TRACE MSPLUS

Service Manual

Revision A
Trace MS Plus™ and Xcalibur™ are trademarks of Thermo Finnigan Corporation. Microsoft® and Windows NT® are registered
trademarks of Microsoft Corporation. Pentium® is a registered trademark of Intel Corporation.

Technical information contained in this publication is for reference purposes only and is subject to change
without notice. Every effort has been made to supply complete and accurate information; however, Thermo
Finnigan Corporation assumes no responsibility and will not be liable for any errors, omissions, damage, or
loss that might result from any use of this manual or the information contained therein (even if this
information is properly followed and problems still arise).
This publication is not part of the Agreement of Sale between Thermo Finnigan Corporation and the
purchaser of a Thermo Finnigan system. In the event of any conflict between the provisions of this
document and those contained in Thermo Finnigan Corporation’s Terms and Conditions, the provisions of
the Terms and Conditions shall govern.
Reference to System Configurations and Specifications supersede all previous information and are subject
to change without notice.

Printing History: Revision A printed in 2002.

The products of Thermo Finnigan are produced under ISO 9001 accredited quality management systems.

Australia: Thermo Finnigan • P.O. Box 239 Rydalmere• Unit 20, Metro Centre • 38 – 46 South Street • Rydalmere, N.S.W. 2116 • [61] (02) 9898-9000
Austria: Spectronex GmbH • Bischoffgasse 26 • A-1120 Wein • [43] (01) 813 9993
Belgium: Thermo Finnigan BVBA • Groenenbrogerlaan 84 • B-2610 Wilrijk (Antwerpen) • [32] (03) 825 06 70
Canada: Thermo Finnigan Canada • 5716 Coopers Avenue, Unit 1 • Mississauga, Ontario • L4Z2E8 • [1] (905) 712-2258
France: Thermo Finnigan France SA • Parc Hightec Sud • 12 avenue des Tropiques • Z.A. de Courtaboeuf BP141 • F-91944 Les Ulis Cédex •
[33] (01) 69 18 88 10
Germany: Thermo Finnigan Analytische Systeme GmbH • Boschring 12 • D-63329 Egelsbach • [49] (06103) 408 0
Italy: Thermo Finnigan Italia S.p.A. • Strada Rivoltana • I-20090 Rodano (Milano) • [39] (02) 95 059 1
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Netherlands: Thermo Finnigan BV • Druivenstraat 33 • NL – 4816 KB Breda • [31] (076) 587 8722
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[86] (010) 6621 0839
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Sweden: Thermo Finnigan AB • Pyramidbacken 3 • S-141 75 Kungens Kurva (Stockholm) • [46] (08) 680 01 01
Switzerland: Spectronex AG • Rotterdam-Str 21 • Basel • CH-4002 • Switzerland • [41] (061) 331 6020
United Kingdom: Thermo Finnigan Ltd. • Paradise • Hemel Hempstead • Herts HP2 4TG • [44] (01442) 233 555
U.S.A.: Thermo Finnigan LC and LC/MS Division • 355 River Oaks Parkway • San Jose, CA 95134-1991 • [1] (408) 965-6000

Notes: The country code is enclosed in square brackets [ ]. The city code or area code is enclosed in parenthesis ( ). For countries other than the U.S.A.,
when you are dialing from within the specified country, dial the 0 of the city code. For countries other than Italy, when you are dialing from outside the country,
do not dial the 0 of the city code.

Published by Technical Publications, Thermo Finnigan, Manchester, UK.

Copyright© 2001 Thermo Finnigan Corporation, a private subsidiary of Thermo Electron Corporation. All rights reserved. Printed in the UK.
 Contents

1. Introduction ..................................................................................................................................1
Purpose..................................................................................................................................1
Audience ...............................................................................................................................1

1. Technical Support ........................................................................................................................3

2.1 The TechWeb ..............................................................................................................................4
Entering the TechWeb ..........................................................................................................4
Principle Features..................................................................................................................6
Technical Bulletins.........................................................................................................6
Spares List......................................................................................................................6
Links ..............................................................................................................................7
Products..........................................................................................................................7
General..................................................................................................................................7

2.2 Product Support ...........................................................................................................................8

1. Routine and Preventive Maintenance ........................................................................................9

3.1 Preventive Maintenance Schedule.............................................................................................10

3.2 Replacing the Rotary Pump Oil.................................................................................................11

3.3 Replacing the Foreline Trap Pellets...........................................................................................13

3.4 Refilling the Reference Vial ......................................................................................................14

3.5 Cleaning the Electronic Fan Filters ...........................................................................................16

The Rear Instrument Fan Filter ...........................................................................................16
The PC fan filter..................................................................................................................16

3.6 Maintaining the ion source(s) ....................................................................................................17

Dismantling the Source for Cleaning..................................................................................17
Cleaning the Source ............................................................................................................21
Replacing Source Components ...........................................................................................22
Source Filament............................................................................................................22
Source Heater ...............................................................................................................23
Thermocouple...............................................................................................................24
Reassembling the Source ....................................................................................................24

3.7 Checking the Electronics Set Up ...............................................................................................25

Setting the Align Voltage....................................................................................................25

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 Contents _______________________________________________________________________

3.8 Checking Performance After a PM ........................................................................................... 27

Checking the Resolution Set-Up......................................................................................... 27
Setting the Mass Position.................................................................................................... 27
Autotune & Calibrating the instrument .............................................................................. 27
Perform the Installation Specifications............................................................................... 28

1. Fault Finding and Corrective Maintenance ............................................................................29

4.1 Troubleshooting Tables............................................................................................................. 30
General System Problems................................................................................................... 30
Communication................................................................................................................... 31
Vacuum............................................................................................................................... 32
Tuning................................................................................................................................. 33
Tuning (Ctd) ....................................................................................................................... 34
Tuning (Ctd) ....................................................................................................................... 35
Tuning (Ctd) ....................................................................................................................... 36
MS Resolution .................................................................................................................... 36
Calibration .......................................................................................................................... 37
Low Sensitivity................................................................................................................... 38
Low Sensitivity (Ctd) ......................................................................................................... 39
Inlet System / Chromatography .......................................................................................... 39
Inlet System / Chromatography (Ctd)................................................................................. 40
Inlet System / Chromatography (Ctd)................................................................................. 41
Inlet System / Chromatography (Ctd)................................................................................. 42
Spectral Problems ............................................................................................................... 42
Spectral Problems (Ctd)...................................................................................................... 43
Source Problems ................................................................................................................. 44

4.2 Resolving Common Problems................................................................................................... 45

Checking the Power Supply Requirements ........................................................................ 45
Rebooting the PC................................................................................................................ 45
Running the simple diagnostic tests.................................................................................... 46
Checking the DC and Rectified RF Voltages............................................................... 46
Polarity Check.............................................................................................................. 46

4.3 Other Corrective Maintenance .................................................................................................. 47

Tracing Air Leaks ............................................................................................................... 47
Confirming an Air Leak ............................................................................................... 47
Locating the Leak......................................................................................................... 47
Column Connections.................................................................................................... 48
Supply Plumbing.......................................................................................................... 48
GC Internal Plumbing .................................................................................................. 49
Cleaning the Pre-filters .......................................................................................................49

ii _____________________________ Trace MS Service Manual _______________________

 _____________________________________________________________________ Contents

Removing the Analyzer Assembly ...............................................................................50

Removing the Pre-filters from the Assembly ...............................................................50
Cleaning of the Pre-filters ............................................................................................51
Checking for Pre-filter Short Circuits .................................................................................51
Re-assembly of the Analyzer into the Instrument ........................................................52
Checking the Set Point of a Pirani Gauge...........................................................................52

______________________ Trace MS Service Manual ______________________________ iii

Contents _______________________________________________________________________

iv ____________________________ Trace MS Service Manual _______________________

 Section 1
1. Introduction

Purpose
This manual has been written in order to offer assistance to field
service engineers (Customer Support Engineers) whilst working on the
Trace MS Plus Plus. Several aspects of the servicing of the Trace MS
Plus Plus are covered:
• Preventative (Routine) Maintenance.
• Fault Finding and Corrective Maintenance.
• PCB Tuning and Set-Up Procedures.
This manual is not exhaustive and further information can be found on
the TechWeb at http://www.thermofinnigan.co.uk/techweb. The
TechWeb is covered in more detail later in the manual.

Audience
Service Managers and Service / Installation Engineers.

This manual is not, under any circumstances to be viewed by End Users.

____________________ Trace MS Plus Service Manual ____________________________ 1

Introduction ____________________________________________________________________

2 ___________________________ Trace MS Plus Service Manual _____________________

 Section 2
1. Technical Support

Technical Support for the Trace MS Plus is available from two

sources:
Finnigan TechWeb and Finnigan Product Support.

Note: Customers should always contact their local Thermo Finnigan

office or agent for support – the majority of issues can be dealt with in
this way.

It is intended that in the future the TechWeb will be the primary source
of technical information for the Trace MS Plus. The TechWeb is the
Product Support department’s technical support web site. It can be
found at http://www.thermofinnigan.co.uk/techweb.

__________________ Trace MS Plus Plus Service Manual __________________________ 3

Technical Support
The TechWeb ___________________________________________________________________

2.1 The TechWeb

The web site is user name registered and password protected since it
contains technically and commercially sensitive information.
To be registered for the TechWeb please email
product.support@thermofinnigan.ms.
Applicants should apply with the following information:
The Name of the Company you work for.
Which region you work in.
Your email address.
Your username and password will then be emailed back to you.

Note: The TechWeb is for authorized personnel only. It is not to be

used by customers or unauthorized people. Authorization can only be
given by the Thermo Finnigan Product Support Department. Misuse of the
web site or the information contained on in will lead to the individual being
removed from the User List.

Entering the TechWeb

Upon entering the TechWeb address into your browser, you will be
presented with the following log in dialogue box:

4 ___________________________ Trace MS Plus Service Manual _____________________

 Technical Support
__________________________________________________________________ The TechWeb

After logging in you will be displayed the following page:

____________________ Trace MS Plus Service Manual ____________________________ 5

Technical Support
The TechWeb ___________________________________________________________________

After entering your name you will be taken to the Home Page.

Principle Features
The TechWeb is constantly being updated and improved and the latest
information can be found here in Technical Bulletins.

Technical Bulletins

Here you will be able to find the latest technical information released
from the factory. They will often give good hints and clues to setting
up systems and software that may not be included in the manuals.

Spares List

Features an interactive guide to finding parts for all of the Thermo

Finnigan product range.

6 ___________________________ Trace MS Plus Service Manual _____________________

 Technical Support
__________________________________________________________________ The TechWeb

Links

These link to O.E.M. suppliers used on some of the product range.

Products

Under products you will be able to navigate to instrument specific

documentation including manuals and schematics.

General
The TechWeb is constantly being updated but if you have any queries,
comments or spot any errors then please contact
product.support@thermofinnigan.ms.

____________________ Trace MS Plus Service Manual ____________________________ 7

Technical Support
Product Support _________________________________________________________________

2.2 Product Support

If you have not been able to find the information you require on the
TechWeb, then the next course of action is to contact the Product
Support Department for some direct help. Contacts for Product
Support can be found on the TechWeb, or alternatively send an email
to product.support@thermofinnigan.ms.

8 ___________________________ Trace MS Plus Service Manual _____________________

 Section 3
1. Routine and Preventive Maintenance

The Trace MS Plus has been designed to be a low maintenance instrument,

which apart from fairly light periodic PM (Preventive Maintenance) requires
simple source cleaning and inspection purely on a “loss of performance”
basis.

Note: Check that the instrument is operational prior to starting any

preventative maintenance. Make a note of any minor anomalies and point
them out to the customer. More serious faults should be rectified before
commencing.

WARNING: Check with the customer whether the instrument has been
exposed to any radioactive, toxic, or biohazardous materials. Suitable
precautions and/or decontamination may be necessary before the
preventative maintenance can begin.

WARNING: Many solvents and oils are hazardous. Ensure that

appropriate precautions are taken when handling such materials.

____________________ Trace MS Plus Service Manual ____________________________ 9

Routine and Preventive Maintenance
Preventive Maintenance Schedule ___________________________________________________

3.1 Preventive Maintenance Schedule

During a Half Yearly PM visit the following actions should be performed:
• Drain and replace the rotary pump oil
• Replace the foreline trap pellets
• Refill the reference vial
• Clean the rear panel filter
• Clean the PC fan filter
• Maintaining the ion source(s)
• Checking the RF Generator Set Up
• Checking the instrument performance after a PM
These topics are covered in more detail below.

10 _________________________ Trace MS Plus Service Manual _____________________

 Routine and Preventive Maintenance
_____________________________________________________ Replacing the Rotary Pump Oil

3.2 Replacing the Rotary Pump Oil

Note: For more information on operating the rotary pump, refer to the
Rotary Pump User Manual, supplied with the TRACE MS PLUS system.

The rotary pump oil should be replaced at least once every six months. At
the same time as you replace the oil, you should also consider replacing the
foreline trap pellets; see Replacing the Foreline Trap pellets later in this
Section.

WARNING: Always wear gloves when changing the oil. Avoid contact
with the oil because it may contain dissolved residue from analyzed
samples. Observe appropriate disposal requirements when discarding the
old oil.

To replace the rotary pump oil, you will require E2 M1.5 Rotary Pump Oil
(P/N FM101067 (4ltr) or 5660010 (1ltr)). Follow the procedure described
below.

Foreline trap

Vent
Oil filler plug

Drain plug
Viewing window

1. Right-click on the TRACE MS PLUS Server icon in the Windows

task-bar.
The server menu is displayed.
2. Choose the Vent menu option to vent the system.

____________________ Trace MS Plus Service Manual ___________________________ 11

Routine and Preventive Maintenance
Replacing the Rotary Pump Oil _____________________________________________________

3. Place a container under the drain plug on the rotary pump.

4. Remove the filler plug from the top of the pump.
5. Remove the drain plug to release the oil.
6. Turn on the pump for 2 or 3 seconds using the TRACE MS PLUS
Server Pump menu option and turn it off using the Vent menu option.
7. The remains of the old oil are displaced from the internal pump
cavity.

Caution: Do not allow the pump to run for more than a few seconds
without oil.

8. Reinsert the drain plug and fill the pump reservoir up to, but not
above, the upper mark.
9. Reinsert the filler plug.
10. Gas ballast the new oil in the pump; for details, refer to the Rotary
Pump User Manual.
11. Right-click on the TRACE MS PLUS Server icon in the Windows
task-bar and choose the Pump menu option to pump-down the system.

12 _________________________ Trace MS Plus Service Manual _____________________

 Routine and Preventive Maintenance
_________________________________________________ Replacing the Foreline Trap Pellets

3.3 Replacing the Foreline Trap Pellets

Note: For more information on operating the rotary pump, refer to the
Rotary Pump User Manual, supplied with the TRACE MS PLUS system.

Absorbent pellets in the foreline trap help maintain the TRACE MS PLUS’s
high vacuum.
The rotary pump oil should be replaced at least once every six months. At
the same time as you replace the oil you should also consider replacing the
foreline trap pellets.

WARNING: Always wear gloves when handling the pellets. Avoid

contact with the pellets because they may contain dissolved residue from
analyzed samples. Observe appropriate disposal requirements when
discarding the old pellets.

To replace the foreline trap pellets, you will require Absorbent Pellets.
Follow the procedure described below.
1. Loosen the foreline trap end cap by a 1/4 turn.
2. Right-click on the TRACE MS PLUS Server icon in the Windows
task-bar.
The server menu is displayed.
3. Choose the Vent menu option to vent the system.
4. Remove the end cap from the foreline trap to gain access to the
inner baskets of pellets.
5. Open a new can of pellets. Bake them in the GC oven for 2 hours at
250 ºC. Allow the pellets to cool and then place them in the foreline trap
basket.
6. Reassemble the foreline trap.
7. Right-click on the TRACE MS PLUS Server icon in the Windows
task-bar and choose the Pump menu option to pump-down the system.

____________________ Trace MS Plus Service Manual ___________________________ 13

Routine and Preventive Maintenance
Refilling the Reference Vial ________________________________________________________

3.4 Refilling the Reference Vial

The reference vial contains a volatile compound, typically PFTBA, that is
used during the tuning and calibration of the instrument in EI mode.
The instrument was tested before being shipped from the factory and the
reference vial filled with approximately 400µl PFTBA. Under normal
circumstances, this should last approximately 6 months.
To refill the reference vial, you will require approximately 400µl of
reference compound.

Reference vial
Cajon union

Follow the procedure described below.

1. Right-click on the TRACE MS PLUS Server icon in the Windows
task-bar.
The server menu is displayed.
2. Choose the Vent menu option to vent the system.
3. Close down Xcalibur.
4. Switch off the TRACE MS PLUS, by means of its circuit breaker,
and allow at least half an hour for the system to cool.
5. Undo the transit bolt at the back of the digital electronics unit and
lower the unit carefully until it rests on the bench.

14 _________________________ Trace MS Plus Service Manual _____________________

 Routine and Preventive Maintenance
________________________________________________________ Refilling the Reference Vial

WARNING: Risk of burns. Solenoid gas valves reach high temperatures

in operation.

6. Unscrew the knurled nut (Cajon union) attached to the tube of the
reference vial.
7. Remove the vial from the instrument.
8. Top up the vial, using approximately 400µl (but no more than
0.5ml) of reference compound.

WARNING: PTFBA, a tertiary amine, is a corrosive compound. Do not

let it come into contact with either your skin or the instrument.

9. Replace the vial in the instrument and refit it to the union.

10. Tighten the knurled nut to finger tightness.
11. Close the instrument and replace the transit bolt at the back of the
digital electronics unit.
12. Switch on the TRACE MS PLUS’s power and restart Xcalibur.
13. Right-click on the TRACE MS PLUS Server icon in the Windows
task-bar.
The server menu is displayed.
14. Choose the Pump option to pump-down the TRACE MS PLUS.
15. Open the Per Method Parameters table on the Tune Page
16. Turn on the Pump Reference Gas button to remove any air.
17. After about 5 seconds, turn off the Pump Reference Gas option
to stop the pumping.
18. Caution. Do NOT leave the Pump Gas option switched on.
19. Test the operation of the reference inlet by observing the Tune page
as you switch the reference gas on and then off again. The peaks should rise
normally as the gas is switched on and then fade away when it is switched
off.

____________________ Trace MS Plus Service Manual ___________________________ 15

Routine and Preventive Maintenance
Cleaning the Electronic Fan Filters___________________________________________________

3.5 Cleaning the Electronic Fan Filters

The Rear Instrument Fan Filter

The rear panel fan filter removes dust from the air used to cool the TRACE
MS PLUS’s electronics. The filter consists of a gauze, held in place by a
plastic cover. It is the gauze that acts as the filter, trapping dust that would
otherwise be drawn into the electronics.
1. Remove the plastic cover from the back of the TRACE MS PLUS.
The cover is held in place by friction, and should come free easily with a
gentle pull.
2. Take the filter out of the room where the TRACE MS PLUS is
situated.
3. Clean the gauze by removing it and tapping it against a hard surface.
The filter is quite robust and will not be damaged.
4. Remove any persistent dust with a vacuum cleaner.
5. Replace the gauze and cover.

The PC fan filter

Refer to the PC manufacturer’s guide.

16 _________________________ Trace MS Plus Service Manual _____________________

 Routine and Preventive Maintenance
______________________________________________________ Maintaining the ion source(s)

3.6 Maintaining the ion source(s)

The ion source(s) should be cleaned as part of a Preventive Maintenance
visit but it is often necessary to clean the source as part of an unscheduled
visit.

Dismantling the Source for Cleaning

This section describes how to dismantle the source for cleaning. Some of the
steps are also required when you replace source components.
The Source Animations, which can be found in the Media Kit supplied with
the instrument and also on the Trace MS Plus Engineer’s CD, provide good
guidance to dismantling the source and should be used to supplement the
information that follows.

Caution: To guard against unwanted contamination from finger grease,

you are recommended to wear clean, lint-free gloves during all procedures
involving handling of the source.

1. Remove the source from the instrument.

2. Remove the wires connecting the source by disconnecting the
pushpins.
3. Remove the source body from the rest of the assembly by removing
the push-on circlips and lifting the body off the base.

Source body removed from the rest of the assembly

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Routine and Preventive Maintenance
Maintaining the ion source(s) _______________________________________________________

4. Remove the four hex nuts and remove the mounting plate.
In CI and combined sources, the source block comes away with the
mounting plate.

Mounting plate removed from body (EI source)

Mounting plate removed from body (CI and combined sources)

5. Slide the magnet assemblies off, noting which is top and bottom.
The filament is always adjacent to the North Pole.

Magnet assemblies removed

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 Routine and Preventive Maintenance
______________________________________________________ Maintaining the ion source(s)

6. Remove the filament and the trap by removing the fixing screws.

Removal of filament and trap

Caution: Handle the filament with particular care and store it safely.

7. For EI sources, remove the source block on the ion exit plate and
then remove the exit plate from the block.

Exit plate removed from source block

8. Undo the two remaining screws to separate the ion block from the
heater block.

Separating the ion block from the heater block

____________________ Trace MS Plus Service Manual ___________________________ 19

Routine and Preventive Maintenance
Maintaining the ion source(s) _______________________________________________________

9. Undo the fixing screw and remove the thermocouple.

Removed thermocouple

Caution: Take care not to bend the arms of the thermocouple.

10. Undo the nut and remove the repeller assembly.

Removed repeller assembly

11. Loosen and remove the reference inlet tube and, for CI and
combined sources, the reagent gas inlet tube.

Removing gas inlet tube

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 Routine and Preventive Maintenance
______________________________________________________ Maintaining the ion source(s)

12. Dismantle the ion lens assembly, noting the relative lens positions
and taking care not to damage the ceramics or spacers.

Dismantled lens assembly

13. The ion block, plates and spacers can now be cleaned, by following
the procedure described in the following section.

Caution: You are advised NOT to remove the source heater elements for
routine cleaning, because the constant bending of its legs will eventually
lead to fractures. For this reason, ultrasonic cleaning of the repeller block is
not recommended.

Cleaning the Source

Only those source components that are exposed to the sample or to the ion
beam require regular cleaning. These are the:
• Ion block
• Repeller assembly
• Ion lenses
• Analyzer entry plate
Other parts, exterior to the ion source, do not require regular cleaning.

Caution: The filament should never be cleaned. Ultrasonic cleaning of the

repeller block is not recommended.

All metal source components, excepting the repeller block containing the
heater element, can be cleaned as described below.

____________________ Trace MS Plus Service Manual ___________________________ 21

Routine and Preventive Maintenance
Maintaining the ion source(s) _______________________________________________________

If a component is visibly dirty or burnt, an abrasive cleaner can be used.

Suitable abrasives include 6000 grade Micromesh (5010009) and 1200
Micromesh (5010010) or aluminum oxide paste.
Rinse the component in clean water.
Clean using an ultrasonic bath and a beaker of methanol.
Rinse in a degreasing agent, such as 1,1,1-trichloroethane.

WARNING: When using solvents, all precautions for their safe use and
disposal, detailed in the appropriate National Health and Safety regulations,
should be followed.

Place the cleaned component in a clean beaker and dry in a GC oven at

100 ºC for 30 minutes.
The trap should not need regular cleaning, but when necessary it should be
removed by disconnecting only the trap wire and removing the holding
screw. Clean as above; that is, abrasively where burnt and ultrasonically. On
refitting the trap, it is aligned automatically if the mounting plate is already
fitted.
The repeller block containing the heater element should be cleaned inside,
using an abrasive, and then rinsed in methanol.

Replacing Source Components

The following pages describe how to replace source components, including:
• Filament
• Source heater
• Thermocouple
• Filament

Caution: Never try to clean the filament: this may cause damage to it.

Source Filament
Follow steps 1 to 3 of the procedure for dismantling the source for cleaning.
Remove the filament fixing screw and take out the old filament. Carefully
fit the replacement filament and refit the fixing screw. The new filament
self-aligns.

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 Routine and Preventive Maintenance
______________________________________________________ Maintaining the ion source(s)

Removed filament

Source Heater
To replace a source heater:
Follow steps 1 to 10 of the procedure for dismantling the source for
cleaning.
Slacken off the two grub screws holding the heater element (only one on CI
and combined sources), and then carefully bend down one leg and retract the
used element.

Heater with grub screws loosened to allow removal of element

Caution: Always allow the heater to cool before disassembly.

Fit a new heater element into the block and carefully bend the leg back up
into place.
Tighten the grub screw(s) until the element is held firmly in place. Do not
over-tighten.

____________________ Trace MS Plus Service Manual ___________________________ 23

Routine and Preventive Maintenance
Maintaining the ion source(s) _______________________________________________________

Thermocouple
To replace a source thermocouple:
Follow steps 1 to 3 of the procedure for dismantling the source for cleaning.
Remove the thermocouple fixing screw and then take out the old
thermocouple.
Carefully fit the replacement filament and refit the fixing screw.

Removing the thermocouple

Note: Only use K0 type thermocouples supplied by Thermo Finnigan. The

connections are keyed by having one male and one female connector.

Reassembling the Source

Reassemble the source following the reverse of the procedure described
earlier for disassembling it.

Caution: Do not over-tighten nuts and screws because this can damage the
ceramic spacers.

24 _________________________ Trace MS Plus Service Manual _____________________

 Routine and Preventive Maintenance
____________________________________________________Checking the Electronics Set Up

3.7 Checking the Electronics Set Up

After all the Maintenance tasks have been completed, the Align Voltage on
the RF Generator should be reset and the Deglitch should be checked.

Setting the Align Voltage

Note: It is necessary to check that the Align Voltage is at maximum after

removing or replacing of any analyzer components. This includes such
operations as cleaning pre-filters or quadrupole removal.

To set the Align Voltage:

1. Undo the transit bolt at the back of the digital electronics unit and
lower the unit carefully until it rests on the bench.

R.F. generator
adjustable
capacitors
R.F. test
points and
adjustment

2. Remove the protection plate on the Analogue unit of the Trace MS

Plus.
3. Place a Voltmeter across test point J13 and J9, visible through the
uncovered area.
4. Set the run/align switch to align.
5. With the DVM set to measure DC Volts, switch the instrument into
Operate using the Tune Page.
6. Adjust the two variable capacitors on the R.F. generator and check
to see if the initial Max RF value can be improved. The capacitors must be
adjusted in a balanced way e.g. if you vary the top cap 1 turn the bottom
capacitor must be varied 1 turn in the same direction. The voltage achieved
should be greater than 3.5V and is typically over 4V.
7. Set the switch back to “run”, and replace the protection plate.

____________________ Trace MS Plus Service Manual ___________________________ 25

Routine and Preventive Maintenance
Checking the Electronics Set Up ____________________________________________________

8. Replace the digital unit and locking screw.

Caution: The Glass capacitors on the RF Generator are very fragile and
will break if over-adjusted.

26 _________________________ Trace MS Plus Service Manual _____________________

 Routine and Preventive Maintenance
__________________________________________________ Checking Performance After a PM

3.8 Checking Performance After a PM

Checking the Resolution Set-Up

Once the instrument is ready to operate again, the resolution of the beam
should be checked and adjusted if necessary.

Note: If you have had to adjust the Align voltage, it is likely that the resolution
will have been altered

1 Obtain a beam on the Tune page using the reference.

2 Check that the tuning parameters are set to the normal values (especially
LM / HM Res sliders set to 12.5).

3 Set each tune window so that the bases of the main isotope of each peak
can be seen.

4 The base of the main isotope of each peak should be 1 amu wide.

5 If this is not the case, then remove the protection plate on the Analogue
unit.

6 Using the resolution trimpots, Low Mass Res (R69), Linearity (R76 –
usually fully acw) and Resolution (R68) set the resolution.

Setting the Mass Position

For each window, after the resolution has been set, check the mass position
of the peaks.
1 Set the span of each window to 1.

2 Adjust the Mass Scale trimpot (R52) until each of the peaks is in the
center of the window.

Autotune & Calibrating the instrument

Run a full Autotune and Calibration as per the instructions in the Trace MS
Plus Getting Started Manual.

____________________ Trace MS Plus Service Manual ___________________________ 27

Routine and Preventive Maintenance
Checking Performance After a PM ___________________________________________________

Perform the Installation Specifications

After a PM the operation of the instrument should be checked. Some End
Users may insist that the instrument achieves a minimum specification.
The most reliable way to check that an instrument is operating as it should is
to perform the installation specifications. These can be found in the Trace
MS Plus Installation Guide. If the instrument has a combined EI/CI
source or separate EI and CI sources then this is a good way to check that
the sources are functioning correctly.

Note: It is better for a Service Engineer to leave site knowing that an

instrument is operating correctly rather than have to return to site the
following day with the End User suffering unnecessary down time.

28 _________________________ Trace MS Plus Service Manual _____________________

 Section 4
1. Fault Finding and Corrective
Maintenance

This Section is intended to help diagnose and offer rectification help to

some of the more common faults that occur on Trace MS Plus systems.
If you encounter a problem that is not covered here, or the suggested remedy
is not successful in rectifying the problem then help should be canvassed
from the Product Support Department at Thermo Finnigan Manchester.
Details of how to contact Product Support can be found in Section 1 of this
manual and also on the TechWeb at www.thermofinnigan.co.uk/techweb.
This Section is divided into the following areas:
• Troubleshooting Tables
These tables can help to rectify the precise nature of a problem and suitable
action to take
• Resolving common problems
Help with rectifying some of the most common problems
• Other Corrective Maintenance
Guidance for useful corrective actions suggested in the Troubleshooting
Tables
• GC Troubleshooting
Help with resolving problems that may occur due to the GC.

____________________ Trace MS Plus Service Manual ___________________________ 29

Fault Finding and Corrective Maintenance
Troubleshooting Tables ___________________________________________________________

4.1 Troubleshooting Tables

For ease of use, the Troubleshooting Tables have been split into the
following topics:
• General System Problems
• Communication
• Vacuum
• Tuning
• MS Resolution
• Calibration
• Low Sensitivity
• Inlet System / Chromatography
• Spectral Problems
• Source Problems

General System Problems

Symptom
System fails to power up
Rear panel fans fail to operate
Probable Cause
System not plugged in at the
mains
Mains supply problems
Fan filter is blocked
Fan is broken
Fan power supply is failing
Remedy
Plug in and switch on
Check that the mains supply is
comparable to that specified in
the Trace MS Plus Pre-
installation Requirements
Guide
Clean the fan filter as described
in Section 3.5 of this manual
Contact local Thermo Finnigan
office for a replacement
Check that the 24V required to
run the fan is working

30 _________________________ Trace MS Plus Service Manual _____________________


__________________________________________________________Troubleshooting Tables
Communication
Symptom
No communication with the
other equipment
The instrument fails to begin
scanning and Xcalibur displays
the message ‘Waiting for contact
closure’
Xcalibur crashes at the start of a
run
____________________ Trace MS Plus Service Manual ___________________________ 31
Fault Finding and Corrective Maintenance
Probable Cause
Loose or incorrectly inserted
cable
PC System crash
Unsupported communications
Incorrect firmware version
A transient break or fluctuations
in the mains power supply has
halted Xcalibur
A malfunction has occurred in
the Trace MS Plus electronic.
A malfunction has occurred in
the GC electronics
The contact closure cable is
incorrectly fitted
The wrong instrument is selected
as the start instrument in the
instrument method file
Xcalibur has become corrupted
or the raw data file is corrupted
Loose RS 232 cable connection
Remedy
Check all the cables between the
Trace MS Plus and the other
peripheral systems are connected
correctly and in the right place.
For more information see the
Trace MS Plus Getting
Connected Guide.
Reboot the PC
Use the contact closure to start
the Trace MS Plus
Check that the firmware on the
peripheral devices is latest issue
– you may need to contact the
supplier of the equipment for
more details
Reboot the PC
Exit Tune or Xcalibur and reset
the instrument’s hardware, using
the switch on the rear of the
instrument.
Try cycling the power to the GC.
If this is unsuccessful then
contact the local Thermo
Finnigan office
Check that the cable connected
properly. Replace if necessary
Check that the start instrument
selected is appropriate for the
equipment you are running with
Delete the raw data file and
reboot the PC. Reload the
software if necessary
Consult your PC hardware
manual and check the connection
Fault Finding and Corrective Maintenance
Troubleshooting Tables ___________________________________________________________

Vacuum
Symptom
Rotary Pump fails to turn on
Turbomolecular pump fails to
turn on
Pumps switch on but instrument
fails to reach “Vac OK” status
Probable Cause
Pump not plugged in
Pump breaker activated
Communications failure
Turbo pump controller cable
disconnected
Air leaking into system
Foreline Trap pellets need
replacing – possibly damp
Rotary pump oil needs replacing
Rotary pump gas ballast open
The rotary pump oil level is low
GC Column is broken or is
leaking at the interface
Faulty Pirani Gauge
Column flow rate is too high
CI gas valve is open or the gas
line is leaking
Remedy
Connect power lead to rear of
instrument
Ensure that green breaker on rear
of instrument is depressed
See later in this Section
Reconnect cable
Check all O-rings, especially on
any parts recently removed
Remove source and refit
Check interface from GC to
source – tighten if necessary
See later in this Section
Refer to Section 3.3 of this
manual
Refer to Section 3.2 of this
manual
Close gas ballast
Check the oil level on the rotary
pump. Add oil if necessary –
refer to Section 3.2 of this
manual
Check the GC column has been
installed properly
Check the ferrules on the GC
interface
Check the Pirani Gauge Set Point
– refer to Section 4.3 of this
manual
Reduce the flow rate
Check the valve and gas line

32 _________________________ Trace MS Plus Service Manual _____________________


__________________________________________________________Troubleshooting Tables
Tuning
Symptom
Low or no signal
No peaks (or very low intensity
peaks) although the source
readbacks are correct
____________________ Trace MS Plus Service Manual ___________________________ 33
Fault Finding and Corrective Maintenance
Probable Cause
Reference vial empty or nearly
empty
Faulty reference solenoid valve
Voltage not being supplied to a
component
Air leak on system
Reference gas pipes are blocked
or missing
There are problems with the
quadrupole or pre-filters
Source lenses poorly aligned
Air is leaking into the system
Detector voltage too low
The source is dirty
The pre-filters are dirty
Remedy
Refill Reference vial – refer to
Section 3.4 of this manual
Check that the solenoid
energizes when the button is
activated in the software. A
“click” can be heard
If there is no “click” then reboot
the software and try again. If it
still fails, replace the solenoid
Check the readbacks in the Per
Method Parameters table.
Ensure that each value is close to
its Set Point
Refer to Section 4.3 for
information on eliminating air
leaks
Check and clean the source –
refer to Section 3.6 of this
manual
Check the RF Generator Set-Up
– refer to Section 3.7 of this
manual
Disassemble the source, as
described in Section 3.6, and
check the lens alignment with the
tool
Refer to Section 4.3 for
information on eliminating air
leaks
Increase the voltage on he Tune
page
Clean the source – refer to
Section 3.6 of this manual
Clean the pre-filters – refer to
Section 4.3 for more information
Fault Finding and Corrective Maintenance
Troubleshooting Tables ___________________________________________________________

Tuning (Ctd)
Symptom
No peaks (or very low intensity
peaks) although the source
readbacks are correct
High mass peaks (502 and 614
m/z) are missing
Tune peaks show signs of
breaking up
Changing a tuning parameter has
no effect on the peaks or there is
a delay before peaks are changed
Probable Cause
Faulty detector supply
Pre-filters are short-circuiting
Bad connection in the ion source
Pre-filters are short-circuiting
Malfunction in system
electronics
Source plates not connected or
short-circuited
Pre-filters are short-circuiting
Remedy
Check that the voltage displayed
on the tune page agrees with the
voltage measured coming from
the supply (Note: Use a High
Voltage probe to measure this)
Refer to Section 4.3 for
information on pre-filters
Disassemble and re-assemble the
source – refer to Section 3.6 of
this manual
Refer to Section 4.3 for
information on pre-filters
Contact Product Support for help
Check the readbacks in the Per
Method Parameters table.
Ensure that each value is close to
its Set Point
Refer to Section 4.3 for
information on pre-filters

Malfunction in system Contact Product Support for help

electronics

Peaks have an irregular shape
The source is dirty
Old or faulty filament
Poor tuning
Source lenses poorly aligned
Clean the source – refer to
Section 3.6 of this manual
Replace the source filament –
refer to Section 3.6 of this
manual
Check the End User’s Tuning –
refer to Trace MS Plus Getting
Started Guide
Disassemble the source, as
described in Section 3.6, and
check the lens alignment with the
tool provided

34 _________________________ Trace MS Plus Service Manual _____________________


__________________________________________________________Troubleshooting Tables
Tuning (Ctd)
Symptom
Large peaks observed at 18, 28
and/or 32 m/z
High mass peaks (502 and 614
m/z) are missing
Tune peaks show signs of
breaking up
Excessive ion energy voltage or
ion repeller voltage is required
Unusual Emission, Filament or
Source current readbacks shown
on Tune View
Autotune fails even though
manual tune has delivered an
acceptable beam
____________________ Trace MS Plus Service Manual ___________________________ 35
Fault Finding and Corrective Maintenance
Probable Cause
Air is leaking into the system
GC carrier gas bottle is nearly
empty
The system is still moist
following a change of column or
source
Pre-filters are short-circuiting
Bad connection in the ion source
Pre-filters are short-circuiting
Malfunction in system
electronics
The source is dirty (ion repeller
voltage >6.0 V)
Pre-filters are dirty (ion energy
voltage >3.0 V)
Poor tuning
The source magnets are inserted
incorrectly
Electrical problem within the
source
Poorly tuned resolution pots
Remedy
Refer to Section 4.3 for
information on eliminating air
leaks
Replace the gas bottle
Leave the system in vacuum for
a little longer
Refer to Section 4.3 for
information on pre-filters
Disassemble and re-assemble the
source – refer to Section 3.6 of
this manual
Refer to Section 4.3 for
information on pre-filters
Contact Product Support for help
Clean the source – refer to
Section 3.6 of this manual
Clean the pre-filters – refer to
Section 4.3 for more information
Check the End User’s Tuning –
refer to Trace MS Plus Getting
Started Guide
Check the alignment of the
magnets: one should have the
"N" pole visible; the other, the
"S" pole. See Section 3.6 for
details of how to disassemble
and re-assemble the source
Disassemble and re-assemble the
source – refer to Section 3.6 of
this manual
Refer to Section 3.8 of this
manual
Fault Finding and Corrective Maintenance
Troubleshooting Tables ___________________________________________________________

Tuning (Ctd)
Symptom
The ratio of Source current to
Emission current shown on the
Tune View is greater than 10:1
The ratio of Source current to
Emission current shown on the
Tune View is greater than 10:1
Peaks are shifted from their
nominal position
Probable Cause
The source is dirty
The source filament has
deteriorated
Air is leaking into the system
The source filament is poorly
aligned
The trap is dirty or has a poor
connection
The source magnets are inserted
incorrectly
Poor calibration
Malfunction in system
electronics
Remedy
Clean the source – refer to
Section 3.6 of this manual
Replace the source filament.
Refer to Section 3 for details
Refer to Section 4.3 for
information on eliminating air
leaks
Disassemble and re-assemble the
source. Refer to Section 3.6 for
details
Clean or replace the trap. Refer
to Section 3.6 for details
Check the alignment of the
magnets: one should have the
"N" pole visible; the other, the
"S" pole. See Section 3.6 for
details of how to disassemble
and re-assemble the source
See TRACE MS PLUS Getting
Started for details of how to
calibrate the system
Refer to Section 3.7 & 3.8 of
this manual

MS Resolution
Symptom
Unresolved peaks at LM/HM
Res at 12.5 and Ion Energy at 1.0
Poor resolution and low
sensitivity – Ion Energy needs to
be >1.5 to get ions
Probable Cause
Resolution Pots need adjusting
DC voltages on quadrupole not
being applied
Dirty pre-filter or quadrupole
Remedy
Set up resolution pots. Refer to
Section 3.8 of this manual
Run diagnostic as per later in this
section. If the check fails then
contact the local Thermo
Finnigan office
Clean pre-filters. If replacement
quadrupole is required then
contact local Thermo Finnigan
office

36 _________________________ Trace MS Plus Service Manual _____________________


__________________________________________________________Troubleshooting Tables
Calibration
Symptom
The instrument will not calibrate
Masses are drifting
Masses are drifting
____________________ Trace MS Plus Service Manual ___________________________ 37
Fault Finding and Corrective Maintenance
Probable Cause
Poor tuning
Low sensitivity
The first peak (lowest mass) in
the acquired spectrum is too
weak
Using the incorrect reference file
Poor resolution
Source temperature is too high or
too low
Air is leaking into the system
Electron energy not at 70 eV
The quadrupole is dirty
Excessive room temperature
fluctuations
High fields
Remedy
Check the End User’s Tuning –
refer to Trace MS Plus Getting
Started Guide
Refer to Low sensitivity earlier
in this section
Alter the calibration range to
start with a strong first peak
Check that the reference file
being used is related to the
calibrant. In most cases this will
be Heptacosa.
Check that the reference file has
not been altered or corrupted and
that the correct masses are in the
file. Reload the software if
necessary
Check the LM/HM Res and Ion
Energy settings on the Tune page
Adjust the source temperature on
the TRACE MS PLUS Per
Method Parameters
Refer to Section 4.3 for
information on eliminating air
leaks
Reset value on the TRACE MS
PLUS Per Method Parameters
Increase the source temperature
to 300°C and leave at that
temperature for 2 hours
Check the room temperature.
Check the operation of the fan at
the rear of the instrument – refer
to Section 3.5 of this manual
Check for other instruments
emitting high fields in close
proximity. Change the
instrument location if necessary
Fault Finding and Corrective Maintenance
Troubleshooting Tables ___________________________________________________________

Note: In the event of having difficulty calibrating the instrument, use the
tuning diagnostics to obtain further information. These are covered later in
this section.

Low Sensitivity
Sensitivity is determined by the ratio of signal to noise. Before attempting
a diagnosis, determine whether the problem is due to a weak signal or
excessive background noise by reference to a previously know good
spectrum.

Symptom Probable Cause Remedy

Excessive Noise Unconditioned GC column / Remove GC interface from
Contaminated GC column Trace MS Plus.
Condition the GC column as per
instructions in the Trace MS
Plus Installation Guide,
although increased Helium flow
may benefit.
Cleave the ends of the column
before refitting
If high background still present
then replace column
Sample run needs to be repeated Repeat sample run – it can often
take up to 3 attempts to achieve
specification
Source is dirty Bake source at 250-260°C for at
least 1 hour
Clean the source – refer to
Section 3.6 of this manual
Liner is dirty Replace or clean the liner
Weak Signal Poor tuning Re-tune the instrument making
sure all parameters are set at
sensible values
There is an air leak Refer to Section 4.3 for
information on eliminating air
leaks
Helium flow not enough Increase Helium flow in method
(max = 1.2)

38 _________________________ Trace MS Plus Service Manual _____________________

 Fault Finding and Corrective Maintenance
__________________________________________________________Troubleshooting Tables

Low Sensitivity (Ctd)

Symptom Probable Cause Remedy
Weak Signal (Ctd) Detector voltage too low Check the detector voltage in the
instrument method file in
Xcalibur – for Installation
methods this should be set at
450V

Inlet System / Chromatography

Symptom
Variable retention times running
repeat samples
Fluctuating Baselines
Probable Cause
GC oven temperature not stable
from run to run
The GC column is in a poor
condition
Poor injection
Air is leaking into the system at
the injector seal or the carrier gas
manifold
Helium pressure varying during
run
Column requires conditioning
Remedy
Monitor temperature of oven
during run, ensure that
temperature ramps OK – if faulty
contact local Thermo Finnigan
office
Condition or change the column
Repeat, with better injection
technique
Refer to Section 4.3 for
information on eliminating air
leaks
Monitor Helium pressure during
run – run pressure checks – refer
to Trace MS Plus Installation
Guide
Remove GC interface from
Trace MS Plus.
Condition the GC column as per
instructions in the Trace MS
Plus Installation Guide,
although increased Helium flow
may benefit.

____________________ Trace MS Plus Service Manual ___________________________ 39

Fault Finding and Corrective Maintenance
Troubleshooting Tables ___________________________________________________________
Inlet System / Chromatography (Ctd)
Symptom
Overly wide peaks
The peaks have flat tops
Chromatogram peaks show
“tailing” (that is, sloping on the
right hand side).
The chromatogram peaks show
an excessive slope on the left
hand side.
Chromatograms show discreet
high intensity contaminant peaks
Rising total ion current (TIC)
baseline.
40 _________________________ Trace MS Plus Service Manual _____________________
Probable Cause
Column needs replacing
The column has been saturated
The injector is not hot enough
Poor GC oven program
The signal exceeds the dynamic
range of the detector
The sample is too concentrated
The injector is not hot enough
The interface temperature is not
high enough
The carrier gas flow is
inadequate
The injection liner is dirty
The GC column or injector has
active sites
The sample is overloading the
column
Poor injection
The GC column is bleeding
Bleeding is occurring from the
septum
The GC column is bleeding
Air is leaking into the system
Remedy
Confirm by Evaluating column –
refer to Trace MS Plus
Installation Guide
Reduce the injection volume
and/or sample concentration
Increase the injector temperature
Alter the GC program. See your
GC user manual for details
Reduce the detector voltage in
the method
Reduce the injection volume
and/or sample concentration
Reset the injector temperature on
the GC
Increase the temperature on the
GC
Increase the flow - see your GC
user manual for details
Replace the liner
Condition or change the column
Reduce the amount and/or
concentration of the sample..
Repeat, with better injection
technique
Condition or change the column
Replace the septum
Condition or change the column
Refer to Section 4.3 for
information on eliminating air
leaks

__________________________________________________________Troubleshooting Tables
Inlet System / Chromatography (Ctd)
Symptom
High baseline.
Baseline falls away slowly from
a high initial value.
Poor reproducibility
____________________ Trace MS Plus Service Manual ___________________________ 41
Fault Finding and Corrective Maintenance
Probable Cause
The sample is dirty
Contaminated rinsing solvent
Air is leaking into the system
Purge valve left closed during
acquisition
Inadequate purge flow rate
Purge left off for too long
Solvent tail peak
The pre-filters are dirty
The ion source is dirty or badly
assembled
Old or damaged source filament
Poor calibration
Poor tuning
Air is leaking into the system
Active sites in the column or
liner
Incorrect column type
Loose connections in the ion
source
Poor injection
Remedy
Clean or re-make the sample
Replace the solvent
Refer to Section 4.3 for
information on eliminating air
leaks
Alter the GC program. See your
GC user manual for details
Increase the purge flow rate
Shorten the purge time
Increase the solvent delay or use
a different solvent
Clean the pre-filters – refer to
Section 4.3 for more
information
Disassemble, clean, and re-
assemble the source. Refer to
Section 3.6 for details
Replace the source filament.
Refer to Section 3.6 for details
See Trace MS Plus Getting
Started for details of how to
calibrate the system
Check the End User’s Tuning –
refer to Trace MS Plus Getting
Started Guide
Refer to Section 4.3 for
information on eliminating air
leaks
Condition or change the column
Change the column
Disassemble and re-assemble
the source. Refer to Section 3.6
for details
Repeat, with improved injection
technique
Fault Finding and Corrective Maintenance
Troubleshooting Tables ___________________________________________________________
Inlet System / Chromatography (Ctd)
Symptom Probable Cause
There is no noise on the mass Acquisition started too soon after
chromatogram tuning
Detector voltage too low
Data compression is set “on”
Poor signal / noise on test Accidental split injection
standards
Column flow rate too high
Spectral Problems
Symptom Probable Cause
The spectra are distorted or The scan speed is too low
skewed
Unstable or poor tuning
Incorrect isotope peak/ratios LM/HM Res settings or Ion
Energy setting too high or too
low in the tune file
Inaccurate calibration
The detector is being overloaded
Air is leaking into the system
42 _________________________ Trace MS Plus Service Manual _____________________
Remedy
Wait a short time and then re-try
Check the detector voltage in the
instrument method file in
Xcalibur – for Installation
methods this should be set at
450V, increase if necessary
Switch off data compression on
the instrument control panel
Repeat with splitless injection
Reduce the flow rate
Remedy
Increase the scan speed so that
there are at least 6 scans across
the peak
Re-tune the system
Check the Tune page set-up with
the reference gas and set the
LM/HM Res and Ion Energy for
good resolution
Re-calibrate – refer to the Trace
MS Plus Getting Started
Manual for details
If any of the peaks have an ion
count of >2e6, reduce the
concentration of the sample or
reduce the detector voltage
Refer to Section 4.3 for
information on eliminating air
leaks

__________________________________________________________Troubleshooting Tables
Spectral Problems (Ctd)
Symptom
The spectra show a high level of
noise
Missing high mass peaks
The total ion current
chromatogram (TIC) has a high
background
Isotope peaks are missing from
the spectrum
____________________ Trace MS Plus Service Manual ___________________________ 43
Fault Finding and Corrective Maintenance
Probable Cause
The source is dirty
The scan speed is too fast. This
will only happen if the Advanced
Mode is activated
The source is dirty
There is bleeding from the
stationary phase of the GC
column
Air is leaking into the system
The carrier gas is of poor
quality
The sample is dirty
Poor calibration
Poor tuning
The ion source is dirty
The sample is too dilute
Detector voltage is too low
Remedy
Clean the source – refer to
Section 3.6 of this manual
Reduce the scan speed. Clear the
Advanced check box on the
instrument method page and
allow Xcalibur to limit the scan
speed
Clean the source – refer to
Section 3.6 of this manual
Condition or change the column
Refer to Section 4.3 for
information on eliminating air
leaks
Replace the carrier gas source
Clean or re-make the sample
See Trace MS Plus Getting
Started for details of how to
calibrate the system.
Check the End User’s Tuning –
refer to Trace MS Plus Getting
Started Guide
Clean the source – refer to
Section 3.6 of this manual
Repeat with a more
concentrated sample
Check the detector voltage in
the instrument method file in
Xcalibur – for Installation
methods this should be set at
450V, increase if necessary
Fault Finding and Corrective Maintenance
Troubleshooting Tables ___________________________________________________________

Source Problems

Note. Refer to Chapter 4 for information on how to maintain and clean the
ion source.

Symptom Probable Cause Remedy

Source not heating. The heater is malfunctioning or Check the heater connection and
is not connected replace, if necessary.
Refer to Section 3.6 for details

The source thermocouple is Replace the thermocouple

faulty

The source thermocouple is not Re-connect the thermocouple

connected properly

Source temperature readback is The source thermocouple is Replace the thermocouple

at maximum (not regulating).
Source is becoming discolored,
is too hot or is hotter than
intended.
faulty
The source thermocouple is not Re-connect the thermocouple
connected properly
The source thermocouple is Replace the thermocouple
faulty
The source thermocouple is not Re-connect the thermocouple
connected properly
The source thermocouple is not Re-connect the thermocouple
connected to the ion block
The source heater is short- Disassemble and re-assemble
circuiting the source. Refer to Section 3.6
for details

44 _________________________ Trace MS Plus Service Manual _____________________

 Fault Finding and Corrective Maintenance
_____________________________________________________Resolving Common Problems

4.2 Resolving Common Problems

The following pages describe how to handle some of the more easily
resolved problems.

Checking the Power Supply Requirements

The Trace MS Plus needs to be connected to a 230Vac power supply running
at 50Hz. The exact requirements of the system can be found in the Trace
MS Plus Pre-installation Requirements Guide. The power requirements
of other equipment being used can be found in the manufacturers handbook.

Note: If the Trace MS Plus is not connected to the correct power supply
then damage could occur to the system

Rebooting the PC
The most common communication problems with Xcalibur can often be
resolved by simply rebooting the PC.
To safely reboot the PC:
1. Try to save any open data files.
Depending on the nature of the problem, this may not be possible. Any
data that is not saved before rebooting the PC will be lost.
2. Close Xcalibur.
3. Exit from Windows in the usual way, selecting Restart in the window.
4. Reboot Xcalibur.

____________________ Trace MS Plus Service Manual ___________________________ 45

Fault Finding and Corrective Maintenance
Resolving Common Problems ______________________________________________________

Running the simple diagnostic tests

In the event of any tuning or calibration problems, the following tests can be
a useful tool in pin pointing the fault.

Checking the DC and Rectified RF Voltages

Set the following parameters, as given in the table and check that the
readbacks in the Per Method Parameters table are close to the values given
in the table. It should be noted that these values change slightly from
instrument to instrument.
Span Ion Energy Ion Energy LMRes HMRes
0 0 0 0 0

Mass Setting DC Gen 1 (V) DC Gen 2 (V) Rectified RF (%)

2 0 0 0
250 -60 60 25
500 -120 120 50
750 -180 180 75
1000 -240 240 100
(Note: The DC voltages must be opposite in polarity, however, DC Gen 1
may also be positive as long as DC Gen 2 is negative.)

Polarity Check
Set the following ionization modes and check that the polarities of the
voltages listed are correct and close to the Set Point in the Per Method
Parameters table.
Ionization Lens 1 Lens 2 Repeller Electron
Mode Energy
EI -ve -ve +ve -ve
CI+ -ve -ve +ve -ve
CI- +ve +ve -ve -ve

Note: It is usual for the Product Support department to ask you to run these
checks when contacting them for support.

46 _________________________ Trace MS Plus Service Manual _____________________

 Fault Finding and Corrective Maintenance
____________________________________________________ Other Corrective Maintenance

4.3 Other Corrective Maintenance

The following pages will give guidance on how to perform some of the
procedures suggested in the Troubleshooting Tables that are not covered
elsewhere in this manual.
These are:
• Tracing Air Leaks
• Cleaning the Pre-filters
• Checking for Pre-filter Short Circuits
• Checking the Set Point of a Pirani Gauge

Tracing Air Leaks

The following pages describe how to trace an air leak, including:
• Confirming an air leak
• Locating the leak

Confirming an Air Leak

To confirm that you have an air leak, set the TRACE MS PLUS Tune View
to look at the Helium and Nitrogen peaks - m/z 4 and 28 respectively; see
Trace MS Plus Getting Started for details of how to tune the system. The
relative abundance of helium to nitrogen should be in the order of 10 : 1. A
value that differs significantly from this (that is, if the proportion of
Nitrogen is much higher than it should be) is confirmation of an air leak in
the system.

Locating the Leak

Once you have confirmed the presence of an air leak, you must locate and
repair it.
A useful method of locating a leak is to spray likely areas with a solvent,
using a syringe or a spray can. If a leak is present, you should be able to
detect solvent molecules diffusing into the system by using the TRACE MS
PLUS Tune View to look for the appropriate mass peak. These peaks should
decrease when the leak is sealed.
Freon is a suitable solvent for this purpose; see the side of the can for the
molecular weight.

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The areas that you should check include:

• Column connections
• Supply plumbing
• GC internal plumbing

Column Connections

If press-fit unions are used on the analytical column, examine these first:
Gently tighten the GC interface column 1/16” Swagelok securing nut by a
fraction of a turn.
Gently tighten the injector column-securing nut by no more than a quarter of
a turn.
Depending on the tightness of the column, the response of the air peak
display will be delayed for between ½ and 2 minutes if the leak is here.

Caution. Be wary of over-tightening ferrules. This can reduce their

lifespan and risk extruding them, where they might absorb analytes.

Supply Plumbing

Make a particular check in this area if any changes are made to the supply
plumbing after commissioning of the instrument.
If the carrier gas cylinder is near the Trace MS Plus:
1. Close the regulator valve and use a leak-checker (a helium sniffing
electronic device would be most useful) to check the cylinder thread and
all exposed seals and joints of the regulator body.
Set the cylinder regulator to at least 50 psig and repeat the leak checking
procedure from the supply to the GC inlet.
If the carrier gas supply comes from a manifold serving a large number of
systems, you can only make an effective check for leaks in new plumbing.
Once you have done this, examine whether the leak might be from another
source. Finally, if necessary, obtain a gas cylinder and plumb it directly into
the system.

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GC Internal Plumbing

To check for air leaks in the GC column:

1. Connect the carrier gas supply to a single injector and remove the
column.
Blank off the base of the injector.
Fit a new septum.
Ensure that the septum support plate is in the correct orientation and that
the liner is installed correctly.
Set the injector to the operating temperature.
Close the top and bottom valves, using the GC keypad.
Increase the column head pressure to about 50 psig and then close the on/off
valve situated below the head pressure regulator.
There should be no noticeable deviation in needle position over a 20-minute
period. (You should mark the dial to avoid parallax errors).
If you detect a leak, localize it as follows:
2. Return the column to its normal head pressure.
Use a freon spray, as described earlier.
Even though the plumbing is at a higher pressure than the surroundings,
enough freon diffuses into the system to be detectable.

Cleaning the Pre-filters

This section gives guidance on:
• Removing the Analyzer Assembly
• Removing the Pre-filters
• Cleaning of the Pre-filters
It is also a good idea to follow the procedure immediately after this one to
ensure that no faults have been introduced to the Analyzer assembly

Note: As with cleaning the source, to guard against unwanted

contamination from finger grease, you are recommended to wear clean,
lint-free gloves during all procedures involving handling of the internal
components of the instrument.

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Other Corrective Maintenance ______________________________________________________

Removing the Analyzer Assembly

1. Right-click on the TRACE MS PLUS Server icon in the Windows task-
bar.
The server menu is displayed.
2. Choose the Vent menu option to vent the system.
3. Close down Xcalibur.
4. Once the instrument has vented, switch off the mains supply and
disconnect the mains cable from the rear of the instrument.
5. Switch off the TRACE MS PLUS, by means of its circuit breaker, and
allow at least half an hour for the system to cool.
6. Undo the transit bolt at the back of the digital electronics unit and lower
the unit carefully until it rests on the bench.
7. At the rear of the instrument, undo the 4 screws holding the top cover to
the instrument then slide the cover off.

WARNING. Risk of burns. Solenoid gas valves reach high temperatures in

operation.

8. Undo the nuts holding the reference pipes into the instrument and
withdraw them fully.
9. Remove the source and slacken the screws that hold the source interface
bracket.
10. Remove the Headamp and Photomultiplier assembly from the
instrument.
11. Disconnect the 3 cables to the detector and undo the 2 screws fixing the
detector to the Housing.
12. Remove the detector assembly and store in a suitable manner.
13. Undo the 4 screws holding the Analyzer assembly to the Housing.
Support the assembly as the screws are removed.
14. Carefully withdraw the Analyzer assembly from the Housing.

Removing the Pre-filters from the Assembly

1. With the RF Generator end of the Analyzer assembly standing on the
bench, undo the 4 screws holding the diaphragm cover and guide rails to
the assembly.
2. Undo the 4 nuts holding the copper wires to the studs on the Pre-filters.

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3. On each Pre-filter undo the Allen grub screw on the Pre-filter and
carefully remove the Pre-filter from the assembly.

Cleaning of the Pre-filters

1. Using Micromesh, clean off any “ion burns”.
2. Sonicate the Pre-filters in clean methanol for at least 30 minutes.
3. Dry the Pre-filters for at least 1 hour in the GC (or other) Oven at
100°C.
4. Re-assemble onto the Analyzer assembly following the reverse of the
procedure to remove them.

Checking for Pre-filter Short Circuits

It may be necessary as part of an unscheduled service visit for an engineer to
check that the Pre-filters are not short circuit. It is also good idea to check
after re-assembly after cleaning to ensure that no faults have been
introduced.
1. If you have not cleaned the Pre-filter rods, follow the steps in the
Removing the Analyzer Assembly above.
2. Diametric Pre-filter rods should be electrically connected to each other.
If they are not it is likely that the copper wire is not connected.
3. The rod either side of a Pre-filter should not be electrically connected to
it.
Touching copper wires can often produce this fault.
4. None of the rods should be electrically connected to ground.
Check that the copper wire is not touching the can. Pre-filters shorted to the
diaphragm cover can also produce this.
5. None of the rods should be electrically connected to the diaphragm
cover.
Check that there is no debris between the end of the Pre-filter and the cover.
6. None of the rods should be electrically connected to the main analyzer
rods.
Check that the copper wire from the Pre-filter is not touching the main
analyzer rods.
Check that the spring load on the Pre-filter is not causing the rod to
touch the main analyzer rod.

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Re-assembly of the Analyzer into the Instrument

Follow the reverse of the procedure Removing the Analyzer Assembly
above.

Checking the Set Point of a Pirani Gauge

On the Pirani gauge there are three pots, an A pot, a V pot and an S pot that
can be exposed by moving the gray slider on the gauge.
The A pot is set at the manufacturers (Edwards) and is a reference voltage at
atmosphere (usually 10V).
The V pot will adjust the reading of the pirani gauge once it is under
vacuum.
The only pot that may need adjusting is the S pot, especially if you have
replaced the pirani gauge.
The S pot defines at what pressure the pirani will give a "Vac OK" signal.
To set the S pot:
1. Locate J22 on the Digital PCB. (It’s near where the pirani gauge cable
is connected to the PCB).
2. Short circuit J22, either by using a jumper connector or by other means
(such as a piece of wire, etc).
3. View the Per Method Parameters on the Tune Page and locate the
Vacuum Gauge (%) readback..
4. Adjust the S pot on the pirani until the Vacuum Gauge (%) reads ~ 23%
- i.e. the pirani will give a "Vac OK" signal when the gauge reads 23%.
5. Remove the short circuit on J22.

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