all 24 spectra
should not exceed 40 minutes.
2. Quality of identification result; Phosphorylase B must be
identified as the highest rank on all positions. 20 of 24 spectra
must have an expectation below 0.01.
2.2.13 Samples
Standard sample preparation methods should be used. Pre-

pare a slide of rabbit Phosphorylase B (Microm BioResources
Inc.) with the composition described in table 1 (Slide C). In-
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Document the results in table 2. During acquisition, spectrum
16 50
processing methods and identification methods can be inserted
into spectrum 2 of processed positions order to save time. 17 25
Spectrum Amount on target (fmol) Expected value 18 25
1 100 19 25
2 100 20 25
3 100 21 25
4 100 22 25
5 100 23 25
6 100 24 25
7 100 Total run time:
8 100 2.2.13.2 Important notes
9 50
· The internal calibrants of slide C are in large excess result-
10 50 ing in the fact that these 2 peptides will be the dominating
ones in the spectra. This is particularly true for the digests of
11 50 low concentration. The quality of the acquisition is best viewed
if a mass window that is narrower than the mass range for the
12 50
calibrants are used.
13 50 · To assure high-quality identification of the material of test
slide C, assure that a high quality system calibration recently
14 50
has been performed.
15 50 · Assure that the sample slide was prepared in less than 48
contents
hours ago. The matrix is degraded with time leading to lower 1 +…Probability N*isotopic mass N). The probability for pep-
sensitivity, something that is critical for samples with low tides containing one or several C13 atoms increases with in-
amount. creasing peptide mass (Increasing number of carbon atoms).
· If the instrument does not pass test for automatic acquisi- The difference between an average and a monoisotopic mass
tion, please contact the person responsible for the acquisition is approximately 0.06%. See Figure 10 and Figure 11 for ex-
optimization procedure if the instrument in question and amples of monoisotopic and average masses for two peptides
specify the problem (to long acquisition time, noise is accumu- of different mass. In the verification, monoisotopic masses are
lated instead of analyte signal, etc). used for mass accuracy measurements in reflectron and aver-
age masses are used for mass accuracy measurements in
PSD (and for the masses reported in high mass sensitivity).
2.2.14 Measurement definitions The software will automatically calculate these masses if the
correct method settings are used (see Ettan MALDI-ToF Pro
2.2.14.1 Monoisotopic and average masses user manual).
Molecules are made up of chemical elements and elements

have naturally occurring isotopes with unique abundance.
Peptides and proteins are rich in carbon, hydrogen, nitrogen
and oxygen. Depending on what type of isotopes that are in-
corporated in a peptide the mass will differ, even though it is
chemically the same compound. For peptides, carbon is the
molecule that dominates the isotopic distribution. Approxi-
mately 99% of all carbon atoms are C12 and 1% are C13. The
monoisotopic mass is the mass of the isotopic peak whose
elemental composition is composed of the most abundant
isotopes of those elements. For peptides this means a peak
corresponding to peptides with only C12 atoms incorporated.
The second isotopic peak corresponds to peptides with one
C13 atom incorporated and so on. The average mass is the
sum of the isotopic masses weighted by the probability for the
occurrence of each isotopic mass (probability 1*isotopic mass Figure 10
contents
Baseline
Figure 12
Figure 11 2.2.14.3 Calculation of signal height

The signal height for a peak is here defined as the difference
between the baseline value and the signal value at the maxi-
2.2.14.2 Calculation of the baseline
mum of the peak of interest. The baseline value should be
calculated in an area +/- 10 Da outside the peak area. See
Here the baseline in a mass spectrum is defined as the aver- Figure 13 for an example.
age value of all sampled signal values in an area, see Figure
12 for an example. The baseline values will therefore change
over the mass range depending on the definition of the area
that it is calculated in.
contents
Signal height
Peak signal R = (m/z)/FWHM
m/z
FWHM
10 Da 10 Da
W
M
H
F
Area for baseline calculation Figure 14
2.2.14.5 Calculation of signal to noise (S/N)

Figure 13 The noise level is here defined as the standard deviation
around the baseline in an area +/- 10 Da outside the peak
2.2.14.4 Calculation of resolution area of interest. The signal to noise is then calculated as the
signal height (2.2.14.3) divided with the noise level. See Figure
The resolution of a peak is here defined as the mass of the 15 for an example. S/N values have to be calculated manually
peak divided with the width of the peak at half the signal height for the tests described above. For practical work the
(2.2.14.3). Resolution calculated in this way is called FWHM calculation can be simplified based on experience.
(Full Width at Half Maximum). See Figure 14 for an example.
Resolution (FWHM) for monoisotopic peaks are calculated
automatically in the software and displayed in the mass list.
These values can be used for the tests described in 2.2.6.
contents
This is a theoretical definition of noise and is fully correct but
difficult to use. To make it user-friendlier we calculate the noise
as follow:
Signal height Noisep-p/2
Peak signal
So the calculation off s/n is done as follows:
signalp-p∗2/noisep-p
2.2.14.6 Calculation of mass errors in PSD
10 Da 10 Da
Mass errors for investigation of PSD mass accuracy should be
calculated in the following way.
(1)Average mass error = (1/n)∗∑√((measured massi-true
mass)2); where j = 1 to n and n = number of fragments.
(2)Maximum fragment error = maximum of all √((measured
mass-true mass)2).
Area for baseline and noise level calculation

2
Noise level = √(1/(n-1))*∑(signal valuej – Baseline)
where j = 1 to number of datapoints (= n) in area defined

above.
Figure 15
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2.3 Acceptance test document
Technical Specification
The following pages contains a copy of the acceptance test

document. This document should be filled in during the instal- Archive in PARC
lation of a Maldi ToF Pro. When the installation is finished and Minimum retention time: 10 years after termination of the product(s) concerned document no.
edition
219223509
AA
all specification has been achieved and demonstrated to the

page 1(6)
title
customer the final page of the acceptance test has to be Maldi Pro acceptance test
project name date
signed by the customer. If the customer does not sign the Protfly
author(s)
Mats Källgren
2003-03-03
project no
986148
acceptance test the installation has not been completed.
approved by
Anders Tangen
Customer:
Department:
Street:
City:
Post code:
Telephone:
Fax:
Email:
User:
Instrument:____________________________
Serial number:________________________________
Version:_____230V ,_____110V
Computer type: ___________________________ Serial number:___________________
RAM size:_____Mb, HDD size:________Gb, Bios version:______________

Monitor type: ______________________Serial number:_______________________
Printer type: _______________________Serial number:_______________________

Operating system:__________________ Serial number:_______________________
Service pack version:_______________
Software type/version: ______________ Serial number:________________________
Valid from 2002-01-01 70-7611-09 / AH
contents
Technical Specification Maldi Pro acceptance test
document no. 219223509
Maldi Pro acceptance test edition AA
document no. 219223509 page 3 (6)
edition AA
page 2 (7)
Reflectron resolution test
Acceptance limit: Resolution> 10000, FWHM (R) for the monoisotopic peak in the isotopic
cluster of 1.5 pmol hACTH 18-39. The result should be obtained accumulating 200 shots per
spectrum in 8-shots mode.
All methods used in these tests are described in the installation guide. The preparation of hACTH 18-39 Resolution
samples for the tests is described in the installation guide. 2465,199 m/z
Linear mode performance Mass accuracy
Mass accuracy with internal calibration

Linear sensitivity test
Acceptance limit: S/N > 3 for the m/z 1672.89 peak of 5 fmol Neurotensin, accumulating 200 Compare measured masses with theoretical, using 100-fmol iodoacetic acid modified
shots per spectrum in 8-shots mode. phosphorylase b tryptic digest.
Acceptance limit: More than 15 masses must be assigned to Phosphorylase B and for 40% of
the assigned masses, the error should be equal or less than 20 ppm, in the mass range 900-
Neurotensin 5 fmol Signal to noise
2500 m/z.
1672,89 m/z
Mass errors
Linear Resolution test total matched <20ppm
First approved
Acceptance limit: A resolution t1000, FWHM (R) should be achieved for the monoisotopic spectrum
peak in the isotopic cluster of 1.5 pmol Ile 7 Ang III, m/z 897,531. The result should be Second approved
obtained accumulating 200 shots per spectrum in 8-shots mode. spectrum
Ile7 Ang III 1.5 pmol Resolution

897,531 m/z Mass error with external calibration
Linear High Mass Test.
The monomer, m/z 66431, the dimer, m/z 132859 and the trimer, m/z 199287 of 5 pmol BSA Compare measured masses with theoretical, using 100-fmol iodoacetic acid modified
should be detected in the spectra. The result should be obtained accumulating 200 shots per phosphorylase B.
spectrum in 8-shots mode. Acceptance limit: More than 15 masses must be assigned to Phosphorylase B tryptic digest
and for 30% of the masses, the error should be equal or less than 100 ppm.
BSA full-length 5 pmol Detected
66431 m/z
BSA dimer at 132859m/z Mass errors
total matched <100ppm
BSA trimer at 199287m/z First approved
spectrum
Reflectron mode performance Second approved
spectrum
Reflectron sensitivity test
2002-01-01 70-7611-09 / AH 2002-01-01 70-7611-09 / AH
contents
Technical Specification Technical Specification
Maldi Pro acceptance test Maldi Pro acceptance test

document no. 219223509 document no. 219223509
edition AA edition AA
page 4 (6) page 5 (6)
Post Source Decay (PSD) performance

Table 2.
Spectrum Amount on target Expectation
(fmol) value
PSD sensitivity test 1 100
2
3
The fragment masses of 60 fmol Hexatyrosine (m/z 997.396) should be detected and 4
annotated. Acceptance limit: In a spectra the following fragment ions must be detected with 5
S/Nt 3, b2=327.36; b3=490.536; b4=653.712; b5=816.888. 6
7
8
9 50
PSD mass accuracy test
10
11
12
Acceptance limit: The average mass error of the fragment masses, m/z 327.36, 490.536, 13
653.712 and 816.888 of 3 pmol Hexatyrosine must be below +/- 1 Da and the mass error of 14
one individual fragment peak must not exceed1.5 Da. 15
16
17 25
Hexatyrosine B2=327.36 B3=490.536 B4=653.712 B5=816.888 18
S/N 19
FRAGMENT M/Z 20
21
ERROR 22
23
24
Test of automatic acquisition.
Total run time:
For 24 positions of a slide, containing 100, 50 and 25 fmol iodoacetic acid modified
Phosphorylase B and after accumulation of 1 spectra on each position, following criteria must
be fulfilled:
Acquisition time. Total acquisition time for all 24 spectra should not exceed 40 minutes.
Quality of identification result; Phosphorylase B must be identified as the highest ranked
candidate on all positions. 20 of 24 spectra must have an expectation below 0.01.
Results should be documented in table 2.
2002-01-01 70-7611-09 / AH 2002-01-01 70-7611-09 / AH
contents
Maldi Pro acceptance test

document no. 219223509
edition AA
page 6 (6)
ACCEPTANCE
Amersham Biosciences personnel have given an introduction on handling and work with the
instrument and the software.
Amersham Biosciences will not be responsible for loss of stored or generated data.
No additional software may be installed on the instrument PCs. If additional software is

installed the service and maintenance contract for that PC/instrument is no longer valid.
I here by fully accept that the Ettan MALDI-ToF Pro has passed all test and works according
specifications. I agree that installation of the instrument has been completed and warranty
begins.
Amersham Biosciences Service engineer / Application specialist
Signature:
Name:
Date: Location/Place:
Customer:
Signature:
Name:
Date: Location/Place:
2002-01-01 70-7611-09 / AH
contents
2.4 Software Installation Oracle Client: Oracle9i Client Release 1 (9.0.1.1)
Installation of Windows operating system will not be coverd Shorthand Installation Guide.doc.
in this manual. If you are attempting to install a client server installation
2.4.1 Oracle installation you also need to install Oracle client runtime
components. Please refer to document below: Oracle9i
Client Runtime Release 1 (9.0.1.1) Shorthand Installation
Guide.doc.
Database Backup: Amersham Biosciences Oracle9i
Before You Begin Database Backup Shorthand Installation Guide.doc.
This guide is shorthand installation requirement information
for Oracle9i on MS Windows. For a detail system 2.4.1.1 Oracle9i Database Installation Guide Release 1
requirements information refer to Oracle documentation (9.0.1.1) for Windows 2000
located on your Oracle CD (1 of 3) at: \Doc\ a90162.pdf
This guide is shorthand installation requirement information for
Oracle is a registered trademark of Oracle Corporation. Oracle9i on Windows 2000.
Oracle9i is trademark of Oracle Corporation. For a detail system requirements information refer to Oracle
documentation located on your Oracle CD.
You should have some Oracle DBA experiences or have
some knowledge about databases to install Oracle Data- Oracle is a registered trademark of Oracle Corporation.
base or Oracle Client and you should have some knowledge System Requirements for FAT and NTFS File Systems
about Network. Oracle Corporation recommends installing on NTFS for
Following shorthand documents can be used to install: Windows 2000.
Oracle9i Database: Oracle9i Database Release 1 (9.0.1.1)
Shorthand Installation Guide.doc Oracle9i Database System Requirements
Amersham Biosiences Specific Product Database:

Amersham Biosciences Oracle9i Database Installation
Guide Realease 1 (9.0.1.1).doc.
contents
Enterprise Manager Client on the same computer, the
minimal processor requirement is a Pentium III 866, the
Requirement Standard Edition
recommended processor requirement is a Pentium III 1
GHz, the minimal RAM requirement is 128 MB and the
Operating System Windows 2000 Note 2 recommended RAM requirement is 256 MB.
Windows 2000 Service Pack Not required; certified with 1 or higher
5
You cannot run Oracle Universal Installer and Oracle Data
Migration Assistant or Oracle Database Configuration
Minimal Processor Note 4 Pentium 166 or Pentium 200 Assistant during the same installation session on a 128 MB
computer. To run these assistants, answer No if prompted to
Recommended Processor Pentium 233 or Pentium 266
migrate or create a database. After installation is complete
RAM Note 5 128 MB (256 MB recommended) and Oracle Universal Installer has exited, run these
assistants.
NTFS file system 6
If your default temp space is less than 400 MB, then
· Oracle home drive 2.7 Gb updates the TEMP user environment variable to a location
with the required amount of space. You must reboot your
· System drive 140 Mb computer for this change to take effect.
Temp Space Note 6 400 Mb
7
Depending on how many applications are running on the
computer, you may need to further increase the paging file
Virtual Memory Note 7 Initial Size 200 MB , Maximum Size size or reduce the size of the System Global Area (SGA) if
400 MB you run out of virtual memory. Note that if temporary files
V i deo 256 Color and the paging file are both stored on the same physical
drive, a situation can occur where the space requirements
for one can limit the size of another. If your system has
limited free space, then first install the oracle9i software.
2
Windows 2000 includes: Windows 2000 Professional, After the installation is finished, create a database with the
Windows 2000 Server, Windows 2000-Advanced Server, Oracle Database Configuration Assistant.
and Windows 2000 Datacenter.
4
If you run the Oracle Intelligent Agent, Oracle Management 2.4.1.2 Install Products on Windows 2000
Server (includes Oracle HTTP Server), and Oracle
contents
Click Cancel in any Oracle Installer dialog box to exit.
To install Oracle9i Products:
1. Start your operating system. If you are running Windows
2000, log on as a member of the Administrators group.
2. Stop all Oracle applications (if any are running).
3. If installing on Windows 2000, Stop all Oracle services (if
any are running). To stop services
a. From the Control Panel, select Administrative Tools and
then select the Services icon.
b. If any Oracle services exist and have the status Started,
select the service, and click stop.
c. Click Close to exit the Services windows.
4. Insert the Oracle9i for Windows 2000 CD-ROM. The operating
system automatically detects your Oracle9i for Windows 2000
CD-ROM. The Oracle9i Autorun dialog box appears and prompts
you to make a selection:
· Install/Deinstall Products
· Explore CD
· Browse Documentation
5. Choose Install/Deinstall Products.

The following pages appears:
contents
The Oracle Installation Setting Destination dialog box
appears:
File Locations
Enter the stage location of your products and the location
where you want to install your product.
Please specify full paths with up to 32 alphanumeric
characters.
6. Click Next.
contents
Source The Select Installation Options dialog box appears:
Path: Enter the full path of the products.jar file from which
the product(s) will be installed. You may also use the
Browse button to find the products.jar file.
Note: Do not leave any fields empty.
7. Accept the default values and then click Next
(Recommended).
The Loading Product Information process bar appears:
8. Click on Product Languages….
Please wait until loading product information is finished.

contents
The Language Selection dialog box appears: The Select Installation Options dialog box appears:
10. Select Oracle9I Database 9.0.1.1.1 and then Click Next.

9. Select English and then Click OK.
contents
The Select Installation Types dialog box appears: The Loading Product Information process bar appears:
11. Select Custom and then Click Next. Please wait until loading product information is finished.
contents
The Select Product Components dialog box appears: See Checked Components:
Choose those products, which are checked in following Continue…

pages.
For information on the status of the installations, see the
Install Status column.
contents
See Checked Components: See Checked Components:
Continue… 12. Click Next.
contents
The Loading Product Information process bar appears: The Select Alternate Location dialog box appears:
Please wait until loading product information is finished. 13. Accept the default location and then click Next.
contents
The Loading Product Information process bar appears: The Create Database dialog box appears:
Please wait until loading product information is finished. 14. Select No and then click Next.
contents
The Loading Product Information process bar appears: The Summary dialog box appears:
Please wait until loading product information is finished. 15. Click Install.
contents
The Install dialog box appears: The Disk Location dialog box appears:
Installation process continues… Insert Oracle9I disk 2 into your disk drive. Installation
process continues…
contents
The Disk Location dialog box appears: The Configuration Tools dialog box appears:
Insert Oracle9I disk 3 into your disk drive. Installation Installation process continues…
process continues…
contents
The Net Configuration Assistant dialog box appears: The Directory Service Access dialog box appears:
16. Click Next. 17. Select No and then Click Next.
contents
The Listener Configuration dialog box appears: The Select Protocols dialog box appears:
18. Click Next. 19. Select TCP(ask your network administrator for help)
and then Click Next.
contents
The TCP/IP Protocol dialog box appears: The Listener Configuration dialog box appears:
20. Accept the default standard port number (ask your 21. Select No and then click Next.
network administrator for help) and then Click Next.
contents
The Net Configuration Assistant dialog box appears: The Naming Methods Configuration dialog box appears:
22. Click Next. 23. Select No and then click Next.
contents
The Net Configuration Assistant dialog box appears: The Configuration Tools dialog box appears:
24. Click Finish. Installation process continues…
contents
The End of Installation dialog box appears: The dialog box appears:
25. Click Exit. 26. Click Yes.
contents
2.4.1.2 Amersham Biosciences Products Database 1. Choose Start > Programs > Oracle – OraHome90 >
Installation for Oracle9i on Windows 2000 Configuration and Migration Tools >
Before you begin: Database Configuration Assistant.
Copy file AmershamBiosciencesRDBMS.dbt to:
(ORACLE_HOME)\oracle\ora90\assistants\dbca\templates
The following pages appears:
Installation Process
contents
The Database Operation Dialog Box appears:
2. Click Next 3. Select Create a Database and then click Next.
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The Database Template Dialog Bx appears: The Database Identification Dialog Box appears:
4. Select AmershamBiosciencesRDBMS and then click 5. Accept the default values and then click Finish
Next. (Recommended).
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The Database Summary Dialog Box appears: The Database Creation Progress dialog box appears:
The installation process takes some time, please wait!
6. Click OK.
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The Database Creation Progress dialog box appears: When Database creation is complete … then the following
dialog box appears:
The installation process takes some time, please wait! 7. Click Password Management…
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The following page appears: Do not change the password for SYS and SYSTEM account
until the entire installation is complete.
8. Unlock Lock Accounts and then see the next page. All database accounts except SYS and SYSTEM have been
locked. Unlock the accounts and change the default
passwords.
Please Note the information in dialog box and keep it save.
9. Click OK.
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following page appears: Create Database Schema
Copy the Product database installation files from your media
into the HD where Oracle Database is installed, se example
below for Maldi installation:
10. Click Exit.
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11. Open an DOS Command Prompt. 12. Go to the Product database directory.
If none of Amersham Biosciences Products Databases are

already installed then for first installation at command
prompt execute:
STARTCRE SCRIPT or STARTCRE DUMP
Otherwise
STARTCRE USCRIPT or STARTCRE UDUMP
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The installation process will begin:
When Product database installation is finished, open .LOG

files in the root directory of Ora90 as below:
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Open file AmershamBiosciencesMaldi.log and search for
ORA-.
fI
installation is successful then you will get message: Cannot

find “ORA-“.
Open file IMALDI.LOG and search for Import terminated

successfully without warnings.
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If installation is successful then you will see:
Instalation is complete.
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Chapter 3
Chapter Contents
3. Interfacing
Interfacing
3.1 Introduction
3.2 Table of connectors
3.2.1 Instrument connections
3.2.2 TCU connections (Tof Control Unit)
3.3 Cables
Contents Chapter Service Manual Ettan Maldi Tof PRO MS 18-1160-04, Rev March 2004
contents
3. Interfacing figure 2: interconnections
3.1 Introduction EttanMALDI-TOF Computer Monitor
Mains outlet
Figure 1 beside shows the mains connection and a fuse table PCB MS 1 Network LPT1
for 100 - 120 V and 220 - 240 V. Printer
Parallel Network
Figure 2 shows the interconnections between Maldi ToF Ms Mains outlet Optional
and computer. Network terminal Mains outlet Network terminal Mains outlet
figure 3: space requirement and connections

Figure 3 shows the interconnection and space requirements.
figure 1: mains connector
Voltage 100-120 / 220-240 V~

Frequency 50-60 Hz
Power, max 900 VA
Mains
witch WARNING!
Mains
inlet For continued protection against risk
of fire, replace only with fuse of the
Mains
fuse
specified type and current ratings.
100 - 120 V~ T8A
220 - 240 V~ T4A
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3.2.2 TCU connectors
3.2 Table of connectors
The connections of the TCU, Tof Control Unit, internal and
external are described on the following pages.
3.2.1 Instrument connections
Connections between instrument and PC and for the PC inter-
nal connections, see figure 2 on previous page.
picture of the TCU from the back
figure 1: Mains connection and Service connections PC1/PC2. PC1 and

PC2 is only used for connection of service equipment.
Mains
PC 1
PC 2
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TCU Backpanel conectors
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TCU Connector/Pin layout
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TCU Connector/Pin layout
contents
TCU Connector/ Pin layout
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TCU Cable Interconnections Block Diagram
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TCU Interconnections Block diagram
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3.3 Cables Connects between the TCU (U01) and the Reflectron HV sup-
List of all cables ply (U06).
8. Turbo cable source.

All cables listed can be found on drawing LT3P2. Cable connects between TCU (U01) and the Source turbo
This is the top level drawing for the electrical layout. controller (U07).
1.TCU mains cable. 9. LED Cable.

Cable connects between the Mains Block and the TCU. Cable connects between TCU (U01) and the LED panel
(U08).
2. Turbo source mains cable.
Cable connects between Mains Block and the Source Turbo 10. Reflectron turbo cable.
Controller. Cable connects between the TCU (U01) and the Reflectron
Turbo Controller (U09).
3. Fan tray mains cable.
Cable connects between Mains Block and the Fan Tray. 11. Linear detector supply input cable.
Cable connects between the TCU (U01) and the Linear detec-
4. Linear amp power source cable. tor supply (U11).
Cable connects between Linear Detector Amp (U02) and the
TCU. 12. Reflectron detector supply input cable.
Cable connects between the TCU (U01) and the Reflectron
5. Sample inlet assy cable. Detector Supply (U12).
Cable connects between sample inlet assy (U10) and TCU
(U01). 13. Pulser controll cable.
Cable connects between the TCU (U01) and the Pulser (U13)
6. Source HV power supply input cable.
Cable connects between the TCU (U01) and the source sup- 14. Backing valve cable.
ply (U05). Cable connects between the TCU (U01) and the Backing
valve (U14).
7. Reflectron HV power supply input cable.
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15. Valves and covers cable. 23. Pulser trigger cable.
Cable connects between the TCU (U01) and (C0245A) which Cable connects between TCU and the pulser (U13).
consists of Vent valve, Inlet valve and covers loop.
24. Computer interface cable.
16. Pirani gauge cable. Cable connects between the computer and the TCU (U01).
Cable connects between the TCU (U01) and the Pirani gauge
(U17). 25. Gate trigger cable.
Cable connects between the TCU ( U01 ) and the gate driver
17. Magnetron gauge cable. (U21).
Cable connects between the TCU (U01) and the Magnetron
Gauge (U18). 26. Laser detect cable.
Cable connects between the TCU (U01) and laser detect assy
18. Laser power cable. (U10).
Cable connects between the TCU (U01) and the Laser (U19).
27. Laser trigger cable.
19. Beam blanking cable. Cable connects between the TCU (U01) and the Laser (U19).
Cable connects between the TCU (U01) and the beam blank-
ing (U20). 28. Linear detector signal cable.
Cable connects between the TCU (U01) and the linear de-
20. Gate power and controll cable. tector amplifier (U02).
Cable connects between the TCU (U01) and the gate driver
(U21). 29. Reflectron detector signal cable.
Cable connects between the TCU (U01) and the flight tube
21. Pulser power supply input cable. (U2).
Cable connects between the TCU (U01) and the pulser supply
(U22). 30. Linear detector amp int power.
Cable connects internally in linear detector amplifier (U02A).
22. Sample motor cable.
Cable connects between the TCU (U01) sample probe con- 31. Sample inlet interconnect.
nection and the sample probe (U23). Cable is located in Sample Inlet assy (U03).
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32. Pulser control internal cable. ac pcb.
Cable is located internally in the pulser assy (U13A).
42. Scope trigger ttl TCU.
33. Valves & covers interconnect. Cable connects between TCU backplane (U01) and the ac
Cable connects to vent valve, inlet valve and and instrument pcb C0257.
covers.
43. Switched mains TCU.
34. Beam blanking control internal. Cable connects from rear of the TCU backplane and finishes
Located internally in beam blanking unit (U20A). on the front of the backplane.
35. Gate power & control internal. 44. Interconnect TCU.

Located internally in the gate driver unit (U21A).
45. HVC interconnect TCU.
36. Sample probe limits.
Connects to sample probe limit switches. 46. AQC interconnect TCU.
37. Pulser trigger cable. 47. Sample phases TCU.

Connects internally in unit (U13A).
48. Beam blanking hv cable.
38. Laser detect signal cable internal. Cable connects between the beam blanking assy (U20A) and
Connects internally in laser detect assy (U10A). the flight tube (U26).
39. Computer interface cable TCU. 49. Switched power supply unit.
Cable is located on TCU (U01) backplane pcb. Located in the TCU (U01).
40. Pulser trigger cable TCU. 50. Laser detect internal power cable.
Cable is located in the TCU (U01) between the backplane and Located in the laser detect assy (U10A).
ac pcb.
51. Mains distribution cable.
41. Gate trigger cable TCU. Cable connects from mains inlert to the mains distribution.
Cable is located in the TCU (U01) between the backplane and
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52. Reflectron turbo mains cable.
Cable connects from the mains block to the reflectron turbo
controller (U09) and the reflectron turbo fan.
53. Sample motor interconnect.
54. Beam blanking hv cable.

Located in the beamblanking assy (U20A).
55. Pulser hv cable internal.
56. LT3-P2 Top level drawing.

LT3-P2. (electrical).
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Chapter 4
Chapter Contents
4. Troubleshooting
Troubleshooting
4.1 Vacuum system
4.2 Mechanics
4.3 Electronics
4.4 Laser and optics
4.5 Software and PC
4.6 Service Equipment
Contents Chapter Service Manual Ettan Maldi ToF PRO MS 18-1160-04, Rev. March 2004
contents
Vacuum problem
No vacuum
Vacuum reading goes up Yes Sample probe does not
No with probe in forward seal in forward position
Pumps on? Start/repair pump position
Yes No
No
Pirani reading ok Clean/replace Pirani. Reading Vacuum reading unstable Yes Replace drive shaft seal
OK? during probe movment?
Yes No No
Vacuum OK
Fill up oil in rotary pump/replace
pump. Replace molecular sieve
No
Magnetron reading ok Clean/replace door o-ring
Clean/replace Magnetron
Yes Repair/replace leaking valve
Clean/replace leaking o-ring
Leakcheck air admit valve
Leakcheck the sample inlet
valve assembly
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No peaks detected:
Some peaks detected, low sensitivity, low resolution
No peaks A big unresolved peak Yes Pulser problem
at low mass?
No
Is interface and interface No Fit interface and interface No
cable firmly fitted? cable firmly. Is the sample good? Use a good known sample
Yes (Bic ink).
Yes
Is the laser shutter open? No Open the shutter. Disconnect and ground beamdump and gate.
Yes
Does the laser fire? No Connect M77, Change Acq,T/R Adjust sample position and laser mirror.
pcb.
Yes
Does the laser hit No Adjust sample position
No
the sample? and laser mirror. Correctly set laser trig level? Check laser trig level
Yes Yes
Are the HV on? No Check HV readbaks. No
Correct acq methode? Adjust focus mass/delay
Yes time. Beam dump set correctly?
Yes
No
Is the sample good? Use a well known fresh sample No high mass peaks in No Low laser energy,
(Bic Ink). linear mode? adjust/replace laser.
Yes
Does the Maldi work No Check the other mode. Ground
in booth modes? beam dump, gate and kicker.
Yes
Is there a zero burst No Replace T/R
in reflectron mode? pcb
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4.1 Vacuum system
4.1.1 Trouble shooting the vacuum system
Typical values for the vacuum are on the Pirani 5e-03 mbar and
on the Magnetron 5e–07 mbar. This is not any absolute figures
that has to be reached, the main thing is that the vacuum
gauges reaches its trip point so the HV can be turned on.
Turbo pump If the instrument can`t reach this values check the following:
-Is the rotary pump on and is the oil level normal.
-Are the turbo pumps on, is the led on each controller green.
The pumps are switched on by the mains switch on the Maldi.
-Does the sample door close, clean the back of the door and
the o-ring, replace the o-ring if it is worn.
-Is the pirani reading OK, but not the magnetron? Check the
cable to the magnetron. Tap on the gauge with a screwdriver
to see if it will turn on. If it turns on by tapping on the magnet-
N2 or dry air ron housing, it needs to be cleaned. See Edwards manual for
a proper cleaning procedure of the magnetron. If the reading
Turbo vent valve is 1e-8 mbar, it is likely that the electronics in the magnetron is
faulty or the magnetron has not been turned on and the magn-
Pump out line etron needs to be cleaned or replaced.
for probe bearing Backing valve -Is only the pirani gauge faulty and the magnetron OK. Check
Pirani
Turbo pump
the cable, remove the gauge and rinse it inside with methanol.
If this does not help, replace it.
Forline trap To turn on the magnetron four events must take place: sample
Door Magnetron
(penning gauge)
door must be closed, both turbo pump up to speed, the panel
interlock switch must be closed, the vacuum reading on the
N2 or pirani gauge must be lower than its set point. All this events
dry air Vent valve Inlet valve
Rotary pump
are represented by a closed contact (activated relay) con-
nected in series on the I/O pcb. When the magnetron is turned
on and the reading has passed its set point it will be possible
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to turn on the HT and start a run. probe in its forward position, loosen the four allen screws that
holds the sample lock compartment in place. Remove the vent
4.1.2 Sample probe seal leak valve and inlet valve assembly by losen the Swagelock nut.
If the vacuum is good with the sample door closed but it is to Remove the sample lock by pulling it outwards. Replace the
low when the door is opened. This indicates a leak between o-ring and inspect the sealing surface of the sample probe.
the sample probe and the lock. The first thing to try is to adjust Reassemble the sample lock compartment in reverse order.
the micro switch for the sample exchange position. Move it The lock will be guided to its correct position by the sample
approximately 0.5 mm clockwise to move the probe further in probe when it is in its forward position. Close the sample door
to the lock. This will improve the seal. The correct position for manualy, reconnect all contacts and switch on the instruments
the micro switch is when the magnetron reading improve a to start up the pump down sequence. The Maldi has to have
little bit when the sample probe reaches the sample exchange good vacuum before it can be tested again.
position and the sample door opens. Make sure that the motor The first thing to look for if the motor does not move is that all
does not have to work to hard to activate the micro switch. If the contacts are in place. Check the 24 V power supply for the
the leak is still there the seal has to be cleaned or replaced. stepper motor. If the voltage is OK, check the micro switches
To get access to the seal in the sample lock the instrument for the motor. If the micro switches is OK, make sure you get
has to be vented. If possible vent the instrument with Nitrogen 24 V pulses to the stepper motor from the I/O pcb. The motor
(to minimize pump down time). When the instrument has been is controlled by IC 34, 35, and 40. If the pulses is OK replace
vented, open the sample door manually. It is important to dis- the motor, if the pulses are missing replace the I/O pcb.
connect the door motor before it is moved manually. This will
prevent back emf from the motor to damaging the driver circuit 4.1.3 Leaking seals at the probe drive shaft
on the I/O pcb. When the sample door is opened and the If there is a fluctuation in the magnetron reading during the
probe is in its inner position it is possible to see the o-ring in movement of the sample probe there is a leaking seal at the
the sample lock. probe drive shaft. To replace the probe drive shaft seals is a
Try first to clean the o-ring and the sealing surface of the lengthy procedure, so make sure that you have necessary o-
sample probe with some methanol on a cotton bud before the rings pn: 18114588 and vacuum grease before you start on
o-ring is replaced. If the o-ring is damaged it has to be re- this work.
placed. To replace the o-ring, the sample probe has to be in It is also recommended to update the probe drive shaft to its
its forward position. If the system is vented the probe has to latest version at the same time, see SI no 10 for part numbers
be moved manually. Disconnect the motors electric contact to and more information. If the drive shaft is the latest version
prevent the I/O pcb to be damaged by back emf. With the only the o-rings should be replaced.
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Vent the instrument. Remove the Laser Optics Bench. Undo do this but you can usually feel when the drive screw has re-
the cables to the Switch Gear assembly and remove the assy engaged. Now very gently push the drive shaft back into it’s
from the drive housing. To do this, undo the grub screw fas- housing, rotating it clockwise at the same time. If you force the
tening the drive shaft coupling to the motor shaft. Undo the shaft in without turning simultaneously you will almost cer-
four allen screws fastening the gear assembly to the drive tainly damage the o-rings. You can feel the resistance as each
housing. Undo the bearing housing and remove the outer o-ring starts to enter it’s proper location. When it is fully in-
bearing with it. Now the drive shaft can be gently pulled and serted simply refit everything as you took them apart. This
rotated anticlockwise. The rotation unscrews the drive screw procedure can result in the sample offset being altered.
from the sample holder. It should slowly come out from its seal
housing. When free ensure the drive screw has fully disen- 4.1.4 Sample probe positioning and sample offset
gaged. If not continue to turn anticlockwise until it has. Re-
move the drive shaft. Two seals are fitted. The seal nearest to The start position is set by the upper (large) micro switch on
the peek drive screw is the high vacuum seal and the other is sample exchange mechanism. The distance the sample probe
the low vacuum seal. These are a tight fit and are difficult to has to move from the start position to where sample no.1 can
remove and refit. Do not scratch the sealing faces on the drive be hit by the laser is called sample offset and is set in the
shaft. Use tweezers and something nonmetallic to jam under Maldi def file. A typical value is about 18000-20000. This is
the seal. Remove the low vacuum seal first. You can slide this actually the number of steps the sample probe has to move to
over the high vacuum seal to remove it. get the first sample in place. It is 320 steps/mm. The proce-
When you have removed both seals make sure you have not dure to set up sample probe offset is described below.
scratched the o-ring groove faces. If there are light scratches
you can remove them with very fine grade emery paper. If 4.1.5 Sample probe offset adjustment and laser beam
there are deep scratches then the drive shaft will need to be targeting
replaced. ALWAYS USE LASER SAFETY GLASSES WHEN WORKING
Ensure you clean the shaft before reassemble. Apply a small WITH THE LASER.
amount of the vacuum grease to the o-ring grooves. Fit the Prepare a slide with marker pen so it easy to identify the sam-
new high vacuum seal and then the new low vacuum seal, ple spots inside the source. Mark for instance spot 1-3 and
which will slide over the other one. Again apply a little more 22-24, it easier to identify the spots if different colours are
grease to the outer circumference of the two o-rings. Now refit used. The source can be illuminated by a torch. Shine the
the drive shaft by first screwing the drive screw back into the light through the laser mirror and lens to illuminate the sample
sample holder. You cannot see what you are doing when you slide inside the source. Load the sample slide and start a run
contents
at position 1. Block the laser beam with a business card or until the peaks are back. Make a not off the knobs position.
similar after the filter wheel assembly. Observe the sample Continue to turn the knob clockwise until the peaks are gone.
slide through the laser mirror, adjust the sample motor offset Make a note off the position. Set the knob to the centre off the
value in the .SED file if you are not on target. It is 320 steps / two positions. Repeat the procedure above for the right knob.
mm. Reduce the laser power if the peaks are higher than 150.
Higher motor offset value => probe moves towards the Repeat the procedure a few times. Small adjustment (a 1/4 of
door a turn) might be needed to get the best sensitivity. The laser is
Lower motor offset value => probe moves towards the now focused.
home position
When a sample is run set the sample target region to 0% and 4.1.5 Leaking valve
100%. Peaks should be visible in both position.
The laser optics is focused during the manufacturing. It needs There are three valves in the Maldi: Air admit valve fitted on
normally only some small adjustments upon installation and the small turbo pump. The function of this valve is to vent the
service. The only time this focusing has to be done is when system when the turbo pumps are of. The valve is opened
the laser is replaced or when the laser bench has been re- when the turbo speed is approximately 50% off max speed.
moved. The valve is controlled by the turbo pump controller. To find
To get easy access to the laser bench and its adjustment the out if the valve is leaking remove the tubing from the valve.
front corner panel with the three leds and the side panel to the Block the inlet of the valve where the tubing was connected
left of the panel with the three leds has to be removed. To with your finger or a swagelok plugg. If the vacuum reading
reach the adjustments of the transparent mirror it is enough to impoves on the magnetron the valve is leaking and needs to
remove the front corner panel with the three leds. Place a be replaced.
sample slide with BIC ink (or some ink from a marker pen that Door
is known to give good peaks) on some off the sample spots
and or matrix on some of the other spots.
Start a run with the Ink method for acquisition. Make sure the N2 or
laser beam hit the lens in the center by fitting the laser focus- dry air Vent valve Inlet valve
ing tool in front of the lens. Adjust the knurled nuts on the
mirror to until the laser spot in the centre hole of the laser Sample inlet valve assembly
focusing tool. Remove the focusing tool. Increase laser power
until ink peaks are visible. Turn the left knurled knob counter
clockwise until the peaks are gone. Turn the knob clockwise
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it can be seen as the pirani reading goes up when the door is
opened. Normaly the reading should improve (drop) or be the
N2 or dry air same when the sample door is in the opened possition.
Turbo vent valve

4.2 Mechanical assembly
V
There are only three moving parts in the Maldi. Rotary and
a
c
Backing tube turbo pumps not included. It is the sample probe, see above,
u
u
Turbo pump
the filter wheel assembly and the sample door.
m
c Magnetron
(penning gauge)
h
a 4.2.1 Filter wheel assembly
m
b
e
The Iris has been replaced by a filter wheel for the regulation
r of the laser power. The filter wheel is rotated by a stepper
motor. It`s min and max position is detected by two micro
Air admit valve switches. At start up, it first check its min and max position,
and then go to the value set in software (called laser in the
On the Sample inlet valve assembly two valves are fitted. It is tune page and in method set up). The number of steps for the
the Vent valve to the left and the Inlet valve to the right side of motor is defined in the Maldi def file (DefEpt.SED se page
the sample door. To leakcheck the Vent valve remove the 125). If the motor does not find its min and max position the
tubing from the valve, block the hole where the tubing was software sends out a error message. The motor is controlled
connected with your finger or a swagelok plug. by IC 16, 27, 37 and RLY 1 on the I/O pcb.
4.2.2 Sample door

The sample door is opened or closed. Its up and down stops
are controlled by two micro switches in the lower position and
Swagelok plug one in the upper position. The lower micro switch should be
If the reading improves the valve assy needs to be replaced. adjusted so that the door stops in front of the sample lock
The inlet valve is more difficult to trouble shoot. If it is leaking opening to give a good vacuum seal. The second switch is
contents
part of the covers loop, it has to be closed if the HV should be on top of the rotary pump and one Active Inverted Magnetron
enabled. If the HV can`t be turned on check this micro switch. (Penning) gauge fitted next to the pulser box. The only re-
It has to be closed by the door mechanism. maining active device is the linear detector.
needed on the knurled nuts to get highest sensitivity. Start a The Linear detector (ETP) is fitted on the inside of the top
run and check if further adjustment is necessary. Make sure flange of the reflectron.
that peaks are present when the adjust target region is set to
0 and 100% (5 and 95%). This is to make sure that the laser The linear amplifier box sits on top of the reflectron chamber
is able to fire on the hole sample. directly connected to the linear detector output.
The reflectron detector that is fitted inside the vacuum system
4.3 Electronics just under the reflectron stack.
This instrument contains dangerous high voltages.
The electronics is controlled by a pc with pcimca pcb. There
Maximum voltage is 20000 V.
are three switches on the instrument. Two main switches (one
Be careful when the panels are removed.
on the back of the instrument and one on the back of the elec-
The electronics in the Maldi is fitted in to a case that contains tronic case). The third switch is a safety interlock switch for
six pcb. The pcb`s are: the high voltages. It has to be pulled out if the high volt-
Low voltage power supply pcb ages should be on when the panels are removed.
Acquisition control pcb On next page is a block diagram of the electronics showing
Transient recorder pcb how the different electronic units are connected with each
24 V power supply pcb other.
High voltage control pcb
4.3.1 HV to the source
On top of the case are five HT power supply fitted. They are The function of the source voltage is to accelerate the ions
for the source, reflectron stack, pulser, reflectron detector and from the source in to the flight tube.
linear detector. The HV to the source comes from one of HV supply on top of
To the right hand side of the source is the pulser located. Just the electronic case and it is controlled by the high voltage
above the laser is a small aluminium box that contains the control pcb. The source voltage is set by the software. The HV
beam blank drive. On the right side of the reflectron chamber could be checked on pin 3 on contact M45 and ground with a
is an aluminium box for the gate pulse circuit and the kicker. DMM (0-10 V where 10V = 20 kV). The source voltage could
There are also two turbo pump controllers fitted on the back of also be checked at the HV lead that goes in to the pulser box
the instrument. Finally there are also one Pirani gauge fitted with a HV probe and a DMM. It should be 18 kV dc in the 20
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COMPUTER
ACQUISITION CONTROL WITH
IO * GAS CELL CONTROL (AC3) COMMS PCB
* SAMPLE MOTOR (IO1) * GATE CONTROL (AC4)
POWER SUPPLY * IRIS MOTOR (IO9) HIGH VOLTAGE CONTROL
* DATA ACCUMULATION
BOARD * SAMPLE PORT MOTOR (IO10) * HP20R - SOURCE (HVC2)
* EXTERNAL COMMS (AC5)
* VALVES (IO5,IO6,IO7) TRANSIENT RECORDER 24V SUPPLY * HP20R - REFLECTRON END (HVC1)
* LASER TRIGGER (AC2)
+5V LOGIC * TURBO PUMP CONTROLLER INTERFACE (IO4) 1GSPS SWITCH OFF FOR ZERO VOLTS
* PULSER TRIGGER (AC1) OPTIONAL
+24V IO * PIRANI GAUGE CONTROL (IO3) INPUT SIGNALS * LINEAR OPERATION * H5P - DETECTOR (HVC7)
* LASER DETECT (AC7) 2GSPS
+/- 5V T.R. * MAGNETRON GAUGE CONTROL (IO2) * REQUIRED CURRNET 2.4A * HP5R - PULSER (HVC4)
* FAST TRANSIENT RECORDER. TRANSIENT
+/- 5V HEAD AMP * HIGH VOLTAGE CONTROL INTERFACE * LINEAR DETECTOR (TR2) * HP2.5P - REFLECTRON DET 2KV (HV10)
TRIGGER (AC8) RECORDER
* COVERS LOOP * REFLECTRON DETECTOR (TR1) * PULSED EXTRACTION UNIT (HVC4)
* BEAM BLANKING CONTROL * GATE DRIVER (HVC6)
* AUTO-SAMPLER / Y AXIS ON ADDTIONAL BOARD * LASER POWER SUPPLY (HVC5)
* GAS CELL DRIVE * BEAM BLANKING (HVC3) TR2 AC8 TR1
IO11 AC1
PS1 PS2 IO2 IO3 IO4 IO5 IO6 IO7 AC8 AC6 TR2 HVC2 HVC4 HVC5 HVC6 HVC3
HVC1 HV7
HV10
IO9 AC2
AUTO
SAMPLER AC7 LIN:0V (OFF)
OPTION SIG?? REFLECTRON
DETECTOR REFLECTRON DETECTOR
IO1 COVERS
UV LASER, OPTICS, IRIS AC4
HP2.5P 4mA HP20R HP5P
(plus port switch)
HVC4
MOTOR & LIMIT SWITCHES
AC3
+2.5KV REF :+/-20KV +2KV
IO10
FIBRE OPTIC & PULSE DETECT
HP5R
SAMPLE MOTOR +/-4KV AC1
HVC2
HVC6
PULSED
SOURCE EXTRACTION UNIT
HP20R -/+4KV HV3 2KV
LID MOTOR. +/-19.6KV (opposite polarity)

AND 375uA BEHLKE HTS80
BEAM GATE PULSE
MICRO SWITCHES GAS CELL DRIVER TR1
250M 5nF BLANK
DRIVE CONTROL
+/-5V TR2
CONICAL DUAL
ANODE MCP
REFLECTRON AMPLIFIER
60 PLATES ELECTRON 5nF
WITH
INCLUDING ENDS MULTIPLIER OFFSET
INLET CHAMBER
ADJUST
GATE ION FLIGHT TUBE
SAMPLE PULSED BEAM GAS +/-500V KICKER
LENS TUBE TUBE
+/-20KV LENS BLANK CELL OR 0V +/-90V
RESISTIVE DIVIDER. (67M)
EDWARDS
MAGNETRON EDWARDS E DWAR DS MAINS BLOCK
IO2
GAUGE TURBO TUR BO (6 OUTPUTS)
AIM-S-MW25 PUMP EXT70 P U MP E X T 70 * TURBO PUMP CONTROLLER(s)
BACKING VALVE (24V,N.O.) IO7 * TCU
* FAN TRAY
* ROTARY PUMP
INLET * BACK PANEL FANS
VALVE
24V N.C.
IO5
PORT ON
EDWARDS
SAMPLE
PIRAINI GAUGE IO4 IO4
PROBE
APG-M-NW16 ROTARY LAST CHANGE : 09/07/99 17:35
VENT PUMP
VALVE IO3
SJ OR IG INAL XX/98 A
24V N.C. EDWARDS TURBO PUMP EDWARDS TURBO PUMP BY MODIF IC AT ION DAT E IS S
CONTROLLER CONTROLLER DR G NO : S AI-02B D S HE E T 1 O F 1
IO6 EXC100L EXC100L
LT3-P 1 E LE C TR IC AL S YS TE M DIAG .
S C IE NT IF IC ANAL Y S IS INS T R UME NT S L T D
S T R IC T LY C ONF IDE NT IAL C OP Y R IG HT S AI LT D 1997
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kV reflectron mode, 9 kV in the 10 kV reflectron mode and 4 more than this it will cause variation in flight time from one
kV in the 5 kV reflectron mode. In linear mode the set voltage shot to another which will result in broader peaks i.e. bad
is equal to the source voltage i.e. 20 kV linear mode sets 20 resolution.
kV to the source. The HV is connected to the extraction lens
and to the sample probe via the pulser box. 4.3.3 Pulse extraction signal
The pulser box is located on the right hand side of the ion
4.3.2 Laser detect signal source in an aluminium box.
The laser is used to increase to energy level of the sample !!!! The lid is floating at 20 kV if it is not grounded when
molecules, so they vaporize and form ions. A fraction of the the box is open and the HV is on. The HV might be on
laser beam is reflected down to a photo transistor by the filter even if the instrument is not in operate. Switch of the
wheel. This is the laser detect signal. The laser detect pcb is
A B C
fitted in a aluminium box under the laser. The laser detect
signal goes in to the electronic case via M34. The trigger level
is adjusted on the acq control pcb by rv1 and measured on
TP6, TP7 is ground. It should be set to trigger on the steepest
flank 0.8-1.2V (A). Avoid an area where it is some ringing on
the signal (B) because that could cause some jitter on the
peaks. On the oscilloscope picture to the right where Ch1 is
laser detect signal on M34. Ch3 is the clock pulse on M35.
The clock pulse is generated on the acquisition pcb by the
laser detect signal and IC 29, 30, 31. This pulse is the start
signal for the hole system. It trigger the extraction pulse, start
the delay for time for the beam dump and the gate. On the
oscilloscope picture below C indicates the time different be-
tween A: laser detect signal and B: clock signal. Since the
clock signal is time zero i.e. starts the acceleration pulse this
is the time deferents between the laser shot and the extraction
puls. This is the delay time that also is called focus mass in
the acquisition method. The variation in time between the two
pulses should not be more that a few nano seconds, if it is
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electronic rack before open the pulser box. Make sure the
ground wire between the pulser lid and the chassie
ground is connected .
The function of the pulser is to extract the ions from the ion
source and get the ions of the same mass focused when they
reach the detectors. This is achieved by keeping the ions in a
constant electric field between the source block and the ex-
traction lens after the laser has been fired. After a well con-
trolled time delay (focus mass) the extraction lens voltage is
dropped and the ions leaves the source and enter the flight
tube. In 20 kV reflectron mode the extractor drops about 3kV
from 18 kV to 15 kV. To check the pulser do as follows. Switch
of the electronics. Open the pulser box, connect a ground
wire between the lid and chassis ground. Connect a HV probe
to the junction of R2 and C1 in the top left corner of the pcb.
Switch on the electronics and start an acquisition. Ch1 is the clock /trigger pulse at M35 on the back of the electronic box,
It is very important to have no time different from one shot to connected to the scope with a coaxial cable. Ch2 uses a HV probe
the next, if the time difference is more than one nano second (1000:1) and show the extraction pulse. It is 3 kV in the 20 kV mode.
it will have negative influence on the resolution.
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correct then the pulser box is faulty or the cable from J8 to the
pulser box.
Make sure SI21 has been performed. This will prevent that R3
burns and damage the pcb.
Ch1 is connected to M35. The cable that feeds the HV in to

the extraction lens has been disconnected and ch 2 is con-
nected to it’s loose end with a HV probe (1000:1). The voltage
is 18 kV but in the picture it looks like it is 7 kV. It is due to
voltage dividing between the high impedance in the probe 100
Mohm and the high impedance in the pulser lid (100 Mohm).
If the extraction pulse does not exist check the incoming sig-
nal on ic3 pin7 see picture to the right. It is difficult to measure Ch1 is connected to M35. Ch2 is connected to TP14 on the T/
the signal on the input of ic3 and on the pins of M32 due to R pcb and ch3 is connected to ic3 pin7 (pin2 on J10) on the
the nature of pecl circuity and the signal is in diffirential mode. pulser pcb.
If no pulses are present follow the signal backwards. Check 4.3.4 Adjustment of pulse extraction unit voltage
the outgoing puls on the T/R pcb on TP14. If the pulses are The amplitude of the pulse is proportional to the lens voltage.
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When the system is in the 20 kV reflectron mode the sample
probe and extraction lens is at 18 kV. The pulser amplitude
should be -3 kV, this voltage will vary from one instrument to
another. It is set to give best resolution. The puls amplitude
can be adjusted with RV1 on the HV control pcb.
4.3.5 Beam dump (low mass reject filter)

The function of the beam dump signal is to block large signal
of low mass, mainly matrix peaks from hitting the detector.
The beam dump signal comes from a small aluminium box
fitted above the laser and goes to a electrode fitted above the
extractor lens in the flight tube. The trigger signal and its delay
is controlled by the I/O pcb. The pulse is 400 V dc on the out
put bnc contact. This voltage is set with RV1 and is measured
between R1 and C7 on the beam dump pcb.
The first thing to do when the beam dump does not work is to
disconnect the cable M123 from the beam dump filter box to
the flight tube. Ground the pin in the bnc feedthrough fitted on
the flight tube. If the feedthrough is not grounded the elec-
trode will charge up and act like a beam dump filter that is on
all the time. With the electrode grounded all masses should
Ch 1 is the signal on M 35. Ch 2 is the extraction puls and ch 3 is the
reach the detector. If more low mass peaks show up with the beam dump signal. When ch 3 drops to zero all ions passes to the detec-
electrode grounded the filter is working. Check the 400V as tor.
described above, set the voltage to its maximum, higher than check the control signal coming in on J1 pin 3 picture 1 on
400 V if possible. If the 400 V is not present verify that the next page. If the control signal is not present continue to trace
24V to the Beam dump pcb is OK, check it in the contact J1 it backwards. The signal comes from the I/O pcb IC 17 pin 7
pin1. Verify that the setting of the filter in the acq method is and can be checked with the I/O pcb fitted in an extender pcb.
correct and enabled. Next step is to use a oscilloscope and See picture 2 on next page. Make sure there is a good conti-
trace the signal backwards. The picture on next page, Ch3 is nuity between the I/O pcb ic 17 pin 7 and the beam dump pcb.
the output signal measured with a 6kV probe connected to the
bnc contact on the beam dump box. If the puls is missing
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Ch 1 is M 35, ch 2 is controle signal going into the beam dump pcb on Ch1 is M 35, ch 3 is ic 17 pin 7 on the T/R pcb. Tis is the starting point
J1 pin 3. for the low mass trigger (beam dump) signal.
4.3.6 Gate and kicker

The Gate and kicker electronics is fitted in a aluminium box on
the right hand side of the reflector chamber. The gate pulse
select the peak of interest in psd mode by applying +/- 400 V
to the gate electrodes at an exact time. This will only allow
ions off a selected mass and its fragments to pass to the de-
tector in psd mode. The timing and set up of the gate pulse is
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TP1 is the testpoint for the 24 V. The 24 V is converted on the
pcb to 5 V, 15 V, -15V, 500 V and -500 V. The 500 V and the -
500 V can be checked on TP 4 and TP 5. The 5V can be
monitored at IC 7 pins 3 & 6 (middle pins on the 3 pins
grouped together). The 15 V can be checked on ic1 pin 3 and
the -15 V can be checked on ic9 pin 3. Use TP 2 as ground .
Ch 2 is the negative out going gate puls and ch 3 is the gate

controller signal. The probe is connected R1s upper leg.
The kicker tilts the ion beam a little bit in the reflectron mode
so the beam will hit the MCP detector at the end of the reflec-
tron. It applies approximately +/-50 volts to the kicker elec-
trodes to give the ions a parabolic curve in the reflector. This Ch 2 is the negative output (TP 7) ch 3 is the positve gate
is to make sure the low mass ions hits the reflectron detector puls (TP 6), use TP 8 as ground.
in psd mod. The adjustment of the kicker should only be done To verify the function of the Gate and kicker electronics the
in psd mod to optimize the intensity of low mass fragment. first thing to measure is the voltage on the pcb as described
The supply voltage is 24 V and comes in on J1 pin 1,3 and 6. above.
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To test that the gate is opening and closing as it should an
oscilloscope is necessary. See picture below.
Same connection as on the picture to the left. Here it is obvi-

ous that the pulses varies from one shot to the next. If a two
Ch 2 is the negative output (TP 7) ch3 is the positve gate puls channel oscilloscope is used use trigger input instead of ch1
(TP 6), use TP 8 as ground. Ch 1 is the trigger. to trigger the scope.
The control signal coming in to the pcb from the Acq pcb can If all the signal is there but it is still problem with the psd mode
be measured on R1 upper leg, use TP10 as ground. See pic- make sure there is not any jitter in the gate puls, see picture
ture 2 on previous page. If the signal is missing make sure the on next side. To solve the jitter problem check the signal as
probe is connected to the right side off R1, the lower side off described above, replace the pcb where the jitter is created.
R1 is connected to ground. If the signal still is missing follow it Make sure there is a good connection between the acq pcb
backward to the Acq pcb. Connect the oscilloscope probe to and the gate and kicker pcb. To set up the gate in a proper
TP8 use TP3 as ground. way see chapter 2.
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If the gate puls is on all the time (constant 400 V to gate elec-
trode) no signal at all will pass the gate electrodes. This will
results in no peaks at all in reflectron mode, the linear peaks
will be there as normal since the gate and kicker electronics is
disabled in linear mode.
If all the signal is there as described above but it is still prob-
lem with the gate or kicker make sure the electrode inside the
Maldi is not shorted to ground or has come lose. To find out if
the electrodes are shorted do as follow: Disconnect the four
pins on the gate and kicker feedthrough, make a drawing of
how they are connected first. Check the resistance between
each pin and ground and between each other, there should
not be any continuity anywhere. To verify if the electrodes has
been disconnected by some reason the system has to be
vented, the refletron has to be removed and a inspection must
be done from the inside. See Chapter 6 paragraph 6.4 for
instructions
4.3.7 Linear detector

If there is no peaks in linear mode but the peaks are normal in
reflectron mode, assuming the run has started in a normal
way, the sample and methods are ok this his a way of find out. The linear detector output is connected directly to the Ch 1 on
DO NOT TRUST CUSTOMERS SAMPLE. IT IS BETTER TO the oscilloscope, ch 2 is used for trigger. Input impedance is
USE KNOWN SAMPLES FOR ACCEPTANCE TEST. IF THE set to 50 ohm. Delay is set to 13.2 uS. The signal from the
SAMPLES ARE NOT AVAILABLE USE BIC INK OR SOME detector is negative.
MARKER PEN WITH KNOWN PEAKS. for the detector, linear amplifier or the T/R pcb. Check that
Ground the beam dump electrode, gate electrodes and kicker the HV to the detector is 2000 V, use a HV probe and a DMM
electrodes. This is done to make sure nothing will block the or a oscilloscope. Measure the readback voltage on pin 3 in
ions from hitting the linear detector. If the peaks are still miss- the connector for the linear detector high voltage power sup-
ing it is a problem with the linear detector, the power supply ply. It should be 8V. This is 80% of full output from the power
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supply, 0,8*2.5kV= 2kV. If there is no hv, check the 24V on pin electrodes. This is to make sure nothing will block the ions
X in the connector for the HV supply. If the 24V is missing it is from hitting the detector. Check the detector supply voltage is
a problem with the cable or the backplane pcb since the 2000 V.
peaks are normal in reflectron mode all HV for source, both
detectors are enabled at the same time. Replace/repair any
faulty cables, pcb or power supply that is found.
The linear amplifier has a gain off 1 and works like a buffer to
protect the T/R pcb. The system can be used without the lin-
ear amplifier for a test run. Remove the linear amp and con-
nect the bnc cable direct to the output from the linear detector.
If the peaks are back fit a new amplifier.
If the peaks still are missing use a oscilloscope to see if there
is any signal coming out from the linear detector. See picture
on next side. Replace the T/R pcb. If there still are no peaks in
linear mode replace the linear detector and the linear detector
pcb. If there still are no peaks in linear mode contact your
local Maldi service specialist for advice.
4.3.8 Linear amplifier

The amplifier has a gain of one. It’s function is to protect the T/
R pcb from high voltage transients. The only adjustment for
the amplifier is RV1. It’s the dc offset adjustment for the ampli-
fier.
4.3.9 Reflectron detector The reflectron detector is connected to ch 1. Ch 2 is con-
If the linear mode is ok, most likely the source is working. nected to M35 and is used as trigger, the delay is set to 24uS.
Make sure your sample and methods is ok, DO NOT TRUST This will display the peak of intrest on ch1 since the flight time
CUSTOMERS SAMPLE. IT IS BETTER TO USE BIC INK OR of the ions for this peak is 24uS.
SOME MARKER PEN WITH A KNOWN SPECTRUM FOR The next thing to check is the reflectron stack and the reflec-
TROUBLE SHOOTING. Use methods that are known to work tron voltage. Check the readback on from the reflectron high
(i.e installation methods). Start the trouble shooting by ground- voltage supply (pin 3 in the contact). In 20 kV mode the read-
ing the beam dump electrode, gate electrodes and kicker
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back voltage should be 10V. If the readback is not 10 V turn connector when the high voltage has been switched on. Be
off the high voltage by turning of the electronic crate. Check very careful with the lose HV connector: The 20 kV from the
the high voltage with a HV probe and a DMM direct in the HV HV supply has enough power to kill. Whit the HV off meas-
ure the resistance between the center pin in the HV
feedthrough and chassis ground. It should be 67,2-68,4 MΩ.
If the detector supply, reflectron supply and the reflectron stack
is ok it is time to check the signal that comes out from the re-
flectron detector with an oscilloscope. Disconnect the bnc
cable that goes to the T/R pcb connector J6. Connect the ca-
ble from the reflectron detector output to Channel 1 on the
oscilloscope. Set the scope as follows: Channel 200mv/div,
50Ω input impedance and 25ns/div. Trig on negative going
edge on channel1, set the trigger level to –80--100mv. See
next page for oscill oscope picture.
If the signal does not show up on the oscilloscope the final
thing will be to inspect the detector (mcp) in the reflectron
chamber and replace them if needed. See 4.3.10 for instruc-
tions. If the problem still exist after this, contact your local serv-
ice specialist for advise.
The settings is almost the same as on the previous picture.

The only different is that average is set to 8, this means that 8
shots is displayed at the same time on the oscilloscope. This
will indicate id the peaks arrive at the same or not. If the
peaks are arriving at different times the accumulated peak will
broaden out and give lower resolution. This type of problem is
called jitter.
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4.3.10 Detector replacement
- Vent the system with pure N2.
-Disconnect Reflectron HT, linear amplifier and HT to the
linear detector (ETP) from the top of the instrument.
-ALLWAYS USE CLEAN DUSTFREE GLOVES INSIDE
THE VACUUM SYSTEM.
-LINEAR DETECTOR REPLACEMENT: Remove then top of
the Maldi by losen 6 allen screws. The ETP detector is fitted
inside the lid. Make shure you have the right crimp butts for
the connection of the detector. Remove the detector by
losen three small screws that holds the detector in place.
Reacemble the instrument in the reverse order. Be careful
with the H.T spring contact for the reflectron stack.
-REFLECTRON DETECTOR REPLACEMENT: Remove
the turbopump from the reflectron chamber. Disconnect M79,
M80 and +/- dc supply to the MCP amp from the left hand side
of the refletor. It is the H.T and output connectors for the MCP.
Remove the four nuts (A) and lift the reflector assy (it is the
hole top part of the Maldi) gently uppwards to remove it from
the Maldi. Place the reflectron assy upside down on a suitable
piece of wood with holes drilled for the bnc`s in the top of the
reflectron. Make shure the reflectron is supported by a table
so it does not fall.
Before any wires are disconnected MAKE A DRAWING OF
ALL CONNECTIONS INSIDE THE REFLECTRON.
Disconnect the internal wires from the feed through flange: HT
and signal. Disconnect the two wires to the gate and the two
wires to the kicker.
A Remove the four allen screws. Turn the mounting plate up
side down.
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Remove the grid holder by loosen the three screws (B). Re-
move the mcp by loosen the three nylon screws (C) that holds
the mcp clamp in place. Replace the MCP assy. Make sure B
the index mark on the MCPs are turned 180 degrees in rela-
tion to each other. Do not forget the spacer between the
MCPs. Tighten the nylon screws in a criscross pattern. Do not
over tighten the nylon screws, the MCP will brake very easily.
Verify that the height of the assy is correct at each set screw
according to picture to the right. Adjust the set screws to the
correct height if needed. This should be done with adjustment
pins (F) in the middle position.
Refit the grid holder. Make shure the grid is grounded by a
wire connected to on of the screws.
Reassemble the reflectron in reverse order. When the Maldi
has been reassembled, start the vacuum pumps. Wait until C F
the vacuum reaches 1e-6 mbar or better on the magnetron,
start to ramp the HT for the MCP from 0V up to 2000 V by
following the procedure below.
Apply voltage in 100V steps, wait 2 minutes. Repeat until the
voltage is 1.0 kV. Wait 2 minutes.
Adjust the voltage in 100V steps, wait 5 minutes. Repeat until 14.4 mm +/-0.1
the voltage is 1.5 kV. Wait 5 minutes.
Adjust the voltage at 50V steps, wait 10 minutes. Repeat until
the voltage is 2 kV.
The adjustments of HT is done on the trim pot Vi in on the
MCP HT supply. The voltage is checked at the readback at pin
13.8 mm +/-0.1 14.4 mm +/-0.1
three in the contact to the MCP HT supply.
Link to replacement of old detector
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4.3.11 High Voltage problem/Arcing this. A dmm can also be used but in some cases the dmm will
not be fast enough to detect the voltage dip.
Arcing in the Maldi is when the high voltage (HV) discharges
to ground. This can be caused by dust, hair or other particles
4.3.11.1 Measure reflectron resistance and all HV feed
that has come in to the vacuum system and shorts the high
through
voltage to ground. Dust and similar things can come into the
Remove the HV cable on the top of the reflector housing for
system with the sample slides or when the system has been
the reflector HV. Measure the resistance between the center
vented or opened for some repair. If the system is suspected
pin in the feedthrough (M131) and ground with a megger. It
to be dusty it has to be vented and the dust, hair has to be
should be between 67,2 MΩ Ω - 68,4 MΩ. If the resistance is not
removed. If the source is dirty the source housing has to be
within this range, the Maldi has to be opened and the fault
opened and the dirt can be blown away with nitrogen or wiped
must be corrected. Most dmm only works up to 40 MΩ and
of with some methanol on a lint free tissue. If the problem is in
does not use 500V as a test voltage as a megger does.
the reflectron stack it has to be blown of with nitrogen or some
Check the resistance in the bnc feedthrough with a DMM for
other pure gas.
the linear and reflectron detectors. The resistance between HT
The arcing can also take place in the feedthrough for the HV.
(M130) for the linear detector and signal output (M132) should
It is caused by some pore in the plastic that the feedthrough is
be > 40 MΩ, between HT (M130) and ground >40 MΩ, be-
made of. The feedthrough can be OK for quit long times and
tween output (M132) and ground > 40 MΩ.
then suddenly the high voltage brakes through the plastic and
It should be >40 MΩ between HT (M80) and output (M129), 11
shorts to ground. The feed through has to be replaced if it is
MΩ between HT (M80) and ground. If the resistance is lower
causing arcing.
the fault has to be corrected.
The effect off arcing can be noticed as reduced resolution
since the arcing will cause the HV to vary from one shot to
4.3.11.2 HV Power supplies
another. This will give variation in flight time and a broadening
The arcing problem can also be with the HV power supplies.
of the peaks i.e. bad resolution when they are accumulated. In
The source power supply and the reflector power supply are
real bad cases no peaks at all will be present due to that the
identical and can swapped with each other for trouble shoot-
HV is shorted to ground. ing. What seems to be a problem with the HV supply can also
In some cases the arcing problem can be found by measuring be a problem with the 24V supply for the HV or the connection
the readback voltage on pin 3 in the connector of each HV to the HV supply. The 24V must be stable and free from ripple.
connector. Pin 3 is connected to the HV output by a internal If the there is ripple on the 24 V supply, it will give the same
resistor network that divides the voltage to a value from 0-10 kind of problem as arcing. See next page for a faulty 24 V
V where 10 V is full output. It is best to use an oscilloscope for power supply.
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4.3.12 Electronics measurement and calibration
I/O Board
· Check that there is no short between:
Test point
TP7 & TP9
TP14 & TP12
TP14 & TP13
TP14 & TP15
TP14 & TP10
TP16 & TP17
· Measure the following voltages:
Test point Min(V) Max(V)Comment
TP7 & TP9 5 5
This is a scope picture of a the ripple on a faulty 24 V power TP14 & TP12 24 24
supply. When the voltage was measured with a dmm the dc
level was 24.0 V and the ac 0. The 24 V is connected to ch1 TP14 & TP15 12 12
with a 10:1 probe. The input is ac coupled. The scope is set to
trigger on ch1. The ripple is about 700mv p-p. The normal TP14 & TP13 5 5
value is about 20mV.
TP14 & RN6 20 20 RN6 pin 1 (mitered corner)
TP14 & TP1 1 1 Adjust the voltage at TP1

with RV2
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Output 0 Adjust the DC offset using RV1
· Connect Jumpers to J5 & J6 and observe the level on oscilloscop
· Measure the following voltages:
Test point Min(V) Max(V)Comment HV Board

Measure the voltage at:
TP16 & TP17 24 24 Test point Min(V) Max(V)Comment
TP6 & TP3 5.6 5.6 Adjust the voltage using RV3 TP15 & TP2 24 24
TP15 & TP4 7.1 7.1 Adj. RV1 to set Pulser ref
TP6 & TP4 3.8 3.8 Adjust the voltage using RV4 TP15 & TP5 8 8 Adj. RV2 to set Gate ref
- Remove Jumpers from J5 & J6 TP15 & TP6 9.9 10.1 Adj. RV3 to set Hmd ref
TP15 & TP7 9.9 10.1 Adj. RV4 to set Spare ref 2
TP15 & TP8 9.9 10.1 Adj. RV5 to set Dynode ref
T/R Board TP15 & TP13 9.9 10.1 Adj. RV7 to set Spare ref 1
Measure the following voltages (Ground test point first):-
TP3 to TP1 : +5V ACQ Board
TP3 to TP13 : 0V Check there is 5V between TP2 and TP5.
TP3 to TP10 : +3V Check TP6-TP7, trigger level.
TP13 to TP12 : +5V Check TP10-TP7, Laser fired puls.
TP13 to TP11 : -5VA Check TP8-TP3, gate trigger.
Adjust/check the offset for the A/D convertor: Check TP9-TP3, pulser trigger.
TP13 to TP5: -1.364V (adjust RV2). The baseline is now set
just below zero. Beam blanker Board
Check the 24V between pins 1 & 6 of the 9 way D connector
Test point Value (V) Comment
Linear Amplifier R1 pin1 & GND 400 Adj. RV1
Use board assembled in box, with lid removed.
· Plug in power cable. Gate Board
· Plug output into scope terminated in 50 ohms.
· Ground the input
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Measure following voltages: value is 40-50 V.
TP1 & TP2 24
IC7 pins 3 & TP10 5 +Kicker(white) -Kicker(green)
IC7 pins 6 & TP10 5
TP3 & TP2 0 +Gate (red) -Gate(black)
TP4 +400 Adj. RV3
Gate and kicker feedthrough
TP5 -400 Adj. RV4
J7 +50 Adj. RV1 adjusted for best low-
J8 -50 Adj. RV2 mass s/n in psd mode
4.3.12 Low intensity of the low mass peaks in psd mode
If the intensity is low on the lower masses in psd mode the

kicker voltage has to be adjusted. The kicker voltage is set at
the factory and should normally not need any adjustment.
Remove the lid from the gate and kicker box. Be careful it is +
500 V dc inside the box.
Start a PSD run with Hexatyrosine (see 2.2.6 Verification
cases).
Find the maximum intensity on the low mass fragment of
Hexatyrosine 136.173, 299.349, 327.360 and 345.370 by
adjusting the pot RV1 and RV2 on the gate pcb, adjust the
+and - voltage in small steps. They should have the same
potential but different polarity. Measure the voltage between –
kicker and GND and also between +kicker and GND. A typical
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4.5 Fault finding -Is it somenoise or random events in the spectrum? If so,
most likely the detector, amplifierand TR pcb is ok.
4.5.1 No peaks or low sesitivity -Run the instrument in linear mode 5kV. Ground the extraction
lens with a pice of wire, the source (sample slide assembly)
-The first thing to check is your method: Acceleration voltage should be connected directly to the source HT supply. This
= 20kV, Low mass reject = 500, single shot, focus mass = will bypass the pulser box. If younow see some peaks at a
900 or 1500 depending on what sample you are running, higher mass and whit lower resolution than normal it is most
accumulate=20 shots, manualy tune the laser power and likely that the pulser or pulser HT is faulty.
sample possitioning to achive max signal. -If it is still no peaks, disconnect the beam dump bnc contact
-Is the vacuum ok, oil level in rotary pump, rotary pump is on the flight tube. Make a run, if the peaks is back replace
runninng, turbo speed ok? the beam dump pcb.
-Is there a sample slide white a sample in the source? -The next thing to check is the gate box. Disconnect gate +/-
-Check all the voltages in the electronic box? in the box, is the peak back? The gate is on all the time and
-Is the HV for the source, pulser, reflector and detector ok? blocking the beam. Replace the gate pcb and tune it up (se
-Do you get HV to the sample probe? procedure on page 109-110.
-Does the laser fire? Check the 24 V and trigger pulse to the -If the peaks is still missing it could be a detector problem: In
laser. The Acqusition control pcb controlles the laser trigger linear mode: Check the bnc conntacts and coaxcial cables.
puls. Check the resistance in the linear detector. It should be >999
-Is the shutter on the laser open? Mohm between HT and output, 35 Mohm betweenHT and
-Is the laser power enough?Turn up the settings in software ground. If the recistance is lower and the peaks is missing
and on the laser it self if nessesary. It is a trim pot in a small the detector needs to be replaced.
hole on top of the laser. Is the laser focused on the correct In reflectron mode: Check the bnc conntacts and coaxcial
sample spot ( se page 120)? cables. Check resistance between HT M121 and output, it
- Is the sample in the right place? Check offset for sample should be > 40 Mohm, >40 Mohm between output M80 and
slide and the focus for the laser. ground, >40 Mohm between HT M121 and ground. If the
-If the peaksare missing in reflectron mode, are they ok in recistance is low and the signal weak, replace the detectore.
linear mode or? If so, this indicates that the ion source is ok
and it could be a detector, amplifier or TR pcb problem.
contents
resistance in the reflector with a megger. It should be 67.3
4.5.3 Low resolution Mohm between HV input for the reflector and ground. The
The first thing to check is the focus mass in your method, it megger normaly uses 500 V to check resistance which is
should be set to the same mass as you check the resolution not so much compared with the 20 kV the reflectron could
at. be operated at. The reflectron H.T could be checked by
The low resolution could also be caused by the sample. meassure the voltage at pin 3 on M46. If the voltage is not
Prepare a new slide whit new matrix and sample. Make constant it´s an indication of arcing in the reflectron. This
shure all the solvets, pipetts and other things used for sample has to be corrected to get a good resolution. So it might
preparation is clean. Check the resolution according to be nessesary to open the reflectron chamber and look for
the specifications using hACT whit 3 pmol concentration at some dark spots which are sign of arcing. The first place to
mass 2465. look for this is around the spring contact in the lid.
Do not trust unknown samples from customer. Low resolution could also be caused by the detector in
Do not use to much laser energy. It is no exact figur for this booth linear mode and reflectron mode. In linear mode
but try to keep the laser energy down so you get a signal of check the possition of the detector and that it is not lose.
about 60 -100 in each scan. Also check the resistance of the detector (page 18). The
Check that the laser detect signal is triggering at the right mcp detector for the reflectron mode should be firmly fit
level, se 4.3.2 for a correct set up procedure. but not overtighend. Lose mcp ore aligned the wrong way
Check the pulser extraction signal, the ratio between the will give low resolution (se page 27 for correct orientation
source voltage and the extraction signal should be set up and fitting). Check the signal cable from the detector to the
correct for a good resolution. If the peaks are very broad bnc feed through, if the cable and the contacts are not
and in the wrong place it could be that the pulser is not correctly
working at all. Se 4.3.3 for a correct setting of the extraction fitted it could be a impedance missmatch and that will
puls. ruin the resolution. This is also some thing to check in the
Check the settings in the DefEpt.SED file according to coaxial cable from the detector to the electronic box and
procedure on page 20. the transient recorder pcb.
Low resolution could also be caused by incorrect reflectron Resolution problems could also be caused by the electronics.
voltage or arcing in the reflectron. Check the voltage on the It could bea problem on thetransient recorder
reflectron power supply (pin 3 on the contact M46) it´s the pcb,aquisition control pcb. The electronics on these pcb
readback voltage from reflectron H.T. and is 0-10 V where are very fast and difficult to trouble shoot so it is recomended
10 V is the max output from the power supply. Check the to replace them.
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4.4 Sample probe offset adjustment and laser beam remove the front corner panel with the three leds. Place a
targeting sample slide with BIC ink (or some ink from a marker pen that
ALWAYS USE LASER SAFETY GLASSES WHEN WORK- is known to give good peaks) on some off the sample spots
ING WITH THE LASER. and or matrix on some of the other spots.
Prepare a slide with marker pen so it easy to identify the sam- Start a run with the Ink method for acquisition. Make sure the
ple spots inside the source. Mark for instance spot 1-3 and laser beam hit the lens in the center by fitting the laser focus-
22-24, it easier to identify the spots if different colours are ing tool in front of the lens. Adjust the knurled nuts on the
used. The source can be illuminated by a torch. Shine the mirror to until the laser spot in the centre hole of the laser
light through the laser mirror and lens to illuminate the sample focusing tool. Remove the focusing tool. Increase laser power
slide inside the source. Load the sample side and start a run until ink peaks are visible. Turn the left knurled knob counter
at position 1. Block the laser beam with a business card or clockwise until the peaks are gone. Turn the knob clockwise
similar after the filter wheel assembly. Observe the sample until the peaks are back. Make a not off the knobs position.
slide through the laser mirror, adjust the sample motor offset Continue to turn the knob clockwise until the peaks are gone.
value in the .SED file if you are not on target. It is 320 steps / Make a note off the position. Set the knob to the centre off the
mm. two positions. Repeat the procedure above for the right knob.
Higher motor offset value => probe moves towards the Reduce the laser power if the peaks are higher than 150.
door Repeat the procedure above a few times. The laser is now
Lower motor offset value => probe moves towards the focused. Some small adjustment (a 1/4 of a turn) might be
home position needed on the knurled nuts to get highest sensitivity. Start a
When a sample is run set the sample target region to 0% and run and check if further adjustment is necessary. Make sure
100%. Peaks should be visible in both position. that peaks are present when the adjust target region is set to
The laser optics is focused during the manufacturing. It needs 0 and 100% (5 and 95%). This is to make sure that the laser
normally only some small adjustments upon installation and is able to fire on the hole sample.
service. The only time this focusing has to be done is when
the laser is replaced or when the laser bench has been re-
moved.
To get easy access to the laser bench and its adjustment the
front corner panel with the three leds and the side panel to the
left of the panel with the three leds has to be removed. To
reach the adjustments of the transparent mirror it is enough to
contents
Sequence of pulses and signals 4.5 Software and PC
There is no service information about software and pc for
the moment.
4.6 Error code list
Laser 70ns (when delay is set to 0. Will increase the same amount as delay)
There is no error code list for the moment.
4.7 Service equipment
Oscill. M35 starts at the same time as Pulser signal below Multimeter
High voltage probe 20kV for multimeter
Megger
TTL to pulser Depends on selected mass in ion reject box Oscilliscope 500 MHz (portable from: Tektronix TDS3052 or
simmilar)
High voltage probe for oscilloscope 100:1 or 1000:1. 4kV
Beam dump or more (Tektronix P6015A)
Special tool kit supplied at service training.
Gate reflectron mode. Gate drops to zero the laser puls is detected.
UV light protection glasses.
Gate linear mode , gate is zero all the time.
Gate psd mode. Max 300ns delay, depend on selected mass for psd
Detector signal linear mode
Detector signal reflectron mode
contents
Chapter 5
Chapter Contents
5. Maintenance
Maintenance
5.1 Vacuum system
5.2 Electronics
5.3 Mechanics
5.4 Preventive Maintenance
5.4.1 SOP
5.4.2 PM visit records
Contents Chapter Service Manual Ettan Maldi Tof PRO MS 18-1160-04, Rev. March 2004
contents
5.1 Vacuum system 5.2 Electronics
From time to time the vacuum lines and connections should Verify that all fans are working; five on the tray under the
be checked. electronic crate, one at the reflectron turbo pump and one to
the left of the H.T supply. Replace not working fans. Check
Once a year, the oil of the rotary pump should be changed, all power supply pcb (first from left): +5V, +24V, +/-(7V to
according the recommendations of the supplier. 12V) unregulated linear low noise supply for Transient Re-
The pirani gauge should be cleaned once a year. corder analog components,+/-(7V to 12V) unregulated linear
The two turbo pumps should only be changed in case of failur. low noise supply for Head amplifier. Also check the 24V on
the 24V power supply pcb (the fifth from left). Make sure
there is no ripple on any voltages.
Verify that the readback on the H.T supplies are ok. This is
done by meassure the readback voltage on pin three in the
contact to each H.T supply. The readback will be 0-10 V and
10V is full output.
Clean the fan filter under the ion source.
Adjustment of electronics.
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5.3 Mechanics 5.4 Preventive Maintenance
Maintenance for the mechanical system. Check the Motor Routine Service and Maintenance
offset by looking through the transparent mirror for the laser The Ettan Maldi ToF has been designed to require a minimum
beam. If the sample spot is out of alignment adjust the motor amount of routine service. Standard service schedules have
offset value in the .sed file until they all are in the right posi- been defined and are shown below along with the necessary
tion. instructions.
If the sample probe motor is noisy the bearing and o-rings for
the drive screw feed through need to be lubricated.
5.4.1 Standard operation procedure for the PM
5.4.1.1 Initial Service slide Test

The first thing to be done, before going into the instrument, is
to run some samples to check the performance of the instru-
ment befor the pm.
Also ask the customer if there was something not ok with the
system during the last year.
Note the values of the Pirani and the Magnetron gauge.
5.4.1.2 Change Oil in the Rotary Pump.

This can be done without venting the Maldi by disconnec-ting
the contact to the backing valve and connect 24 Vdc to the
valve. Be shure you hear the valve click. This will isolate the
rotary pump from the rest of the vacuum system. The valve
can be closed 10-15 minutes without disturbing the function of
the turbo pumps.
Unplug the power to the rotary pump. Disconnect the Pirani
contents
gauge cable. Now break the vacuum in the backing line by three attempts then you have introduced a leak and
removing the Pirani gauge. Unscrew the oil fill plug on the top rechecking of the o-ring and groove will be needed. Make
of the rotary pump. Place a oil container in front of the pump, shure there is no scratches on the door.
undo the oil drain plug. The oil will be hot so be careful. Allow
the oil to drain until it is just dripping. Now replace the drain
plug and refill with new oil. Fill to ¾ full. Replace the oil fill plug 5.4.1.4 Clean the dust filters.
and Pirani gauge. Reconnect the rotary pump main’s cable. The dust filter is located at the bottom of the instrument. It
Reconnect the Pirani cable and then switch off the 24v to the is secured with Velcro patches. If the filter is dirty then simply
backing valve. Replace the original backing valve cable. New unfasten it. Clean or replace it.
oil should be gas ballasted for about 15 minutes. To do this,
simply loosen the gas ballast screw on top of the rotary pump
until you can hear the pump snoring. Tighten the gas ballast 5.4.1.4 Cleaning the Pirani Gauge.
knob after 15 minutes. Use Oil pn:18-1157-20 for it. Do not Use the same procedure as changing the rotary pump oil, see
use Edwards Ultragrade 19. Routine service, except that you are going to clean the gauge,
not change the oil. When you have removed the gauge re-
move the circlip holding the gauge in place. Rinse the gauge
5.4.1.3 Clean the sample door o-ring and groove. internaly with methanol a few times. Shake the gauge a few
Open the sample door. Ease out the o-ring from it’s groove. times to make shure there is no methanol left in the gauge.
Be careful not to scratch it when doing this. Wipe with metha- Refit the Pirani gauge.
nol and a lint free cloth. Wipe around the groove. Inspect the
o-ring and groove for any residual dust, dirt or scratches. Re-
place the o-ring if it is damaged. If any scratches are evident 5.4.1.5 Checking the vacuum lines and connections.
across the groove these should be gently rubbed away with All vacuum tubing and connections of the vacuum system
fine abrasive paper, along the direction of the groove, but only should be checked. Specialy the plastic tubing that goes from
if a leak has been identified previously. Take care to thor- the inlet valve to the probe bearing at the back of the ion
oughly clean away any dust if this if it has been done. Refit source (the pump out probe bearing tube).
the o-ring. Close the door and ensure correct operation.
Sometimes if the door has been open for an extended time
5.4.1.6 Cleaning the magnetron.
the lock may fail to pump down on the first try. Simply close
the door again if it opens on default. If it still fail after two or Turn off the pumps to vent the Maldi. Remove the magnetron
by losening the red nut on the clamp ring (the magnetron is
contents
located on the right side of the Maldi, under the pulser box).
Remove the circlip from the inside of the magnetron with a
pair of pliers. Take out the two ”buckets” from the inside of the
magnetron. Unscrew the white piece of plastic from the other
side of the magnetron, take out the center pin from the magn-
etron. Place the two buckets, the circlip and the center pin in a
beager filled with methanol. Sonicate the beager with its con-
tents in a ultrasonic bath for 15 minutes. Rinse with deionised
water several times. Let all the parts dry. If the parts are really
dirty it migth be nessesarry to add 10-15% of formic acid to
the methanol and follow the procedure above. Be careful with
the formic acid, it is a strong acid. It should only be used with
safety gloves, safety glasses and a lab coat in a vent hood.
Reasembly all the parts in reverse order. Start all the pumps.
Leave the system to pump down. It can take some time for
the system to reach a good vacuum since some parts from
the magnetron has been weat.
5.4.2 Preventive Maintenance Visit Records
On the following pages are copies of the pm visit recores.
contents
PREVENTIVE MAINTENANCE VISIT RECORD
Customer: Date: ........... ............... ..............
Serial No: ..................................
Job No: .....................................

Contract No: .............................
Engineer:...................................................
Modification status: Accessories:
Check Action* √ Remarks

1 Status information I
Pirani Reading: mbar
Magnetron reading: mbar
Motor Offset:
Laser threshold:
2 Pre pm test T See page 2-4
2.1 Perform the entry test T
3 Overall condition I,C
3.1 Check all connections I,C
3.2 Clean the Maldi C
4 Vacuum System I,C,R
4.1 Change of oil in the rotary pump R Special Pump Oil to Maldi 18-1157-20
4.2 Change the door O-ring R Door O-Ring 44,2 x3 FPM 18-1150-37
4.3 Inspect all vacuum hose and I,
connections.
5 Electronics I,T
5.1 Clean fanfilter, inspect all fans C,I
5.2 Measure voltages on psu pcb M
7 Mechanics I,A,L
7.1 Check the motor offset I,A
7.2 Lubricate the door assy L
8 Laser I,A
8.1 Check alignment of the laser I,A
8.2 Check laser treshold value New laser treshold value =___
9 Slideloader I,C,L,A
9.1 Check the adjustment of the SL I,C,L,A,T
9.2 If necessary recalibrate M
10 Software T,M
Update the Ettan Maldi software M Version 2.0 SP2
Perform a backup of the Oracle DB M
Perform an update of Protein DB M
11 Final Test T See page 5-7
Action Codes: A = Adjust, C = Clean, I = Inspect, L = Lubricate,

R = Repair/ Replace if worn or damaged, T = Test, M = Modify
Pre pm test
This test should be performed as the first thing to do on a pm visit, whiteout any tuning or
adjustments. This is to determine the function and performance of the Maldi before the pm.
There are no specifications to achieve for this test. All methods used in these tests are
described in the installation guide. The preparation of samples for the tests is described in the
installation guide.
Linear mode performance
Measure the s/n for the m/z 1672.89 peak of 5 fmol Neurotensin .The result should be obtained
accumulating 200 shots per spectrum in 8-shots mode.

1672,89 m/z
Linear Resolution test
The resolution, FWHM (R) should be determed for the monoisotopic peak in the isotopic cluster
of 1.5 pmol Ile 7 Ang III, m/z 897,531. The result should be obtained accumulating 200 shots
per spectrum in 8-shots mode.

897,531 m/z
Run 5 pmol BSA accumulating 200 shots per spectrum in 8-shots mode. The monomer, m/z
66431, the dimer, m/z 132859 and the trimer, m/z 199287 should be detected in the spectra.

66431 m/z
BSA dimer at 132859m/z
BSA trimer at 199287m/z
Reflectron mode performance

Measure the s/n for the m/z 1672.89 peak of 5 fmol Neurotensin .The result should be obtained

1672,89 m/z
The resolution FWHM (R) for the monoisotopic peak in the isotopic cluster of 1.5 pmol hACTH
18-39 should be determend. The result should be obtained accumulating 200 shots per
hACTH 18-39 Resolution

2465,199 m/z
Mass accuracy
Compare measured masses with theoretical, using 100-fmol iodoacetic acid modified
phosphorylase b tryptic digest.
Mass errors
total matched
<20ppm
First approved
spectrum
Second approved
spectrum
Mass error with external calibration
phosphorylase B.
Mass errors
total matched
<100ppm
First approved
spectrum
Second approved
spectrum
PSD sensitivity test
The fragment masses of 60 fmol Hexatyrosine (m/z 997.396) should be detected and
annotated. In a spectra the following fragment ions S/N should be determed, b2=327.36;
b3=490.536; b4=653.712; b5=816.888.
The average mass error of the fragment masses, m/z 327.36, 490.536, 653.712 and 816.888 of
3 pmol Hexatyrosine should be determed.
Hexatyrosine B2=327.36 B3=490.536 B4=653.712 B5=816.888
S/N
FRAGMENT M/Z
ERROR
be fulfilled:
Table 2.
(fmol) value
1 100
2
3
4
5
6
7
8
9 50
10
11
12
13
14
15
16
17 25
18
19
20
21
22
23
24
Total run tim:
Post pm test
This test should be performed after the pm. This test is the same as the installation test and the
specification is the same. This is to verify that Maldi fulfill all specification after the pm.
All methods used in these tests are described in the installation guide. The preparation of
samples for the tests is described in the installation guide.
Linear mode performance
Acceptance limit: S/N > 3 for the m/z 1672.89 peak of 5 fmol Neurotensin, accumulating 200
shots per spectrum in 8-shots mode.

1672,89 m/z
Linear Resolution test
Acceptance limit: A resolution ≥1000, FWHM (R) should be achieved for the monoisotopic peak
in the isotopic cluster of 1.5 pmol Ile 7 Ang III, m/z 897,531. The result should be obtained

897,531 m/z
The monomer, m/z 66431, the dimer, m/z 132859 and the trimer, m/z 199287 of 5 pmol BSA
should be detected in the spectra. The result should be obtained accumulating 200 shots per

66431 m/z
BSA dimer at 132859m/z
BSA trimer at 199287m/z
Reflectron mode performance

Acceptance limit: S/N> 3 for the m/z 1672.89 peak of 5 fmol Neurotensin .The result should be
obtained accumulating 200 shots per spectrum in 8-shots mode.

1672,89 m/z
Acceptance limit: Resolution> 10000, FWHM (R) for the monoisotopic peak in the isotopic
cluster of 1.5 pmol hACTH 18-39. The result should be obtained accumulating 200 shots per
hACTH 18-39 Resolution

2465,199 m/z
Mass accuracy
phosphorylase b tryptic digest.
Acceptance limit: More than 15 masses must be assigned to Phosphorylase B and for 40% of
the assigned masses, the error should be equal or less than 20 ppm, in the mass range 900-
2500 m/z.
Mass errors
total matched
<20ppm
First approved
spectrum
Second approved
spectrum
Mass error with external calibration
phosphorylase B.
Acceptance limit: More than 15 masses must be assigned to Phosphorylase B tryptic digest
and for 30% of the masses, the error should be equal or less than 100 ppm.
Mass errors
total matched
<100ppm
First approved
spectrum
Second approved
spectrum

PSD sensitivity test
The fragment masses of 60 fmol Hexatyrosine (m/z 997.396) should be detected and
annotated. Acceptance limit: In a spectra the following fragment ions must be detected with
S/N≥ 3, b2=327.36; b3=490.536; b4=653.712; b5=816.888.
Acceptance limit: The average mass error of the fragment masses, m/z 327.36, 490.536,
653.712 and 816.888 of 3 pmol Hexatyrosine must be below +/- 1 Da and the mass error of one
individual fragment peak must not exceed1.5 Da.
Hexatyrosine B2=327.36 B3=490.536 B4=653.712 B5=816.888

S/N
FRAGMENT M/Z
ERROR
be fulfilled:
Table 2.
(fmol) value
1 100
2
3
4
5
6
7
8
9 50
10
11
12
13
14
15
16
17 25
18
19
20
21
22
23
24
Total run tim:
Chapter 6
Chapter Contents
6. Disassembling
Disassembling
6.1 Removing panels
6.2 Vacuum pumps
6.3 Flight tube
6.4 Detector system
6.5 Slide Loader
6.7 Pcb and power supplies
contents
6.1 Removing panels
The first panel to remove is the curved front panel with the
blue LED. It is hold in place by a screw in the lower left
corner.
The second panel is the front of the ”chimney”. It is secured
by the curved panel with the LED, two screws at the top.
Also the lid of the chimney has to be removed before the
front of the chimney can be removed. When this has been
removed, it is only to lift the front panel up and remove it.
The panel is hanging on some screw heads that is fitted in
the chassie of the maldi.
The third panel to remove is the right front panel. It is hold
in place by some screws that is hidden under the front of
the ”chimney”.
The fourth panel to remove is the back of the ”chimney”.
Losen the vent tube hold in place by some tie wrap then it is
only to lift the panel upwards.
The fifth panel is the top that cover all HT supplies. This
panel is just to lift it of the maldi.
The sixth panel to remove is the back panel. It`s secured by
al allen screw from the top. When the allen screw has ben
removed, lift the panel up and forward to remov it.
To remove the last panel which covers the sides, losen
three screws at each side and slide the wrap a round
panels off.
To refit the panels the order is reversed from above and it
requires a black belt in origami to get them in place.
contents
6.1 Vacuum pumps If a separate 24 V power supply is not avilabel the system
has to be vented by switching of the main switch on the
When doing service on a vacuum system you should
right side of the instrument. The system should be vented to
always use clean dustfree rubber gloves so you do not
dry N2 and not to air. This is to reduce the pump down time
leave finger prints inside the vacuum system. When the
after venting the Maldi. When the rotary pump is back in
system is opend keep all parts and openings coverd whit
place it should be switched on for one minute before the 24
alumina foil to keep the inside as clean as possible. Small
V is removed from the isolation valve. It could be a good
dust particles and hair could cause discharges and arcing
idea to replace/service the pirani gauge at the same time as
inside a vacuum camber when voltages up to 20 kV is
the rotary pump. It is fitted on top of the rotary pump and
applied to the different parts inside.
hold in place by a clamp ring. The only service that can be
All connections between the pumps are made by stainless done is to replace the oil inthe rotary pump. In the turbo
steel bellow tubing. The bellow tubing is connected to the pumps there are no service to be done.
pump by a stainless steel clamp ring and the sealing is
The system has to be vented if the turbo pumps should be
done whit a viton o-ring.
removed. Each turbo pump is hold in place by four clamps
When reassembly a vacuum system, make shure that and four screws. Remove all contacts and valves from the
all o-rings and sealing surfaces are clean and dust free. turbo pump, losen the screws that holds the turbo pump in
They could be cleaned whit metanol and a lint free place a 1/4 of a turn in a crisscross pattern, repeat until the
tissue. pump is lose. Remove the pump. When putting back the
The first thing to do when removing the rotary vacuum pump it is important to make shure to get the o-ring in the
pump is to separate the pump from the rest of the vacuum right place and thighten the screws that holds the pump in
system by activating the isolation valve with a external 24 V place in a crisscross pattern and 1/4 of a turn each time.
supply. It is done by disconnecting the normal contact and This is done to achive a good seal between the pump and
connect the 24 V supply to the pins on the valve. When the the vacuum chamber and not to bend the flange of the
valve is activated the rotary pump can be switched of and pump. To get acces to the source turbo pump it might be
removed from the system by losen the clamping ring and nessesary to remove the laser and the pulser from the
the screw under the Maldi (this screw is a transport screw instrument.
and should be removed when the system is installed). The The magnetron (penning) gauge should only be removed
system will keep the vacuum for about 15 minutes whitout when the system is vented. See in the magnetron manual
the rotary pump. The rotary vacuum pump can now be from Edwards on how to dissassembly the magnetron
removed and replaced/serviced whitout venting the system. gauge.
contents
6.3 Flight tube
There is no reason to open up the flight, because that is
only a empty tube. If you still has to open it contact your
local service specialist for advice.
contents
6.4 Detector system
- Went the system with pure N2.
-LINEAR DETECTOR REPLACEMENT:Remove then top of
the connection of the detector. Remove the detector by losen
three small screws that holds the detector in place.
-REFLECTRON DETECTOR REPLACEMENT Old style
detector: Remove the turbopump from the reflectron chamber.
Disconnect M79 and M80 from the left hand side of the A
refletor. It is the connectors for the MCP (reflectron detector).
Loosen the four nuts (A) and lift the reflector gently uppwards
to remove it from the Maldi. Place the top part of the Maldi on
a clean bench. Cover the openings on the instrument with
alumina foil. Loosen the four allen screw (B) and remove the
alumina plate that holds the MCP, Gate electrode and Kicker
electrodes.
contents
Be careful with the eight ceramic distances when you lose
the (B) allen screw. Turn the alumina pice up side down.
Losen the three nylon screw (C). Remove (D). Make a note
of the mark on the left side of the MCP. Do not touch the
MCP with your fingers, use tweezers one the edges of the
MCP when the plates has to be moved. The mark on the
top one should be to the right and the bottom one to the left.
Be careful and keep the parts as clean and dustfree as
possible. The reassemble is in the reverse order. Be careful
when thigtening the nylon screews (C), thigtnen the
screews a 1/4 of a turn each time to achive a uniform
pressure on the detector plates. Do not over thigten the
screews, the MCP are very fragile and brake easily. Do not
expose the plates to air for a long time since the coating on
the detectors will oxidice, they will also absorbe humidity
from the air which have to evaporate from the plates before
the HT is applied to to the detectors in the vacuum
chamber. If not, the water in the tiny holes of the plate will
explode and ruin the MCP.
C D MCP
Link to replacement of the new detector.
contents
6.5 Slide Loader
See Slide Loader service manual.
contents
The laser is fitted on a bench to the left of the ion source. It
is mounted with three allen screws (a) from the underside of
the bench. To remove the laser it is just to disconect the
contacts for 24V and laser trigger at the back of the laser
box and remove the two allen screw at the bottom.
The filter thats regulate the laser power is fitted just after the
laser and is hold in place by two screws (b) on the
underside of the bench were also the Laser detect box is
fitted. To remove the Filter assy a contact has to be
disconnected. There are no parts to service inside the laser,
it is replaced as a units.
Laser and Filter assy. a b
contents
6.7 Pcb´s and power supply
The electronics are fitted in a alumina box on the back of
the instrument. To get acces to the box the back pannel has
to be removed. To get acces to the pcb´s a panel on the
alumina box has to be removed by lose 20 screws from it
and three bnc contacts has to be disconnected. Four nuts
and washer has to be removed from the bnc contacts
before the alumina panel can be removed.
The five H.T supplies are fitted on two rods on the top of the
electronic box. Each H.T power supply is fitted whit four
screws. All pcb´s and power supplies are not supposed to
be repaird on seit, they are replaced when needed.
contents
Chapter 7
Chapter Contents
7. Spare Parts
Spare Parts
7.1 Spare Parts
7.2 Exploded View Panels
contents
7.1 Spare part list
Instrument
Ettan Maldi -Tof PRO MS 240 V Version:
18-1156-53
Ettan Maldi -Tof PRO MS 120V Version:
18-1156-54
contents
Manuals
Service Manual: 18-1160-04
Instrument Handbook: 18-1144-00
User Manual: 18-1144-01
Site preparation guide: 18-1144-63
contents
Computer and Software
Ettan Maldi-Tof Pro MS

Computer, Compaq PC
Ettan Maldi TOF Pro software 2.0SP2.

18-1175-88
ORACLE DATABASE LICENSE 9I:

18-1162-58
PCI Interface board

this card is located in the PC
18-1146-56
contents
PCB 1
PSU 20KV HP20R/211 Refl.
18-1157-19
PSU 2.5KV HP 2.5N Refl.det.
18-1146-55
PSU 2.5KV HP 2.5P Linear detector
18-1172-39
PSU 2.5KV HP 2.5N Linear detector, used on early Maldi Pro
18-1146-55
PSU 5kV HP 5R/1M Pulser
18114653
PSU 20KV HP20R/212 Source
18-1157-18 REFLECTRON
PULSER
MCP
ETP
SOURCE
24 V Switched Power Supply board (PSU)
18-1146-57
Power supply PCB
18-1159-98
Transient recorder board
18-1159-94
Acqusition control board
18-1159-96
Main I/O board
18-1146-18
HV control board
C
NO
NC
18-1146-17
contents
PCB 2
Linear head Amplifier
18-1146-52
Gate and kicker pcb

18-1146-51
Pulser assy
18-1145-71
Beam blanking assy (beam dump, low mass filter)
18-1146-50
Laser detect assy

18-1146-72
Backpanel/plane boards (located behind the aluminium
panel with all D-sub connectors.)
18-1145-97/18-1145-98
Magnetron
18-1146-12
Magnetron cable assy
18-1145-77
NW 25 C clamp
18-1146-14
Maldi door assy
18-1169-77
contents
Laser and optical system
Laser N2 OEM VSL-3371 LSI

18-1145-73
E.U. 19-9000-86
Filter wheel assy
18-1160-01
ND filter motor assembly
18-1161-47
Laser detect assy
18-1146-72
LSI
M52
contents
Vacuum system main parts
Turbo pump large EXT 250

18-1146-33 E.U. 19-9000-98
Turbo pump EXT 70 ISO-K63 small
18-1146-00 E.U. 19-9000-91
Turbo pump controller EXC 100 L
18-1146-02 E.U. 19-9000-93
Rotary Pump E 2 M 1.5
110 V 18-1164-36
230 V 18-1164-37
Magnetron gauge AIM-S-NW 25
18-1146-12
Magnetron gauge cable
18-1145-77
Pirani gauge
18-1146-03
Pirani gauge cable
18-1145-76 C
Air admit valve (vent valve fitted on small turbo)

18-1162-86
contents
Vacuum system equipment
S.S. Vacuum line NW 10x250

18-1146-05
Cross NW 10 AL
18-1146-06
Clamp half claw ISO 63
18-1146-07
Clamp ring NW 10/16
18-1146-08
NW 10/16 Viton on ST carrier
18-1146-10
NW 10 to 1/8 NPT
18-1146-09
NW 10 viton on AL carrier
18-1146-11
NW 25 viton on ST ST carrier
18-1146-13
NW 10 elbow
18-1146-15
contents
Reflectron Assembly
Clamp bulkhead NW 16
18-1146-32
Pumping Kit Assembly
NW 25/10 reducer aluminium
18-1146-35
NW 10 x 750 tubing flexible
18-1146-36
Elbow NW 25
18-1146-37
Tee piece NW 25
18-1146-38
Clamp craw full ISO 63
18-1146-39
Blank NW 25
18-1146-40
NW 25 clamp ring ST ST
18-1146-42
18-1146-43
18-1146-49
contents
O-Ring 44.2x3 FPM
O-rings in the area drive lens HSG Assy
18-1150-37 door o-ring
O-Ring 114 x 5.7 Viton 1143.57

18-1145-84
O-Ring 164 x 5.7 Viton 1643.57
18-1145-85
O-Ring 44.5 x 3.0 Viton 0445.30
18-1145-86
O-Ring 32.92 x 3.5 Silicone
18-1145-87 o-ring for the sample lock, seals against the probe when
the door is open
O-Ring 10 x 2.4 Viton 0096.24
18-1145-88 o-ring to brass bushing for the sample slide assy
O-Ring 18 x 2.5 Viton 0176.24
18-1145-89
O-Ring 27.5 x 3.0 Viton 0275.30
18-1145-90
O-Ring 26.6 x 2.4 Viton 0246.24
18-1145-91
O-Ring 22 x 3 Viton 0215.30
18-1145-92
O-Ring 12 x 2.5 Viton 0120.25
18-1145-93
O-Ring 42.5 x 3.0 Viton
18-1145-94
contents
O-rings in the area reflectron assembly

18-1146-27
O-Ring 155 x 5.7 Viton 1543.57

18-1146-28
O-Ring 174 x 5.7 Viton 1743.57

18-1146-29
O-Ring 175 x 3 Viton 1745.30

18-1146-30
O-ring 12 x 2.5 Viton 0120.25

18-1145-93 duplicate
contents
O-Rings in the area Pumping Kit assembly
O-Ring 22 x 2. 5 Viton 0216.24

18-1146-45

18-1146-46
O-Ring 27.5 x 3.0 Viton 0275.30

18-1145-90 duplicate

18-1146-48
contents
Parts Drive/Lens HSg Assembly
Spring Extension 0.51 x 4.78

18-1145-95
Torque Disc Backlash Free 19 mm

18-1145-96
Brass bushing
18-1159-99
The bushing is located under this cover, it is the bearing
and seal for the sample slide transport meccanism.
Drive shaft complete
18-1172-40 Drive shaft new design. See Si no 10 for more
info.
contents
Detectors
ETP
18-1157-16
linear detector pcb
11-0002-79
MCP high speed detector assy

The complete detector has no part number
18-1165-95 MCP plates 5um matched pair
contents
High Voltage System
PSU HP 5R/1M
18-1146-53 E.U. 19-9001-02
PSU HP 2.5/1M
18-1146-54 E.U. 19-9001-03
PSU HP 2.5 N
18-1146-55 E.U. 19-9001-04
PSU HP20R/211 REFL
18-2257-19
PSU HP20R/212 SOURCE
18-2257-18
Feedthrough assy
18-1145-80
Feedthrough assy short pulser box
18-1145-69
Slim fan 230 V
18-1149-92
Slim fan 120 V
18-1160-00
contents
Switch Gear Assembly
Switch Gear Assy

18-1145-79 E.U. 19-9000-87
micro switch large

spur gear
spur gear ZG 0.5 - 120 + 6 bore M3
spur gear modified
spur gear 6.35 bore M3
stepper motor wired assy
small micro switch
bush flanged
contents
Electrical Parts
Fuse 204V 20 mm antisurge

18-1146-23
Fuse Filter Inlet 10A

18-1146-24
Inlet Boot 10A

18-1146-25
Fan 110V
18-1146-22
Fan 240V
18-1146-21
110 Volt Parts
A. Fan 110 volt ( Slim for HV ) 2

B. Fan 110 volt ( Electonic Tray ) 4
C. Rotary pump 1
The picture shows an old fan tray. The new fan tray has 5
D. Fuse 10Amp 1 fans.
E. Fuse 4Amp 1
F. Main inlet 6Amp 1
contents
Cables
Cable 277A Pulser HV INT

18-1145-70
Inlet Valve Cable Assy

18-1145-75
Pirani Gauge Cable Assy

18-1145-76
Magnetron Gauge Cable Assy

18-1145-77
Computer Interface Cable

18-1145-78
contents
Valves
Valve Solenoid IPVA 10 EK

18-1146-04
single valve
Sample Inlet Valve Assembly

18-1146-16
Con O-RIng 7/16 stayt to 1/4

Tee SW Union SM
Tube Adapter Male Npt
Solenoid Valve
Male 1/8 Npt to 1/8 Swage
Tube Nylon Black 1/8 OD x 30 M
Tee Male Run
Hose Insert
Tube Nylon Natural 1/4 Idx 30 M
Adaptor 1/4 Tbue To 1/4 Hose
Tube LPDE 3/8 in OD to 1/4 in ID
Adaptor 1/8 Npt to 1/4 in ID
Loctite 542 Gasket Sealer 10 ml
contents
PC Boards Switched PSU 24 V (TCU)
Switched PSU 24V 4.8A Linear
18-1146-57
E.U.
19-9001-06
contents
PCB Power Supply
Power Supply Board
18-1159-98
E.U.
contents
PCB Backplane Assy
Backplane Board
18-1145-98
E.U.
19-9000-89
contents
PCB Acqusition Control
Acqusition Control Board
18-1159-96
E.U.
contents
PCB T/R Assy
Transient Recorder Board
18-1159-94
E.U.
contents
PCB I/O Assy
Input-/Output - Board
18-1146-18
E.U.
19-9000-95
contents
PCB HV Assy
High Voltage Control Board
18-1146-17
E.U.
19-9000-94
contents
Pulser Assy IT 2-3
Pulser Box Assembly
18-1145-71
E.U.
19-9000-84
Assembly contains:
Pulser board
Capacitor 5000 pF 20 kV
Front Cover
contents
Beam Blanking Assy
Beam Blanking Board
18-1146-50
E.U.
19-9000-99
Beam Blanking Assy contains:
Beam Blanking board

Box
contents
Gate Driver Assy
Gate Drive Board
18-1146-51
E.U.
Gate Driver Assy contains:
Gate Driver Board

Box
contents
Linear Amplifier Assy
Linear Preamplifier Board
18-1146-52
E.U.
19-9001-00
Linear Amplifier Assy contains:

Box
contents
PCB Assy PCI I/F
PCI Card
18-1146-56
E.U.
19-9001-05
contents
PCB Laser Detect Assy
Laser Detect Board
18-1145-72
E.U.
19-9000-85
Laser Detect Assy contains:
Laser Detect Board

Box
contents
Sample slides and equipment
Sample slide Kit

18-1147-18
containing 24 spot sample slides
Sample Tray Kit
contents
Automatic Slide Loader
18-1147-63
contents
Instrument Service Miscellenous
Installation Ettan Maldi TOF

18-1145-20
Maldi TOF MS Full Cover Agreement

18-1145-11
Maldi TOF MS PM Agreement

18-1145-13
Maldi TOF MS 3 Year Extended Warranty

18-1145-14
contents
Instrument Cover
Top Cover
56-3104-14
Tube Panel
the numbers underneath are internal Umea Factory 56-3104-16
numbers
Fan Cover
56-3104-17
Upper Cover
56-3104-18
Side Panel
56-3104-20
Sample Inlet
56-3104-12
Front Corner Rear Panel

56-3104-11 56-3104-15
Main Cover
56-3104-19
contents
Chapter 6
Chapter Contents
6. Disassembling
Disassembling
6.1 Removing panels
6.2 Vacuum pumps
6.3 Flight tube
6.4 Detector system
6.5 Slide Loader
6.7 Pcb and power supplies
contents
6.1 Removing panels
The first panel to remove is the curved front panel with the
blue LED. It is hold in place by a screw in the lower left
corner.
The second panel is the front of the ”chimney”. It is
secured by the curved panel with the LED, two screws at
the top. Also the lid of the chimney has to be removed
before the front of the chimney can be removed. When this
has been removed, it is only to lift the front panel up and
remove it. The panel is hanging on some screw heads that
is fitted in the chassie of the maldi.
The third panel to remove is the right front panel. It is hold
in place by some screws that is hidden under the front of
the ”chimney”.
The fourth panel to remove is the back of the ”chimney”.
Losen the vent tube hold in place by some tie wrap then it
is only to lift the panel upwards.
The fifth panel is the top that cover all HT supplies. This
panel is just to lift it of the maldi.
The sixth panel to remove is the back panel. It`s secured
by al allen screw from the top. When the allen screw has
ben removed, lift the panel up and forward to remov it.
To remove the last panel which covers the sides, losen
three screws at each side and slide the wrap a round
panels off.
To refit the panels the order is reversed from above and it
requires a black belt in origami to get them in place.
contents
6.1 Vacuum pumps If a separate 24 V power supply is not avilabel the system
has to be vented by switching of the main switch on the
When doing service on a vacuum system you should
right side of the instrument. The system should be vented
always use clean dustfree rubber gloves so you do not
to dry N2 and not to air. This is to reduce the pump down
leave finger prints inside the vacuum system. When the
time after venting the Maldi. When the rotary pump is back
system is opend keep all parts and openings coverd whit
in place it should be switched on for one minute before the
alumina foil to keep the inside as clean as possible. Small
24 V is removed from the isolation valve. It could be a
dust particles and hair could cause discharges and arcing
good idea to replace/service the pirani gauge at the same
inside a vacuum camber when voltages up to 20 kV is
time as the rotary pump. It is fitted on top of the rotary
applied to the different parts inside.
pump and hold in place by a clamp ring. The only service
All connections between the pumps are made by stainless that can be done is to replace the oil inthe rotary pump. In
steel bellow tubing. The bellow tubing is connected to the the turbo pumps there are no service to be done.
pump by a stainless steel clamp ring and the sealing is
The system has to be vented if the turbo pumps should be
done whit a viton o-ring.
removed. Each turbo pump is hold in place by four clamps
When reassembly a vacuum system, make shure that and four screws. Remove all contacts and valves from the
all o-rings and sealing surfaces are clean and dust turbo pump, losen the screws that holds the turbo pump in
free. They could be cleaned whit metanol and a lint place a 1/4 of a turn in a crisscross pattern, repeat until the
free tissue. pump is lose. Remove the pump. When putting back the
The first thing to do when removing the rotary vacuum pump it is important to make shure to get the o-ring in the
pump is to separate the pump from the rest of the vacuum right place and thighten the screws that holds the pump in
system by activating the isolation valve with a external 24 V place in a crisscross pattern and 1/4 of a turn each time.
supply. It is done by disconnecting the normal contact and This is done to achive a good seal between the pump and
connect the 24 V supply to the pins on the valve. When the the vacuum chamber and not to bend the flange of the
valve is activated the rotary pump can be switched of and pump. To get acces to the source turbo pump it might be
removed from the system by losen the clamping ring and nessesary to remove the laser and the pulser from the
the screw under the Maldi (this screw is a transport screw instrument.
and should be removed when the system is installed). The The magnetron (penning) gauge should only be removed
system will keep the vacuum for about 15 minutes whitout when the system is vented. See in the magnetron manual
the rotary pump. The rotary vacuum pump can now be from Edwards on how to dissassembly the magnetron
removed and replaced/serviced whitout venting the system. gauge.
contents
6.3 Flight tube
There is no reason to open up the flight, because that is
only a empty tube. If you still has to open it contact your
local service specialist for advice.
contents
6.4 Detector system
- Went the system with pure N2.
-LINEAR DETECTOR REPLACEMENT:Remove then top of
the connection of the detector. Remove the detector by losen
three small screws that holds the detector in place.
-REFLECTRON DETECTOR REPLACEMENT Old style
detector: Remove the turbopump from the reflectron
chamber. Disconnect M79 and M80 from the left hand side of A
the refletor. It is the connectors for the MCP (reflectron
detector). Loosen the four nuts (A) and lift the reflector gently
uppwards to remove it from the Maldi. Place the top part of
the Maldi on a clean bench. Cover the openings on the
instrument with alumina foil. Loosen the four allen screw (B)
and remove the alumina plate that holds the MCP, Gate
electrode and Kicker electrodes.
contents
Be careful with the eight ceramic distances when you lose
the (B) allen screw. Turn the alumina pice up side down.
Losen the three nylon screw (C). Remove (D). Make a note
of the mark on the left side of the MCP. Do not touch the
MCP with your fingers, use tweezers one the edges of the
MCP when the plates has to be moved. The mark on the
top one should be to the right and the bottom one to the
left. Be careful and keep the parts as clean and dustfree as
possible. The reassemble is in the reverse order. Be
careful when thigtening the nylon screews (C), thigtnen the
screews a 1/4 of a turn each time to achive a uniform
pressure on the detector plates. Do not over thigten the
screews, the MCP are very fragile and brake easily. Do not
expose the plates to air for a long time since the coating on
the detectors will oxidice, they will also absorbe humidity
from the air which have to evaporate from the plates
before the HT is applied to to the detectors in the vacuum
chamber. If not, the water in the tiny holes of the plate will
explode and ruin the MCP.
C D MCP
Link to replacement of the new detector.
contents
6.5 Slide Loader
See Slide Loader service manual.
contents
The laser is fitted on a bench to the left of the ion source.
It is mounted with three allen screws (a) from the underside
of the bench. To remove the laser it is just to disconect the
contacts for 24V and laser trigger at the back of the laser
box and remove the two allen screw at the bottom.
The filter thats regulate the laser power is fitted just after
the laser and is hold in place by two screws (b) on the
underside of the bench were also the Laser detect box is
fitted. To remove the Filter assy a contact has to be
disconnected. There are no parts to service inside the
laser, it is replaced as a units.
Laser and Filter assy. a b
contents
6.7 Pcb´s and power supply
The electronics are fitted in a alumina box on the back of
the instrument. To get acces to the box the back pannel has
to be removed. To get acces to the pcb´s a panel on the
alumina box has to be removed by lose 20 screws from it
and three bnc contacts has to be disconnected. Four nuts
and washer has to be removed from the bnc contacts
before the alumina panel can be removed.
The five H.T supplies are fitted on two rods on the top of
the electronic box. Each H.T power supply is fitted whit
four screws. All pcb´s and power supplies are not
supposed to be repaird on seit, they are replaced when
needed.
contents
Chapter 7
Chapter Contents
7. Spare Parts
Spare Parts
7.1 Spare Parts
7.2 Exploded View Panels
contents
7.1 Spare part list
Instrument
Ettan Maldi -Tof PRO MS 240 V Version:
18-1156-53
Ettan Maldi -Tof PRO MS 120V Version:
18-1156-54
contents
Manuals
Service Manual: 18-1160-04
Instrument Handbook: 18-1144-00
User Manual: 18-1144-01
Site preparation guide: 18-1144-63
contents
Computer and Software
Ettan Maldi-Tof Pro MS

Computer, Compaq PC
Ettan Maldi TOF Pro software 2.0SP2.

18-1175-88
ORACLE DATABASE LICENSE 9I:

18-1162-58
PCI Interface board

this card is located in the PC
18-1146-56
contents
PCB 1
PSU 20KV HP20R/211 Refl.
18-1157-19
PSU 2.5KV HP 2.5N Refl.det.
18-1146-55
PSU 2.5KV HP 2.5P Linear detector
18-1172-39
PSU 2.5KV HP 2.5N Linear detector, used on early Maldi Pro
18-1146-55
PSU 5kV HP 5R/1M Pulser
18114653
PSU 20KV HP20R/212 Source
18-1157-18 REFLECTRON
PULSER
MCP
ETP
SOURCE
24 V Switched Power Supply board (PSU)
18-1146-57
Power supply PCB
18-1159-98
Transient recorder board
18-1159-94
Acqusition control board
18-1159-96
Main I/O board
18-1146-18
HV control board
C
NO
NC
18-1146-17
contents
PCB 2
Linear head Amplifier
18-1146-52
Gate and kicker pcb

18-1146-51
Pulser assy
18-1145-71
Beam blanking assy (beam dump, low mass filter)
18-1146-50
Laser detect assy

18-1146-72
Backpanel/plane boards (located behind the aluminium
panel with all D-sub connectors.)
18-1145-97/18-1145-98
Magnetron
18-1146-12
Magnetron cable assy
18-1145-77
NW 25 C clamp
18-1146-14
Maldi door assy
18-1169-77
contents
Laser and optical system
Laser N2 OEM VSL-3371 LSI

18-1145-73
E.U. 19-9000-86
Filter wheel assy
18-1160-01
ND filter motor assembly
18-1161-47
Laser detect assy
18-1146-72
LSI
M52
contents
Vacuum system main parts
Turbo pump large EXT 250

18-1146-33 E.U. 19-9000-98
Turbo pump EXT 70 ISO-K63 small
18-1146-00 E.U. 19-9000-91
Turbo pump controller EXC 100 L
18-1146-02 E.U. 19-9000-93
Rotary Pump E 2 M 1.5
110 V 18-1164-36
230 V 18-1164-37
Magnetron gauge AIM-S-NW 25
18-1146-12
Magnetron gauge cable
18-1145-77
Pirani gauge
18-1146-03
Pirani gauge cable
18-1145-76 C
Air admit valve (vent valve fitted on small turbo)

18-1162-86
contents
S.S. Vacuum line NW 10x250

18-1146-05
Cross NW 10 AL
18-1146-06
Clamp half claw ISO 63
18-1146-07
Clamp ring NW 10/16
18-1146-08
NW 10/16 Viton on ST carrier
18-1146-10
NW 10 to 1/8 NPT
18-1146-09
18-1146-11
NW 25 viton on ST ST carrier
18-1146-13
NW 10 elbow
18-1146-15
contents
Reflectron Assembly
Clamp bulkhead NW 16
18-1146-32
Pump Kit Assembly
NW 25/10 reducer aluminium
18-1146-35
NW 10 x 750 tubing flexible
18-1146-36
Elbow NW 25
18-1146-37
Tee piece NW 25
18-1146-38
Clamp craw full ISO 63
18-1146-39
Blank NW 25
18-1146-40
NW 25 clamp ring ST ST
18-1146-42
18-1146-43
18-1146-49
contents
O-Ring 44.2x3 FPM
O-rings in the drive lens HSG Assy
18-1150-37 door o-ring
O-Ring 114 x 5.7 Viton 1143.57

18-1145-84
O-Ring 164 x 5.7 Viton 1643.57
18-1145-85
O-Ring 44.5 x 3.0 Viton 0445.30
18-1145-86
O-Ring 32.92 x 3.5 Silicone
18-1145-87 o-ring for the sample lock, seals against the probe when
the door is open
O-Ring 10 x 2.4 Viton 0096.24
18-1145-88 o-ring to brass bushing for the sample slide assy
O-Ring 18 x 2.5 Viton 0176.24
18-1145-89
O-Ring 27.5 x 3.0 Viton 0275.30
18-1145-90 also used in the pump kit
O-Ring 26.6 x 2.4 Viton 0246.24
18-1145-91
18-1145-92
O-Ring 12 x 2.5 Viton 0120.25
18-1145-93 also used in the reflectron assy
18-1145-94
contents
O-rings in the reflectron assembly

18-1146-27
O-Ring 155 x 5.7 Viton 1543.57

18-1146-28
O-Ring 174 x 5.7 Viton 1743.57

18-1146-29
O-Ring 175 x 3 Viton 1745.30

18-1146-30
O-ring 12 x 2.5 Viton 0120.25

18-1145-93 alsoused in the drive lens hsg assy
contents
O-Rings in the Pump Kit area
O-Ring 22 x 2. 5 Viton 0216.24

18-1146-45

18-1146-46
O-Ring 27.5 x 3.0 Viton 0275.30

18-1145-90 also used in the drive lens hsg assy

18-1146-48
contents
Parts Drive/Lens HSg Assembly
Spring Extension 0.51 x 4.78

18-1145-95
Torque Disc Backlash Free 19 mm

18-1145-96
Brass bushing
18-1159-99
The bushing is located under this cover, it is the bearing
and seal for the sample slide transport meccanism.
Drive shaft complete
18-1172-40 Drive shaft new design. See Si no 10 for more
info.
contents
Detectors
ETP
18-1157-16
linear detector pcb
11-0002-79
MCP high speed detector assy

The complete detector has no part number
18-1165-95 MCP plates 5um matched pair
contents
High Voltage System
PSU HP 5R/1M
18-1146-53 E.U. 19-9001-02
PSU HP 2.5/1M
18-1146-54 E.U. 19-9001-03
PSU HP 2.5 N
18-1146-55 E.U. 19-9001-04
PSU HP20R/211 REFL
18-2257-19
PSU HP20R/212 SOURCE
18-2257-18
Feedthrough assy
18-1145-80
Feedthrough assy short pulser box
18-1145-69
Slim fan 230 V
18-1149-92
Slim fan 120 V
18-1160-00
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Switch Gear Assembly
Switch Gear Assy

18-1145-79 E.U. 19-9000-87
micro switch large

spur gear
spur gear ZG 0.5 - 120 + 6 bore M3
spur gear modified
spur gear 6.35 bore M3
stepper motor wired assy
small micro switch
bush flanged
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Electrical Parts
Fuse 204V 20 mm antisurge

18-1146-23
Fuse Filter Inlet 10A

18-1146-24
Inlet Boot 10A

18-1146-25
Fan 110V
18-1146-22
Fan 240V
18-1146-21
110 Volt Parts
A. Fan 110 volt ( Slim for HV ) 2

B. Fan 110 volt ( Electonic Tray ) 4
C. Rotary pump 1
The picture shows an old fan tray. The new fan tray has 5
D. Fuse 10Amp 1 fans.
E. Fuse 4Amp 1
F. Main inlet 6Amp 1
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Cables
Cable 277A Pulser HV INT

18-1145-70
Inlet Valve Cable Assy

18-1145-75
Pirani Gauge Cable Assy

18-1145-76
Magnetron Gauge Cable Assy

18-1145-77
Computer Interface Cable

18-1145-78
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Valves
Valve Solenoid IPVA 10 EK

18-1146-04
single valve
Sample Inlet Valve Assembly

18-1146-16
Con O-RIng 7/16 stayt to 1/4

Tee SW Union SM
Tube Adapter Male Npt
Solenoid Valve
Male 1/8 Npt to 1/8 Swage
Tube Nylon Black 1/8 OD x 30 M
Tee Male Run
Hose Insert
Tube Nylon Natural 1/4 Idx 30 M
Adaptor 1/4 Tbue To 1/4 Hose
Tube LPDE 3/8 in OD to 1/4 in ID
Adaptor 1/8 Npt to 1/4 in ID
Loctite 542 Gasket Sealer 10 ml
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PC Boards Switched PSU 24 V (TCU)
Switched PSU 24V 4.8A Linear
18-1146-57
E.U.
19-9001-06
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PCB Power Supply
Power Supply Board
18-1159-98
E.U.
contents
PCB Backplane Assy
Backplane Board
18-1145-98
E.U.
19-9000-89
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PCB Acqusition Control
Acqusition Control Board
18-1159-96
E.U.
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PCB T/R Assy
Transient Recorder Board
18-1159-94
E.U.
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PCB I/O Assy
Input-/Output - Board
18-1146-18
E.U.
19-9000-95
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PCB HV Assy
High Voltage Control Board
18-1146-17
E.U.
19-9000-94
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Pulser Assy IT 2-3
Pulser Box Assembly
18-1145-71
E.U.
19-9000-84
Assembly contains:
Pulser board
Capacitor 5000 pF 20 kV
Front Cover
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Beam Blanking Assy
Beam Blanking Board
18-1146-50
E.U.
19-9000-99
Beam Blanking Assy contains:
Beam Blanking board

Box
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Gate Driver Assy
Gate Drive Board
18-1146-51
E.U.
Gate Driver Assy contains:
Gate Driver Board

Box
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Linear Amplifier Assy
18-1146-52
E.U.
19-9001-00
Linear Amplifier Assy contains:

Box
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PCB Assy PCI I/F
PCI Card
18-1146-56
E.U.
19-9001-05
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PCB Laser Detect Assy
Laser Detect Board
18-1145-72
E.U.
19-9000-85
Laser Detect Assy contains:
Laser Detect Board

Box
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Sample slides and equipment
Sample slide Kit

18-1147-18
containing 24 spot sample slides
Sample Tray Kit
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Automatic Slide Loader
18-1147-63
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Instrument Service Miscellenous
Installation Ettan Maldi TOF

18-1145-20
Maldi TOF MS Full Cover Agreement

18-1145-11
Maldi TOF MS PM Agreement

18-1145-13
Maldi TOF MS 3 Year Extended Warranty

18-1145-14
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Instrument Cover
Top Cover
56-3104-14
Tube Panel
the numbers underneath are internal Umea Factory 56-3104-16
numbers
Fan Cover
56-3104-17
Upper Cover
56-3104-18
Side Panel
56-3104-20
Sample Inlet
56-3104-12
Front Corner Rear Panel

56-3104-11 56-3104-15
Main Cover
56-3104-19
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8.8 High voltage control board
Chapter 8
8.9 Backpanel board
8.10 Backplane pcb

Circuit Diagrams
8.11 PCI bus interface
Chapter Contents
8.12 24 V PSU PCB
8.1 Block diagram
8.13 Gate PCB
8.2 Electronic system drawing
8.14 Pulser board
8.3 TCU interconnection block diagram
8.15 Beam dump PCB
8.4 Power supply PCB
8.16 Linear Preamplifier PCB
8.5 Transient recorder board
8.17 Laser detect PCB
8.6 Acquisition control board
8.18 Reflectron detector
8.7 Main I/O board
8.19 Linear detector
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8.1 Block Diagram
AC5
COMPUTER
ACQUISITION CONTROL WITH
IO * GAS CELL CONTROL (AC3) COMMS PCB
* SAMPLE MOTOR (IO1) * GATE CONTROL (AC4)
POWER SUPPLY * IRIS MOTOR (IO9) HIGH VOLTAGE CONTROL
* DATA ACCUMULATION
BOARD * SAMPLE PORT MOTOR (IO10) * HP20R - SOURCE (HVC2)
* EXTERNAL COMMS (AC5)
* VALVES (IO5,IO6,IO7) TRANSIENT RECORDER 24V SUPPLY * HP20R - REFLECTRON END (HVC1)
* LASER TRIGGER (AC2)
+5V LOGIC * TURBO PUMP CONTROLLER INTERFACE (IO4) 500MSPS SWITCH OFF FOR ZERO VOLTS
* PULSER TRIGGER (AC1) OPTIONAL
-5.2V ECL * PIRANI GAUGE CONTROL (IO3) INPUT SIGNALS * LINEAR OPERATION * H5P - DETECTOR (HVC7)
* LASER DETECT (AC7) 2GSPS
-2V ECL * MAGNETRON GAUGE CONTROL (IO2) * REQUIRED CURRNET 2.4A * HP5R - PULSER (HVC4)
* FAST TRANSIENT RECORDER. TRANSIENT
+24V IO * HIGH VOLTAGE CONTROL INTERFACE * LINEAR DETECTOR (TR2) * HP2.5P - REFLECTRON DET 2KV (HV10)
TRIGGER (AC8) RECORDER
+/- 5V T.R. * COVERS LOOP * REFLECTRON DETECTOR (TR1) * PULSED EXTRACTION UNIT (HVC4)
+/- 5V HEAD AMP * BEAM BLANKING CONTROL * GATE DRIVER (HVC6)
* AUTO-SAMPLER / Y AXIS ON ADDTIONAL BOARD * LASER POWER SUPPLY (HVC5)
* GAS CELL DRIVE * BEAM BLANKING (HVC3) TR2 AC8 TR1
IO11 AC1
PS1 PS2 IO2 IO3 IO4 IO5 IO6 IO7 AC8 AC6 TR2 HVC2 HVC4 HVC5 HVC6 HVC3
HVC1 HV7
HV10
IO9 AC2
AUTO
SAMPLER AC7
OPTION SIG?? REFLECTRON REFLECTRON
DETECTOR
DETECTOR HP20R
IO1 COVERS
UV LASER, OPTICS, IRIS AC4 HP5P
(plus port switch) HP2.5P 4mA REF :+/-20KV
HVC4
MOTOR & LIMIT SWITCHES
AC3 +2KV
IO10 +2.5KV LIN:0V (OFF)
FIBRE OPTIC & PULSE DETECT
HP5R
SAMPLE MOTOR +/-4KV AC1
HVC2
HVC6
PULSED
SOURCE EXTRACTION UNIT
HP20R -/+4KV HV3 2KV
LID MOTOR. +/-19.6KV (opposite polarity)

AND 375uA BEHLKE HTS80
BEAM GATE PULSE
MICRO SWITCHES GAS CELL DRIVER TR1
250M 5nF BLANK
DRIVE CONTROL
+/-5V TR2
CONICAL DUAL
ANODE MCP
REFLECTRON AMPLIFIER
60 PLATES ELECTRON 5nF
WITH
INCLUDING ENDS MULTIPLIER OFFSET
INLET CHAMBER
ADJUST
GATE ION FLIGHT TUBE
SAMPLE PULSED BEAM GAS
LENS TUBE TUBE +/-500V KICKER
+/-20KV LENS BLANK CELL
OR 0V +/-90V
RESISTIVE DIVIDER. (67M)
EDWARDS
MAGNETRON EDWARDS EDWARDS MAINS BLOCK
IO2
GAUGE TURBO TURBO (6 OUTPUTS)
AIM-S-MW25 PUMP EXT70 PUMP EXT70 * TURBO PUMP CONTROLLER(s)
BACKING VALVE (24V,N.O.) IO7 * TCU
* FAN TRAY
INLET * ROTARY PUMP
VALVE * BACK PANEL FANS
24V N.C.
IO5
FORE LINE
PORT ON TRAP
EDWARDS
SAMPLE
PIRAINI GAUGE IO4 IO4
PROBE
APG-M-NW16 ROTARY LAST CHANGE : 09/07/99 17:35
VENT PUMP
VALVE IO3
SJ ORIGINAL XX/98 A
24V N.C. EDWARDS TURBO PUMP EDWARDS TURBO PUMP BY MODIFICATION DATE ISS
CONTROLLER CONTROLLER DRG NO : SAI-02BD SHEET 1 OF 1
IO6 EXC100L EXC100L
LT3-P1 ELECTRICAL SYSTEM DIAG.
SCIENTIFIC ANALYSIS INSTRUMENTS LTD
STRICTLY CONFIDENTIAL COPYRIGHT SAI LTD 1997
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TCU Interconnections Block diagram
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8.4 Power supply pcb picture of board location
8.4.1 Description
8.4.2 Board Layout
8.4.3 Electronical Schematics
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picture of the board
8.4.1 Description
The power supply assy supplies most of all the low voltages in
the system.It is located in the TCU unit in slot 1.
Before insert a new board to exchange, please control that the

right mains voltage is set with the microswitches.
(according the label, here 115V AC)
This has the following supplies :

+5V for Acquisition Control PCB and IO PCB
+5V for transient recorder
+24V for IO PCB
+/-(7V to 12V) unregulated linear low noise supply for
Transient Recorder analog components.
+/-(7V to 12V) unregulated linear low noise supply for Head
amplifier.
See schematic page 192-194.
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Testprocedures for the PCB +14V and +27V unregulated (depends on load)
Maldi Pro has only 5V and 24V. -2V and -5.2V are only used Measure the voltages on TP2 wrt TP1. Should be between -
old Maldi with 500 MSPS. 14V and -27V unregulated (depends on load)
Initial inspection. Not needed if new power supply.
Check the quality of the soldering. ””Remove the sense plates from the power supply, returning
Check the quality of the crimping by gently tugging on thw the wires to the correct positions.””
wires. Measure between J1-C7 (-) and J1-C2(+). This should read
Check that connectors J1 and J2 are sitting correctly on the +5.1V. Ensure the polarity is correct.
board. Measure between J1-C12 (-) and J1-C17(+). This should
Check that the plate (B88) is firmly fitted onto the back of J2 read +5.1V. Ensure the polarity is correct.
ensuring that the warning label is visible. Measure between J1-C25 (-) and J1-C22(+). This should
Check that the backplate (B80) is firmly fitted onto the back read +2V. Ensure the polarity is correct.
of the board ensuring that the warning label is visible. Measure between J1-C28 (-) and J1-C31(+). This should
Check that holes H2, H13, H14, H15, H16 are earthed read +24V. Ensure the polarity is correct.
together. These holes form the connection to the backplate Add a sticker ”Warning!! NOT for use with 500MSPS
of the power supply and can be checked by using the systems”, (unless no conflict will arise).
screws on the backplate. Sign and date the pretest Label.
Check that the switch’s on the power supply module, SW1-3
are set to the appropriate voltage 220 or 110.
Connect the mains to the Ground, Neutral & Live on the
power supply.
IF USING AN ELECTRONICS CRATE TO TEST THE
SUPPLY, REMOVE ALL OTHER PCBS FROM THE UNIT.
Not needed if new power supply.
””With the sense plates still connected measure the voltages
on the supply and trim until the voltages are 24V, 5.0V, 5.2V
and 2V.””
Measure the voltages across TP7 (+) wrt TP8 (-) and TP5
(+) wrt TP6 (-). The output voltages should be around 9V.
Measure the voltages on TP4 wrt TP3. Should be between
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8.4.2 Board Layout
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Linear Detector Power
TP 1 : 0V
TP 2 : +5V
Linear Detector Power

TP 3: 0V
TP 4: -5.2V
Transient Recorder Linear Power

TP 5: -6 V +/- 2V
TP 6:
Transient Recorder Linear Power

TP 7:
TP 8:
Remark: see also drawing sheet 1
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Testpoints and Voltages to adjust
+ 5V
-5,2V
- 2V
24V
-2 and -5.2V are only used on Maldi whit 500 Msamples/

sec transient recorder pcb.
Detector linear power

-10V
10V
Transient recorder linear power

-10V
10V
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8.4.3 Electronical Schematics
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picture of board location
8.5 Transient recorder board
8.5.1 Description
8.5.2 Board Layout
8.5.3 Electronical schematics
Contents Chapter Service Manual Ettan Maldi TofPro MS 18-1160-04, Rev March 2004
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and the Reset signal
8.5.1 Description · A ‘Start’ signal is sent. This is synchronised to the sampling
This takes analog signals from the detectors, digitises them clock, then passed on to trigger the pulsed extraction unit.
and stores them in memory. It uses an 8 bit ADC at a · The ‘Start’ takes the ADC out of reset. This also leads to
maximum sampling rate of 1GSPS. It’s input bandwidth is resynchronising of the data into the De-multiplexer which
approximately 800MHz. It is controlled by the Acquisition follows the ADC in the data path, and to providing the data
Control Board. It can digitise at three speeds ; 1GSPS, enable to the FIFOs at the appropriate time.
500MSPS and 250MSPS. These represent the three mass · The ADC has demultiplexed data output; there are two
ranges of the instrument. It has a HF relay to switch channels a 500MHz.
between the linear detector signal and reflectron detector
signal. · This data passes De-multiplexer where it emerges as a
62.5MHz 128bit word.
It has split power planes, as the power for the digital circuits
is kept separate from the power for the analog circuits. · This 128 bit word is stored in the FIFOs.
It has an input offset DAC to set the baseline. The DAC is · Successive data is written into the FIFOs until they are full.
used to test the PCB. · This memory full signal is passed to the Acquisition Control
Board.
It has a PAL to provide issue information to the software.
The sampling clock is reduced in frequency when not in · The Acquisition Control Board then stops the acquisition
use, in order to provide superior EMC performance. by removing the ‘Start’ signal.
A 500MHZ oscillator is used, which is frequency doubled · The Acquisition Control Board then reads the data out of
using a PLL. This is then divided by factors of 2 and 4. One the FIFOs and adds it to the accumulator memory.
frequency is select from the 3 generated via the Acquisition See schematic
Control Board. A 4th frequency can be selected, but this is Sheet 18 is a block diagram showing data path timing &
generated on the Acquisition Control Board for test and synchronisation
control purposes. This is a high speed board, and where
signals cannot be easily routed point to point, low skew
splitter chips are used such as 100EL15 and 100EL11.
Basic Sequence Of Operation.
· The FIFO memory is reset using the test & control clock
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Measure the following voltages (Ground test point first):-
Testprocedures for the board TP3 to TP1 : +5V
T/R Board TP3 to TP13 : 0V
TP3 to TP10 : +3V
Equipment used :-
TP13 to TP12 : +5V
ENSURE THAT THE MAIN POWER SUPPLY IN THE TCU IS TP13 to TP11 : -5VA
18-1159-98 ISSUE BD OR ABOVE !!! TP3 to pin 5 (attached to copper area) of
Ensure no cable other than the mains cable are attached to IC15,IC17,IC13,IC8,IC14,IC9,IC20 & IC22 : +3V
the TCU. TP13 to C322 pin 1 (no via) : +2.5V
Ensure that the TCU is switched off at the mains. TP13 to TP5 : -1.364V (adjust with RV2)
Connect up (2),(3),(4) & (5). Program IC12 using the JTAG port on J13 (if not done
Fit extender card into slot 23. already)
Examine the device under test (D.U.T.). Fit programmed IC27 into SKT1 (if not done already)
Check the right componets are fitted in the correct orientation. Run the test program (testall) on the computer.
Not fitted :- C321 Adjust the baseline to just below zero as instructed (if
Check for solder bridges, dry joints and pads not soldered. neccessary)
Check the following resistances :-
TP3 to TP1 : 53 ohms (0VD to 5VD)
TP3 to TP13 : < 0.1 ohms (0VD to 0VA)
TP3 to TP10 : 86 ohms (0VD to 3VD)
TP13 to TP12 : 670 ohms (0VA to +5VA)
TP13 to TP11 : 6.2 Kilo-ohms (0VA to -5VA).
TP3 to pin 5 (attached to copper area) of
IC15,IC17,IC13,IC8,IC14,IC9 & IC22 : 62K
TP3 to pin 5 (attached to copper area) of IC20 & IC22 : 14K
Switch on unit prior to inserting the board in order to check
voltages.
Measure between J1-C1 (0VD) and J1-C11 (5VD). This
should read +5V. Ensure polarity is correct. Fit board on to the
extender card.
Switch on mains to the TCU.
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8.5.2 Board Layout
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8.6 Acquisition control boar d picture of board location
8.6.1 Description
8.6.2 Board Layout
Contents Chapter Service Manual Maldi Tof Pro MS 18-1160-04, Revised March 2004
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· If the gate is used, then at some time during the
8.6.1 Description acquisition, determined by the gate delay, a pulse is output
This board communicates with the computer. It then to the gate unit, whose width is determined by the gate
controls the timing of data acquisition. It does this by pulse width register.
controlling when the laser is fired, when the pulsed · The acquisition control board waits for the transient
extraction is triggered, when the transient recorder recorder memory to fill up. A signal is then passed back.
acquires, when the gate is activated etc. It reads the data
· The acquisition control board reads the transient recorder
from the transient recorder, sums it to previously acquired
boards data, and adds it into the accumulator memory.
spectra (if required) and then sends the data packet to the
computer via an on board buffer. The IO board has to · If it has been requested, the accumulator memory is
arbitrate with this board in order to send status to the transferred to the output buffer, where the data can be sent
computer. to the computer. (It is possible to accumulate spectra faster
then they can be sent to the computer).
Basic Sequence Of Control
· If data is being sent to the computer this happens in
· The computer sends instructions to set up the mode of
parallel with other operations on the acquisition control
operation, the pulsed extraction, the gate delay, gate pulse
board.
width and the mass range.
· The acquisition control board stops if only a single spectra
· The computer sends an instruction to start.
was required
· The laser is fired using a TTL trigger.
· Otherwise it will wait until the laser has re-changed before
· The laser light pulse is detected by the laser detect unit acquiring the next spectra.
and passed to this board.
See schematic page 200 onward.
· The received pulse is latched and passed down a
The Acqusition control card has one Voltage adjustment.
programmable delay line.
Laser detect level: TP6 - 2 V TP7 - GRD
· The output of the delay line is passed on to the transient
Adjust RV1 till read 2V at TP6. This is a start point, it
recorder board and is also used to trigger the delay to the
should be set to trigger on a clean step flank of the laser
gate pulse (if used).
detect pulse.
· On the transient recorder board the pulse is synchronised
to the sampling clock. It is then used to start the acquisition
of data and to trigger the pulsed extraction unit.
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Testprocedures for the Board Fit extender card into slot 31.
(1) Test Software Plug the DUT onto the extender card.
(2) Computer Switch on mains to the TCU.
(3) PCI interface board PCB017B Check there is 5V between TP2 and TP5.
(4) Computer interface cable C0231A If the board has not been programmed, program it now.
(5) Fully tested TCU, populated with PCBs Run the test program (testall ver3.0 or greater) on the
(6) Test Board LV LT3 PCB035A. computer.
(7) Multimeter. Go to the Acquisition Control Board Test Menu (H).
(8) Extender Card. Run the automatic tests (A).
(9) Oscilloscope. ** Pulsed Extraction Delay **
(10) BNC to BNC RG58 coax cable > 1m long. 2off. Use the laser trigger signal from the upper BNC on the
transient recorder board.
Ensure no cable other than the mains cable are attached to
the TCU. Take a length of coax to M34 on the back of the crate
(second from bottom BNC)
Ensure that the TCU is switched off at the mains.
Plug the laser detect cable SMB (RG197 cable) into the
Connect up (2),(3),(4) & (5). board (bottom SMB connector, J9)
Examine the device under test (D.U.T.). Set the laser detect threshold to 1V adjusting RV1
Check the right componets are fitted in the correct monitoring TP6 wrt GND (TP7).
orientation. Plug the scope trigger cable SMB (RG197 cable) into the
Not fitted :- R1, J4, J5, J6 , J8 top tranisent recorder board SMB connector (J7).
Check for solder bridges, dry joints and pads not soldered. Trigger the scope using a probe on TP10 (Laser Fired).
Check the resistance between TP2 & TP5. This should be Ground is TP7.
~36 ohms. Montior the TTL signal to the pulser. (TP9 or IC29 pin 6).
Check the resistence between TP3 & IC29 pin 1,2,3 & 4. Ground is TP3.
This should be 270 ohms. Scope setup : Trigger at left, Timebase 200nS/div for max
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delay, 20ns/div for min delay. J2 C22.
It is useful to set the scope to ”infinite persistance” for this Plug the scope trigger into the TCU scope tigger output on
test. the backpanel (bottom BNC, M35) and use this as a TTL
Run the Pulser Delay test (G). trigger, rising edge.
If this completes successfully, the laser detect is OK. Run the Gate Pulse Width test. (I). Check the scope trigger
can be seen on the scope.
The Delay counter has 8 bits. Each bit is set in turn. Finally
all the bits are set. ** Gate pulse Width **
The first delay (all bits zero) should be ~27nS from Laser On the other channel montior the TTL signal to the Gate.
Trigger. (TP8 or IC29 pin 7).
This is zero point for pulse delay. Scope setup : Trigger at left, Timebase 50nS/div. Run the
Gate Pulse Width test (I). The width counter has 4 bits. It
The second delay (l.s. bit set high) should also be ~32nS counts fron 0 to 15.
(+5ns).
The 1st pulse should be 20nS wide. Each successive pulse
The third delay (2nd ls bit set high) should be 37nS (+5ns). grows by 20nS, to a maximum of 300nS.
See following table...
Look at the differential PECL verion of signal at IC29 pins 1
1 2 3 4 5 6 7 8 9 10 delay number & 2.
00 01 02 04 08 10 20 40 80 ff hex value loaded Set scope offset to 3.5V. Set volts/div to 500mV. A positive
27 32 37 47 67 106 187 345 658 1280 delay from laser going 500mV pulse should be seen on pin 3.
pulse in nS. A negative going complimentary pulse should be seen on
Each succussive delay should be twice the previous pin 4.
(bearing in mind the 27nS offset). ** Gate Delay **
Look at the differential PECL verion of signal at J2 C22 & J2 Scope setup : Trigger at left, Timebase 5uS/div for max
C23. delay, 50ns/div for min delay. Run the Gate Delay test (H).
Set scope offset to -3.5V. Set volts/div to 500mV. positive The Gate Delay counter has 11 bits. Each bit is set in turn.
going 500mV pulse should be seen on pin J2 C23. Finally all the bits are set.
A negative going complimentary pulse should be seen on The first delay (0) is not valid and does not produce a pulse.
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8.6.2 Board Layout
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8.7 Main I/O Board picture of board location
8.7.1 Description
8.7.2 Board Layout
Contents Chapter
contents Service Manual Maldi Tof Pro MS 18-1160-04, Revised March 2004
8.7.1 Description picture of the board
The I/O control board is located in the TCU unit in slot 5.
The I/O control pcb contols a list of functions , and they are as
follows.
:Sample Motor
:Iris Motor
:Sample Port Motor
:Valves ( Inlet, Vent, backing )
:Turbo pump controllers
:Pirani gauge
:Magnetron gauge
:High voltage control Interface
:Covers loop
:Beam blanking control
Contents Chapter
Testprocedures for the board TP14 GRD
The I/O pcb has several test points. Lets first check and be
sure that there are no shorts between: TP1 (1V adjust)
TP14 GRD
(TP7 and TP9)
(TP14 and TP12)
(TP14 and TP13)
First we need to connect Jumpers to pin 1&2 of J5 and pin1
(TP14 and TP15)
& 2 of pin of J6.
(TP14 and TP10)
Now measure at the following Test points:
(TP16 and TP17)
TP17 24V
TP16 GRD
The following are the voltages you should see at these test
points.
Adjust TP3 for 5.6V, use RV3.
TP7 +5V (+/- 0.1V )
TP6 is the GRD. ( Magnetron set point)
TP9 Grd
Adjust TP4 for 3.8V , use RV4.
TP12 +24V (+/- 0.1V)
TP6 is the GRD. (Pirani set point)
TP14 Grd
TP15 12V (+/-0.1V) Remove Jumpers from J5& J6!!!!!!!!!

TP 14 GRD
TP13 5V (+/- 0.1V)

TP14 GRD
RN6 pin 1 20V
Contents Chapter
· Test Software. Check that there is no short between TP7 & TP9.
· Computer. Check that there is no short between TP14 & TP12.
· PCI interface board PCB017B. Check that there is no short between TP14 & TP13.
· Computer interface cable C0231A. Check that there is no short between TP14 & TP15.
· Fully tested TCU, populated with PCB’s. Check that there is no short between TP14 & TP10.
· Test Board LV LT3 PCB035A. Check that there is no short between TP16 & TP17.
· Multimeter. Switch SW2 according to the instrument type LT2/LT3.
· Extender Card. Connect PCB022A (D.U.T.) ono the extender card.
· Oscilloscope. Connect PCB035A to M8 on the backpanel of the TCU.
· 2 Jumper connectors. On PCB035A toggle SW2, SW3, SW4 & SW5 down-
· 2 off Resistor Link 2K2 with crimp ‘D’ pins. wards (over-ride)
· Sample motor rig including limit switches. Connecting ca- Ensure SW1 & SW8 are in the centre position (“OFF”)
ble. Switch on TCU at the mains.
· Iris motor rig including limit switches. Connecting Cable. Measure 5V between TP7 & TP9
· Inlet port rig including limit switches. Connecting Cable. Measure 24V between TP14 & TP12.
Measure 12V between TP14 & TP15.
Ensure no cable other than the main’s cable are at- Measure 5V between TP14 & TP13.
tached to the TCU. Measure 20V between TP14 & RN6 pin 1 (mitred cor-
Switch TCU off at mains. ner).
Connect up (2), (3), (4) & (5). Measure the voltage between TP14 & TP1. Adjust the
Fit extender card into slot 47. voltage at TP1 with RV2 to be 1V.
Examine the device under test (D.U.T.). Connect Jumpers to J5 & J6
Check the right components are fitted in the correct Measure 24V between TP16 & TP17.
orientation. Measure the voltage between TP6 & TP3. Adjust to 5.6V
Check for solder bridges, dry joints and pads not sol- using RV3.
dered. Measure the voltage between TP6 & TP4. Adjust to 3.8V
using RV4.
Carry out a “Simulated Switch on Sequence” as detailed
on a separate page of this document.
While the “Simulated Switch on Sequence” is underway,
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monitor the pulses from the stepper motor drive on J2 at the switches is correctly displayed.
C18, C19, C20 & C21. Observe a 24V square wave. Select the iris motor ensuring the selected motor status
Set the scope to 20V/div and 2ms/div. The pulses are bits readback correctly (J).
present while LED3 is on. Once the sequence is com- Move the iris motor from limit to limit checking the op-
plete the I.O. board is initialised. eration of the limit switches (M, R and K).
Ensure that the sequence completes as described. Check the switches stop the motor and that the status of
Once the I.O. board has initialised correctly, switch off the switches is correctly displayed.
the unit. Using Test Board LV LT3 PCB035A, set signal out (J7)
Plug in a tested sample motor rig into the connector to 2.8V with RV1.
marked M27 on the backpanel. Link J7 to J6 (SIG. OUT. to VACUUM SIGNAL).
Plug a tested iris motor rig into the backpanel connector Select the Magnetron ADC channel. Read back should
marked M12. be 2.8V +/-0.2V (L).
Switch on the unit again. The sample motor should start Remove the IO board from the extender and refit nor-
to move. If it does not then switch off immediately to mally into the unit.
avoid driver chip damage. Investigate before re-applying
power. I/O PCB Simulated sample Exchange Sequence
Carry out a “simulated exchange sequence” as detailed
on a separate page of this document. When the TCU is switched on, the I.O. board (P022)
Use the test software to manipulate the board. enters an “exchange sequence”.
Test the accumulator board to ensure that it is working. It drives the sample probe into the sample inlet.
Check that the I.O. Board Type is shown as “3”. In order to run the TCU without an instrument it is nec-
Perform a “Basic IO Test” to show that communication essary to simulate inputs.
with the computer is working, then use the “IO Interac- This is done with the Test Board P035A. There are
tive Menu”. switches to simulate the inputs required.
Make sure a sample exchange is not underway. During the sequence observe the LED on the test board
Select the sample motor ensuring the selected motor and the IO board.
status bits readback correctly (J). On the IO board LED3 will be on (green) when the sam-
Move the sample motor from limit to limit checking the ple motor is being driven.
operation of the limit switches (M, R and K). On the IO board LED4 will be on (red) while the ex-
Check the switches stop the motor and that the status of change sequence still underway.
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On the IO board LED5 will be on (red) when the direc-
off. (Motor changed direction & moving)
tion of the sample motor is towards the port.
LED14 will go off (inlet valve)
The following instructions refer to the Test Board P035A
LED15 will go off (backing valve)
unless otherwise stated: -
Switch SW1 to the centre (“OFF”) position.
Ensure SW1 & SW8 are in the centre position.
Switch SW1 to the down (DATUM) position.
Ensure SW2, SW3, SW4 & SW7 are in the down (over-
On the IO board LED3 & LED4 will go off.
ride) position.
Switch SW1 to the centre (“OFF”) position.
Ensure SW6 is in the up position.
Switch On TCU (or send “Exchange” message).
The following LED’s should be on - LED1, LED3, LED4,
LED5, LED8, LED9 & LED10.
The following LED’s should be off - LED6, LED7,
LED13, LED14 & LED15.
On the IO board LED3, LED4, LED5, LED8, LED6,
LED9 should be on. LED7 should be off.
Switch SW1 to the up position. (Simulate motor limit).
LED9 will go off. (Limit reached)
On the IO Board LED3 will go off. (Sample has reached
inlet port)
LED13 will go on (vent valve on).
Switch SW7 up (lid open).
LED13 will go off (vent valve closed).
Switch SW7 down (lid closed again).
LED15 will go on (backing valve)
LED14 will go on (inlet valve - sample inlet is being
pumped)
Wait for 20 seconds. This is the minimum pump down
time.
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On the IO board
Service Manual Maldi Tof Pro MS
LED3 will come on and LED5 will go
18-1160-04, Revised March 2004
schematics
8.7.2 Board Layout
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8.8 High Voltage Control Board
8.8.1 Description
8.8.2 Board Layout
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This is the description of the high voltage control PCB.

It is located in the TCU unit slot 6. Counting from left to right
it is in position six. The high voltage PCB has many functions,
which are listed below:
Source (HP20R)
Reflectron (HP20R)
(Switch off for zero volts)
Detector (HP5)
Pulser (HP5R)
Reflectron detect 2kv (HP2.5P)
Pulsed extraction unit
Gate driver
Laser power supply
Beam blanking
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Testprocedures for the board TP9-10V (+/- 50mV)
Using the test software set ” Source DAC ” to 0xFFFF
The high voltage PCB has many test points which will need to
checked and adjusted at times. You will also need to use TP14-5V (+/- 50mV)
diagnostics software to do some of the following tests. All the Using the test software set ” Reflectron DAC ” to 0x8000
following Test will use TP 15 as the ground connection.:
TP14-10V (+/- 50mV)
TP 2 -24V (+/- 50mV) Using the test software set ” Reflectron DAC ” to 0xFFFF
TP 4 -7.1V (+/- 50mV)
TP1- 1V Adjust RV1 to set Pulser Ref Check in the test software status that the Source supply
TP 5 - 8v (+/- 50mv) Adjust RV 2 to set Gate Ref Positive and the Pulser supply negative readback is asserted.
Measure the voltage at the following test point:
TP 6 -9.9V to 10.1V Adjust RV 3 to set HMD Ref
TP 7 -9.9V to 10.1V Adjust RV 4 to set Spare Ref 2 TP15 Grd & TP3 24V (+/-50mV)
TP 8 -9.9V to 10.1V Adjust RV 5 to set Dynode Ref
TP13 -9.9V to 10.1V Adjust RV 7 to set Spare Ref 1 Using the test software select ”Negative Ion” E
Check in the test software status that the ”Source supply
The following will use the test software: Negative and the pulser supply Positive ” readback is
asserted.
TP224V (+/- 50mV) Measure the voltage at the following test point:
TP175V (+/- 50mV) TP15 Grd & TP3 0V

Check the test software status that the ”High Voltage On ”
Readback is asserted.
TP182.5V (+/- 50mV)
Check the test software status, that the ”High voltage On”
Readback is asserted.
TP95v (+/- 50mV)
Using the test software set ”Source DAC ” to 0x8000
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• Test Software. Fit Resistor link on backpanel of the TCU on the connec-
• Computer. tor marked M26 between pins 2 & 3.
• PCI interface board PCB017B. Switch on TCU at the mains.
• Computer interface cable C0231A. Carry out a “simulated exchange sequence” as detailed
• Fully tested TCU, populated with PCB’s. below
• Test Board LV LT3 PCB035A. Using the test software (IO interactive) select “Linear
• Multimeter. Mode” (V).
• Extender Card. Using the test software select “Positive Ion” (E).
• 2 off Resistor Link 2K2 with crimp ‘D’ pins. Observe the Leeds on the IO board in slot 47.
• Oscilloscope. On the IO board the bottom 5 LED’s should all be on
except the lowest one.
Check the correct components are fitted in the correct No LED’s should be on the board under test.
orientation. Using the test software select “HV request” (F).
Check for solder bridges, dry joints and pads not sol- The bottom LED of the IO board should illuminate.
dered. Ensure no cable other than the main’s cable are Check in test software status that the “High Voltage On”
attached to the TCU. readback is asserted.
Switch TCU off at mains. On the D.U.T. the LED1, LED3 should be on.
Connect up (2), (3),(4) & (5). On the D.U.T. the LED2, LED4 should be off.
Fit extender card into slot 59. Use TP15 as a ground point.
Examine the device under test (DUT). Measure +24V at TP2.
Check that there is no short between TP15 & TP2. Measure +5V at TP17.
Connect PCB021A (D.U.T.) ono the extender card. Measure +2.5V at TP18.
Connect PCB035A to M8 on the backpanel of the TCU. Using the test software set “Source DAC” to 0x8000. (A)
On PCB035A toggle SW2, SW3, SW4, SW6 downwards Measure +5V at TP9.
(over-ride). Using the test software set “Source DAC” to 0xFFFF. (A)
On PCB035A toggle SW5 & SW7 upwards. Measure +10V at TP9.
Ensure SW1 & SW8 are in the centre position (“OFF”). Using the test software set “Reflectron DAC” to 0x8000.
Fit Resistor link on backpanel of the TCU on the connec- (B)
tor marked M5 between pins 2 & 3. Measure +5V at TP14.
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Using the test software set “Reflectron DAC” to 0xFFFF. LED2 should illuminate.
(B) Measure +24V at R8 pin 1 (mitred corner).
Measure +10V at TP14. Using the test software, deselect “HV request” (F)
At TP4 using RV1 set the “PULSER REF” to +7.1V Attach scope probe to TP18. Test trigger point to 2.4V.
At TP5 using RV2 set the “GATE REF” to +8.0V Using the test software, select “HV request” (F)
At TP6 using RV3 set the “HMD REF” to +10.0V (+/-0.1) View the 2.5V reference ramping up to full scale in
At TP7 using RV4 set the “SPARE REF” 2 to +10.0V(+/- around 0.5 second.
0.1) Using the test software, select “Blanking On”. (X)
At TP8 using RV5 set the “DYNODE REF” to +10.0V (+/ Using the test software, set “Blanking Time To 0x7F”. (Y)
-0.1) Attach a scope probe to J1 C13.
At TP13 using RV7 set the “SPARE REF 1” to +10.0V Trigger the scope using the “Scope Trigger” BNC output
(+/-0.1) on the back of the TCU (M35)
Check in test software status that the “Source Supply
Positive” readback is asserted.
Check in test software status that the “Pulser Supply
Negative” readback is asserted.
At TP3 measure +24V.
Using the test software select “Negative Ion” (E)
Check in test software status that the “Source Supply
Negative” readback is negated.
Check in test software status that the “Pulser Supply
Positive” readback is negated.
At TP3 measure +0V.
On the DUT the LED1, LED4 should be on.
On the DUT the LED2, LED3 should be off.
Check in test software status that the “Flight path - Lin-
ear” readback is asserted.
Using the test software select “Reflectron Mode”. (V)
Check in test software status that the “Flight path - Re-
flectron” readback is asserted.
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8.8.2 Board Layout schematics
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location of the board
8.9 Backpanel Board
8.9.1 Description
8.9.2 Board Layout
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8.9.1 Description
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8.9.3.1 Block Diagram of Backpanel Board
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8.9.3.2 Power Supply board Slot
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8.9.3.3 Transient Recorder Board Slot
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8.9.3.4 Acquisition Control Board Slot
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8.9.3.5 Spare I/O Board Slot
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8.9.3.6 I/O Board Slot
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8.9.3.7 High Voltage Control Board Slot
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8.10 Backplane Board
8.10.1 Description
8.10.2 Board Layout
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8.10.4.1 Description
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8.10.4.2 Board Layout
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8.10.4.3 Electronical
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picture of the board location
8.11 PCI Bus Interface
8.11.1 Description
8.11.2 Board Layout
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The PCI card is responsible for the communication and data

transfer between instrument and the PC.
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schematics
8.11.2 Board Layout
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8.12 24 V Power Supply (PSU) picture of the location of the board
8.12.1 Description
8.12.2 Board Layout
8.12.3 Electronic schematics
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8.12.1 Description of the board picture of the board
The 24 Volt switched power supply is responsible for linear

operation and supports the HV control board,
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8.12.3 Electronic schematics
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8.13 Gate PCB
8.13.1 Description
8.13.2 Board Layout
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The gate pcb is located in the box at the base of the reflectron
stack. To gain access to the pcb remove all the screws and
remove the cover. There are several test points and
adjustments on this pcb. To test the pcb do the following.
Find J1, this is the 10 pin molex connector. Apply 24v to pin 1,
this is the power connection.
Pin 2 - Grd
Pin 4 - Polarity
Pin 7 - Reflectron-on
Pin 9 - Gate-Ref
Pin 10 - Gate-Ref-Rtn
Measure the following voltages.
Tp1 (24V) and Tp2 (Grd) (24V +/- 50mV)
IC7 pin 3 (5V) and Tp10 (Grd) (5V +/- 50mV)
IC7 pin 6 (5V) and Tp10 (Grd) (5V +/- 50mV)
Tp3 and Tp2 (0V)
Next Apply +24V to pin4 on J1 (Reflectron-On) and measure

the following voltages.
Tp J1 pin 3 (24V +/- 50mV)
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Measure the following.
Next apply +8V to J1 pin 9 (Gate-Ref) and check voltages and
adjust if needed.
Tp11 (Low) and Tp10 (Grd) (Low < 0.7V)
Tp 4 +400v Adjust Rv3 Tp9(High) and Tp10n (Grd) (High > 2.0V)
Tp 5-400V Adjust Rv4
Tp7(-400V) and Tp J4 (Grd) (-400V)
J7 +90V Adjust Rv1
Tp6(+400V) and Tp J4 (Grd) (+400V)
J8 -90V Adjust Rv2
Now we will set the TTL input to the input driving circuit to a
Next apply +24V to J1 pin4 (Polarity) Check the following. High state (> +2.0V)
Measure the following.
Tp J7(-90V)
Tp J8(+90V) Tp11 (High) and Tp10 (Grd) (High > 2.0V)
Tp 9 (Low) and Tp 10 (Grd) (Low < 0.7V)
Next apply a signal to J2 (SMB connector). Tp7 and Tp J4 (0)
This input requires a differential PECL pulse. Tp6 and Tp J4 (0)
The input can be generated from a TTL pulse.
The chip to use is a Synergy SY100ELT22ZC TTL- PECL Now apply a positive going 40ns wide TTL pulse to the input
driver. For an example of the input driving circuit see driving circuit and observe both pulses at the same time.
schematic # P023B05.
On the schematic, see the bottom center for the Tp7 (-400V to 0 to -400V) and Tp J4 (Grd)
SY100ELT22ZC. Rising pulse to 0 then falling back
The input driving circuit and the unit under test should share
the same ground. Tp6 (+400V to 0 to +400V) and Tp J4 (Grd)
Set the TTL input to the input driving circuit to a low state Falling pulse to 0 and rising back
(<+0.7V). Use RV5 and RV6 to make the pulses start at the same point
in time.
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schematics
8.13.2 Board Layout
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8.14 Pulser Board
8.14.1 Description
8.14.2 Board Layout
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8.14.1 Description
The Pulser unit is responsible for the Pulsed extraction

function and also for the swithced polarity, to measure
positive or negative ions.
The pulse is triggered by the acquisition control board.
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Testprocedure for the board For an example of the input driving circuit see schematic
sheet P023B05.
• Multimeter. On the schematic, see bottom centre for the
• High voltage probe. SY100ELT22ZC integrated circuit.
• Oscilloscope >250Mhz bandwidth 1M ohm input im- The input driving circuit & the unit under test should
pedance. share the same ground.
• Scope probe 1.25Kv max input bandwidth >250MHz. Apply a positive going 150Us wide TTL pulse to the
100:1 input driving circuit at 8Hz.
• Input driving circuit. Using the oscilloscope between ground point at R1 pin 2
• TTL pulse generator. (No mitre on the ident) and J10 pin 2, observe a positive
• 24V power supplies. going TTL pulse 150Us wide with an amplitude > 3.5V
Switch off the TTL pulse generator.
Place the assembled PCB on mounting pillars on a Apply voltages to J9 (spade connector) as follows:
workbench. Pin 1 (HV in) -1KV
Apply the following voltages to connector J2 Use the Multimeter in conjunction with the high voltage
Pin 1 (polarity) +24V probe.
Pin 2 (ground) 0V Use J6 as a ground point.
Pin 3 (power) +24V On the spade terminals of the relays nearest to IC2
Apply the following voltages to connector J9 Test equip- (Behlke switch) measure the following: -
ment required: RLY1 and RLY2 should be 0V.
Electronic Multimeter RLY3 and RLY4 should be -1KV.
Oscilloscope > 250MHz Bandwidth On the spade terminals of the relays furthest from IC2
Pin 1 (HV in) +0V (Behkle switch) measure the following: -
Measure +5V between J10 pin 1 and 3. RLY1 and RLY4 should be -1KV.
Apply a signal to J4. RLY2 and RLY3 should be 0V.
This input requires a differential PECL pulse. Apply voltages to J9 (spade connector) as follows: -
The input can be generated from a TTL pulse. Pin 1 (HV in) 0V.
The chip to use is a Synergy SY100ELT22ZC TTL-PECL
driver.
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Apply voltages to J2 (3-way Molex connector) as fol- Pin 1 (HV in) 0V.
lows: - Apply voltages to J2 (3-way Molex connector) as fol-
Pin 1 (Polarity) 0V (negative ion). lows: -
Pin 2 (Ground) 0V. Pin 1 (Polarity) 24V (positive ion).
Pin 3 (Power) 24V. Pin 2 (Ground) 0V.
Apply voltages to J9 (spade connector) as follows: - Pin 3 (Power) 24V.
Pin 1 (HV in) +1KV. Apply voltages to J9 (spade connector) as follows: -
Use the Multimeter in conjunction with the high voltage Pin 1 (HV in) -1KV.
probe. Measure a negative going pulse with amplitude of -1KV
Use J6 as a ground point. on the scope.
On spade terminals of the relays nearest IC2 (Behkle The falling edge should be sharp, and the rising edge
switch) measure as follows: will climb slowly.
RLY1 and RLY2 should be +1KV. The pulse should remain at -1KV for 100uS.
RLY3 and RLY4 should be 0V. The falling edge should have a fall time (10% to 90%) of
On spade terminals of the relays furthest from IC2 less than 20nS.
(Behkle switch) measure as follows: -
RLY1 and RLY4 should be +1KV.
RLY2 and RLY3 should be 0V.
Apply the TTL pulse as described above.
Attach the scope probe ground to J6.
Attach the scope probe tip to the M5 ring terminal on the
wire from J5.
Measure a positive going pulse with amplitude of +1KV
on the scope.
The rising edge should be sharp, and the falling edge
will drop slowly.
The pulse should remain at +1KV for 100uS.
The rising edge should have a rise time (10% to 90%) of
less than 20nS.
Apply voltages to J9 (spade connector) as follows: -
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schematics
8.14.2 Board Layout
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8.15 Beam Dump Board picture of board location
8.15.1 Description
8.15.2 Board Layout
Contents Chapter Service Manual Maldi Pro Tof MS 18-1153-59, Revised March 2004
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The beam dump assy is located on the first shelf from the
bottom of the unit and is connected to the TOF tube by a
cable.
The beam dump has only on adjustment. Listed below is the
proper procedure for this adjustment.
You need to apply 24V between pin 1 (24V) and pin 6 (Grd) of
the 9way D connector.
The test point R1 pin 1 (mitered corner on ident) & Grd.

Value 400V Adjust Rv1.
The beam dump is used to redirect the lower mass ions that
are mainly from the matrix so the detector does not saturate.
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Testprocedures for the board
Beam blanker Board
Apply 24V between pins 1 (24V) & 6 (GND) of the 9 way D

connector
R1 pin1 (mitred corner on ident) & GND

400 Adj. RV1
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8.16 Preamplifier Board picture of board location
8.16.1 Description
8.16.2 Board Layout
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The pre amp is for the linear detector operation only. It is

located at the top the reflectron stack. There is only one
adjustment for this PCB.
To check or adjust pcb. Open cover of box and leave the pcb
assembled in the box, there is no need to remove it.
Plug in the power cable.
Plug output into a scope terminated in 50 ohms.
Ground the output.
Check the output for 0V and adjust the dc offset using RV1
and observe the level on the oscilloscope.
Then you are done.
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Use board assembled in box, with lid removed.

· Plug in power cable.
· Plug output into scope terminated in 50 ohms.
· Ground the input

Output 0 Adjust the DC offset using RV1
and observe the level on oscilloscop
• +/-5V power supply
• Power Cable based on cable C201A
• Twin Peaks generator
• Oscilloscope
• BNC terminated coaxial cable
Use board assembled in its box, with the lid removed.
Plug in the power cable.
Plug output into scope terminated in 50 ohms.
Plug “twinpeaks generator” into the amp input.
Observe the “twin peaks” signal on the scope.
Adjust the DC offset using RV1.
Observe the change of offset on the scope.
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8.17 Laser detect PCB
8.17.1 Description
8.17.2 Board Layout
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The laser detect board is located underneath the iris unit.

The detected laser signal is transferred vai a BNc cable to
the acquisition control board.
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• Laser and iris assembly with beam splitter & laser

detect box.
• 24V Power supply and cables to laser and detect box.
• Scope.
• TTL trigger for laser & scope trigger
• Means of controlling the iris aperture (Control unit,
Computer & cables).
Set iris aperture to a minimum.

Add coaxial cable between output & scope. Terminate in
560 ohms.
Apply 24V to D connector. 24V to pin 1. Ground to pin 2.
Trigger laser.
Observe a pulse on the scope. The initial edge must rise
above 2.5V.
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8.17.2 Board Layout
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8.18 Reflectron detector
8.18.1 Description
8.18.2
8.18.3
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8.18.1 Description
The N5 detector is a new faster design of the detector that

has a higher sensitivity for ions with low masses, specially
in psd mode. This has been achived by give the mcp a
perpendicular angel towards the ion beam. A spacer is
placed between the mcp to increase the gain in the
detector. The detector has also a grid fitted infront of the
mcp to give the ions a post source acceleration. The
potential between the grid and the mcps is 200 V.
The detector comes pre adjusted from the factory and
should not need any further adjustments. If it is needed, the
angel of the detector can be adjusted with two knobs on the
detector flange to achive maximum resolution and picture of the N5 detector.
sensitivity.
MCP
Distance washer
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HT 2000V
10 M MCP assy
1M
Grid
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8.19 Linear detector detector
Linear detector (ETP) and linear detector pcb.

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Linear detector pcb
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Schematic of the linear detector
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1 volt.
LOAD REGULATION: -Less than 10ppm for load changes from 100uA to
maximum. (Measured at maximum voltage).
HP Series Data Sheet OVERLOAD

current limit.
PROTECTION: -Flashover and short circuit proof. Re-entrant
TEMPERATURE CO-EFFICIENT:-25ppm/ oC or better (except HP60P &

HP1, HP2.5, HP5, HP10, HP20, HP30 & HP60 HP60N 150ppm/ oC).
PRECISION HIGH VOLTAGE MODULES DRIFT: -Typically 0.01% per hour Measured at constant input voltage, 0.02% per 8
hours load current & ambient temperature after 1 hour warm up.
1kV, 2.5kV, 5kV, 10kV, 20kV, 30kV & 60kV

CONTROL:
High Stability, Low Ripple
High frequency FET oscillator
INTERNAL potentiometer.
Internal control or externally programmable
EXTERNAL potentiometer or 10V analogue signal. (0 to +10V gives zero to
Short circuit and flashover proof maximum output, tolerance +2%). Input impedance > 100Kohm.
24 hour burn in
Low radiated magnetic field READOUT: -Voltage monitor 0 to +10V represents zero to maximum
output, tolerance +2%(Source resistance 10 kohm).
Pin Connection & Safety Instructions
CURRENT MONITOR: - Optional on all units . Note- simple current monitor
includes the internally used feedback current. Precision current monitor removes this
ELECTRICAL SPECIFICATION current to give a true reading (only available on HP10P & N, HP20P & N & HP30P & N).
RIPPLE AT FULL
UNIT TYPE POLARITY OUTPUT OPERATING TEMPERATURE: -0 oC to +50 oC
LOAD
HP1P POSITIVE 10 volts to 1kV at STORAGE TEMPERATURE: --35 oC to +85 oC
10mV peak to peak
HP1N NEGATIVE 10mA
HP2.5P POSITIVE R.F.I.:
-Steel case for low radiated magnetic field.
10 volts to 2.5kV at
10mV peak to peak
HP2.5N NEGATIVE 4mA
SYNCHRONISATION: -Oscillator frequency can be locked to a suitable external
HP5P POSITIVE frequency.
10volts to 5kV at 2mA 20mV peak to peak
HP5N NEGATIVE
MECHANICAL SPECIFICATION
HP10P POSITIVE 20 volts to 10kV at
50mV peak to peak
HP10N NEGATIVE 1mA SIZE:
HP20P POSITIVE 50 volts to 20kV at
200mV peak to peak HP1, HP2.5 & HP5 - 148 x 98 x 47mm
HP20N NEGATIVE 0.4mA HP10 - 200 x 98 x 47 mm
HP30P POSITIVE 100 volts to 30kV at HP20 & HP30 - 210 x 120 x 60 mm
300mV peak to peak HP60 - 240 x 140 x 60 mm
HP30N NEGATIVE 0.25mA
HP60P POSITIVE 200 volts to 60kV at FIXINGS:HP1P & N, HP2.5P & N, HP5P & N, HP10P & N have M4 studs. All other
10V peak to peak
HP60N NEGATIVE 0.1mA units have mounting holes.
OUTPUT: By 0.5 metre screened cable (HP20, HP30 & HP60 1 metre). N.B.
INPUT VOLTAGE: -24 volt d.c. +10% at less than 1A. Negative input terminal Reducing the cable length may increase the ripple voltage.
common to HV earth return.
INPUT CONNECTOR: Molex 10 pin, mating connector supplied.
OUTPUT VOLTAGE: -See table above.
LINE REGULATION: -Less than 10ppm of maximum voltage for input changes of Applied Kilovolts Ltd., 38-40 Eastbrook Road
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technician who is fully aware of the particular dangers associated with
SAFETY & INSTALLATION high voltage switch mode power supplies. Metallic or conductive tools
INSTRUCTIONS (December 1996) should not be used to adjust any of the potentiometers. The unit has no
user serviceable parts and should not be dismantled.
FOR HP & KS SERIES DO NOT HANDLE OR TOUCH THESE UNITS WHEN THE SUPPLY
IS CONNECTED. AFTER DISCONNECTION FROM THE SUPPLY,
PLEASE READ CAREFULLY BEFORE INSTALLING OR ALLOW 30 SECONDS BEFORE HANDLING SO THAT ALL THE
CAPACITORS CAN DISCHARGE. To ensure that the output is fully
OPERATING THIS POWER SUPPLY discharged short to ground before touching any high voltage circuit.
Care should be taken not to operate the unit outside the specified limits
given above, failure to do so may damage the unit.
COMPLIANCE WITH SAFETY STANDARDS

The unit is designed to meet Normalised European Safety Standards and
hence installation of the power supply unit into the equipment should
comply with the following requirements.
a. A PROTECTIVE EARTH must be provided for safety in accordance

with EN61010 Part 1 : 1993 : Clause 6.5.1. The case of the units should be
bonded to this protective earth.
b. The output is classed as hazardous and must therefore not be accessible

to operators. The output must be isolated from accessible circuits by
Pin 5 Control link, see diagrams Double Insulation or a protective screen as defined in EN61010-1.
Pin 1 Synchronisation (HP Series above.
only). c. The unit is intended to be installed in an electrical enclosure and should
not be accessible to the operator. Access should be restricted to authorised
Pin 6 Link to pin 5 for external
Pin 2 + 24 Volt power input. service personnel only, with use of a tool. Care should be taken to prevent
control.
access to the interior of the unit and protect against items (e.g. tools or
Pin 3 Voltage monitor. 0 to +10V wires) inadvertently entering the interior of the unit.
Pin 7 Analogue voltage input 0
represents 0 to max. output. to +10V gives 0 to max. O/P. INSTALLATION
Tol... HP Series + 2%, Input impedance
Pin 8 HP Series I monitor (if The outputs of these units are considered hazardous and should be
> 100 kohms.KS series + 3%.
fitted). KS Series + 500V tap (if installed such that they cannot become accessible. The output should be
fitted). connected such that the shortest creepage and clearance path is to a
Source resistance 10 kohms.
protective earth connection. ENSURE that a LOW IMPEDANCE
Pin 4 Control link, see diagrams Pin 9 Signal 0 volt return. connection is made to the unit chassis from the system PROTECTIVE
EARTH. The safety earth conductor must not contain any switches or
above.
Pin 10 Power 0 volt return. fuses.
Under worst case conditions the unit draws a current of 1A (HP) and 0.5A
GENERAL (KS) and any input supply cable must be of a suitable type and rating. The
unit is not fitted with a fuse and so should be operated from a limited
On receipt the unit should be carefully unpacked and inspected to ensure supply. Fuses may be fitted externally to the unit to protect unit and
that no transit damage has occurred. Provided that this inspection is interconnecting wiring etc. but these should be rated to prevent nuisance
satisfactory and reveals no evidence of damage then installation can failures. Care should be taken in the design of the interconnecting wiring
proceed. within the system to ensure that connectors with hazardous voltages
cannot be connected to accessible circuits.
If an electrical test is to be carried out prior to fitting the power supply, it
is essential that the person undertaking this work be a qualified electronics Ensure that the output is connected to the load prior to operation of the
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technician who is fully aware of the particular dangers associated with unit and that a good low impedance high voltage joint is made. Sharp
high voltage switch mode power supplies. Metallic or conductive tools points on either the high voltage or return joint should be avoided as this
should not be used to adjust any of the potentiometers. The unit has no will cause corona which will make the output appear noisy. In general a
user serviceable parts and should not be dismantled. tracking distance (creepage distance) of 25mm (1 inch), per 10kV to earth
is advised as a minimum to ensure no breakdown or corona occurs, a
DO NOT HANDLE OR TOUCH THESE UNITS WHEN THE SUPPLY much greater distance will be required under adverse conditions. Care
IS CONNECTED. AFTER DISCONNECTION FROM THE SUPPLY, must be taken not to damage the cable inner when forming the
ALLOW 30 SECONDS BEFORE HANDLING SO THAT ALL THE connections.
CAPACITORS CAN DISCHARGE. To ensure that the output is fully
discharged short to ground before touching any high voltage circuit. During arcing currents exceeding 1000 Amps will flow. It is important
that these currents return to the high voltage power supply by the shortest
Care should be taken not to operate the unit outside the specified limits possible route using the screen (shield) of the output cable. Failure to
given above, failure to do so may damage the unit. observe this will result in the control terminals of the unit seeing large
voltage spikes during arcing and radiation of electromagnetic interference.
COMPLIANCE WITH SAFETY STANDARDS
Adequate ventilation should be provided to keep the unit cool and the
The unit is designed to meet Normalised European Safety Standards and ventilation inlets should not be covered in any way. The ambient air
hence installation of the power supply unit into the equipment should temperature around the inlet must not exceed 45 C (KS), 50 C (HP). The
comply with the following requirements. unit will operate in any orientation, however it is not recommended to
operate with the side fitted with the silk-screen as the lowest face.
a. A PROTECTIVE EARTH must be provided for safety in accordance
with EN61010 Part 1 : 1993 : Clause 6.5.1. The case of the units should be OPERATING NOTES
bonded to this protective earth.
1/ HIGH VOLTAGES ARE DANGEROUS. ENSURE THE OUTPUT IS
b. The output is classed as hazardous and must therefore not be accessible FULLY DISCHARGED BY SHORTING TO GROUND BEFORE
to operators. The output must be isolated from accessible circuits by TOUCHING ANY HIGH VOLTAGE CIRCUIT.
Double Insulation or a protective screen as defined in EN61010-1.
2/ The unit is short circuit proof but care should be taken that the high
c. The unit is intended to be installed in an electrical enclosure and should voltage cannot be shorted into one of the control pin connections.
not be accessible to the operator. Access should be restricted to authorised
service personnel only, with use of a tool. Care should be taken to prevent 3/ KS SERIES ONLY. R101 sets the oscillator frequency, in the event of
access to the interior of the unit and protect against items (e.g. tools or this pot being disturbed it can be reset by adjusting for minimum input
wires) inadvertently entering the interior of the unit. current at full load and full output voltage.
INSTALLATION 4/ POWER SUPPLIES ARE DISPATCHED WITH INTERNAL

POTENTIOMETER SET TO MAXIMUM. TURN DOWN TO ZERO
The outputs of these units are considered hazardous and should be BEFORE CONNECTING TO 24 VOLT SUPPLY.
installed such that they cannot become accessible. The output should be
connected such that the shortest creepage and clearance path is to a APPLIED KILOVOLTS Ltd. 38/40 Eastbrook Rd. Po
protective earth connection. ENSURE that a LOW IMPEDANCE
connection is made to the unit chassis from the system PROTECTIVE Sussex. BN41 1PB. U.K.
EARTH. The safety earth conductor must not contain any switches or
fuses. Tel: +44 1273 439440 Fax: +44 1273 4394
Under worst case conditions the unit draws a current of 1A (HP) and 0.5A
Home | Top of Page | Datasheet HP or KS | Current Monitor | Email
(KS) and any input supply cable must be of a suitable type and rating. The
unit is not fitted with a fuse and so should be operated from a limited
supply. Fuses may be fitted externally to the unit to protect unit and
interconnecting wiring etc. but these should be rated to prevent nuisance
failures. Care should be taken in the design of the interconnecting wiring
within the system to ensure that connectors with hazardous voltages
cannot be connected to accessible circuits.
Ensure that the output is connected to the load prior to operation of the
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9.8 Edwards compound molecular pumps
Chapter 9
Appendix
Chapter Contents
9. Appendix
9.1 User manual
9.2 Instrument handbook
9.3 Site preparation guide
9.4 Edwards rotary pump
9.5 Edwards rotary pump parts list
9.6 Edwards turbo pump
9.7 Edwards turbo pump controller

Contents Chapter Service Manual Ettan Maldi Tof Pro MS 18-1153-59, Revised March 2004
contents

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Service Manual

ETTAN Maldi ToF Pro MS

Valid for: Maldi Tof Pro MS

Service Manual Code No. 18-1160-04

Copyright© 2002 Amersham Biosciences

5. Maintenance & Adjustments

8. Circuit diagram / Layout

1.1 MALDI time of flight MS

The Maldi Time of flight mass spectrometer seperates ions

The Ettan Maldi Tof is the first generation of Mass Spectrom-

The Maldi ToF incorporates a patented Harmonic field reflec-

The Harmonic field reflectron facilitates single step

1.3.2.1 Technical Specification

Mains Voltage 100 - 120 V 50/60 Hz

Sensitivity Refl. mode: 5 fmol(<1 fmol*)

at 4:1 signal to noise

Sensitivity Lin. mode: <5 fmol (<1 fmol*)

at 4:1 signal to noise

Mass accuracy: 25 ppm (int. calibr.),

100 ppm (ext. calibr.) Indicators

Ion gate resolution: 100 (m1/m2-m1) Mains

Acquisition Rate 1 GHz

and a Multi Channel Plate assembly (MCP) which is used in

1.3.4.1 List of components in vacuum system

1.3.4.2 The function of vacuum pumps and gauges

1.3.4.4 Pump down sequence

Digestion External calibration

High-pass filters Ion source

Monoisotopic molecular weight Peak area

Proteomics Run list

Separates ions in time as they travel down a flight tube. Time-

2.2 Acceptance test

2.3 Acceptance test document

2.4 Software Installation

2.1.2 Components check 2.1.6 Measure reflectron resistance and all HV

2.1.9 Conditioning 2.1.10 Calibration

2.2.2.8 Lab consumables.

2.2.3.1.3 Preparation of 50 ml BUFFER B (50 vol% ACN, AmBio Order #

2.2.3.5.6 5 pmol BSA; Slide B spot 20-24

2.2.5.1 Protein Digest PRO acquisition method

Figure 3A-E. Different laser profiles.

The amount of laser energy delivered at the sample surface is

2.2.9 Description of the auto tuning algorithm

2.2.9.1 Included parameters

The first auto tuning parameter can be found in the MALDIDEF

Figure 4. The slide subdivision parameter is defined in the slide details

2.2.9.2.1 Fast scan mode

2.2.9.2.2 Initial and refine mode

During initial mode, changes in laser and position are alter-

Figure 8. Examples of the difference in incremental changes between

Set to 30 Set Set according to

set according to 2.2.11.1

set according to 2.2.11.3

2.2.10.3.1 Auto tune set-up

Set according to Set according to Set according to

cover as much of the expected fragment ion range without

The following section describes the software methods that

2.2.12.3 Acquisition method

Slide possdition Amount on target (fmol)

2.2.13.1 Test for verification of automatic acquisition and

Assure that a current system calibration has been performed.

Standard sample preparation methods should be used. Pre-

Spectrum Amount on target (fmol) Expected value 18 25

7 100 Total run time:

RAM size:_Mb, HDD size:Gb, Bios version:__________

Printer type: _Serial number:_

Software type/version: Serial number:__________