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LCMS-8040 Triple Quadrupole Liquid

Chromatograph Mass Spectrometer (LC-


Wendy Gavin

LC/MS General Guide

Version 1

November 2015

Table of Contents

1. References. page 3
2. LC/MS Instrument page 4
3. Basics of LC/MS.. page 6
4. Atmospheric Pressure Ionization.. page 7
a. Electrospray Ionization.. page 7
b. Atmospheric Pressure Ionization.. page 8
5. Triple Quadrupole page 10
a. Tandem MS/MS. page 14
b. Isotopes.. page 14
6. Liquid Chromatography.. page 16
7. Analysis Modes. page 18
8. Sample Preparation. page 21
9. Data Acquisition. page 22
10. Data Analysis page 33
11. Report.. page 36
12. After 5pm Batch Run. page 37
13. Shutdown.. page 38

1. References
LC-MS Training Manual pdf.
Steps for LC-MS pdf.
EEM-07-002-A Level 1 Safety Training.pdf
RES-07-001-ETIC Emergency evacuation.pdf

2. LC/MS Instrument-Shimadzu LC/MS 8040
A. LC Unit

B. Pumps LC-20AD



C. Degasser Unit


D. Auto-Sampler


Cools samples

3. Basics of LC/MS

Liquid Chromatography Mass Spectrometry (LC/MS) is an analytical technique that combines the
separation capabilities of liquid chromatography with the mass analysis capabilities of mass
spectrometry. LC/MS is oriented towards specific detection and potential identification of chemicals in
the presence of other chemicals (mixture).

Liquid Chromatography is a fundamental technique used to separate a sample into its individual
components. The separation occurs based on the interactions of the sample with the mobile phase and
stationary phase. Liquid chromatography separates the components of the sample based on differences
in their affinity for the stationary phase or mobile phase. LC can separate of wide range of organic
compounds from small-molecule metabolites to peptides and proteins.

Traditional detectors for LC include: refractive index, electrochemical, fluorescence, and ultraviolet-
visible (UV-Vis). Such detectors quantify substances based on retention time and quantitate substances
based on peak intensity and peak area. Chromatography offers great resolution, but quantifying and
quantitating substances accurately can be difficult, especially when components elute at the same time.

Mass Spectrometry (MS) offers highly sensitive detection technique that ionizes the sample components
using various methods. The resulting ions are separated in vacuum based on their mass-to-charge ratio
and the intensity of each ion is measured. MS detectors generate valuable information about molecular
weight, structure, identity, quantity, and purity of the sample. MS detectors increase confidence of
qualitative and quantitative analyses.

MS is a more sensitive and more specific detector than all other LC detectors. It can analyze compounds
without a suitable chromophore. It can identify compounds in unresolved chromatography peaks,
reducing the need for perfect chromatography.

LCMS unit consists of a unit for separating components (HPLC), an ion source that ionizes the sample, an
electrostatic lens that introduces the generated ions, a mass analyzer that separates ions based on their
mass-to-charge ratio, and a detector unit that detects the separated ions.

4. API-Atmospheric Pressure Ionization

The atmospheric pressure ionization unit ionizes the sample sent from the LC under atmospheric

Ion sources ionize the analyte molecules and separate the resulting ions from the mobile phase.
Atmospheric pressure ionization (API) ionizes analyte molecules first, at atmospheric pressure. These
analyte ions are mechanically and electrostatically separated from neutral molecules. Ions generated
are stripped of solvent, focused into a beam, then delivered to the quadrupole. Electrospray ionization
(ESI) and atmospheric pressure chemical ionization (APCI) are two common API techniques. ESI is best
suited for ionic compounds of high polarity, where APCI is good for low or medium polarity compounds.


The ESI source operates at atmospheric pressure. The sample solution is sprayed from a small tube into
a strong electric field in the presence of nitrogen to assist desolvation. The liquid aerosolizes as it exists
the capillary at atmospheric pressure, the desolvating droplets shedding ions that flow into the mass
spectrometer, induced by the effects of electrostatic attraction and vacuum. ESI can be used for a wide
range of samples such as natural products, proteins, peptides, biological macromolecules and

The principle of ionization for an ESI probe is that the sample solution is drawn into a capillary tube with
a high voltage of around 3 to 5 Kv applied to it. Nebulizer gas is blown out around the outside of the
capillary tube, spraying the solution and generating fine droplets that are electrostatically charged with
the same sign as the applied voltage. During the course of movement, the charged droplets are subject
to vaporization of the solvent and they disintegrate when the repulsive force among the charges
exceeds the surface tension of the liquid. Through repetition of vaporization and disintegration, very
fine droplets are achieved, and ultimately it is thought that sample ions are released in the vapor phase.

The ionization process does not fragment the sample into smaller charged particles. Instead, it turns the
sample into smaller droplets which in turn will be further desolvated into even smaller droplets. This
creates molecules with attached protons. These protonated and desolvated molecular ions will pass
through the mass analyzer to the detector where the mass of the sample can be determined.

ESI allows for the production of multiply charged species. This results in the ability to analyze very high
molecular weight species. One sees a distribution of ions for peptides and proteins.


Solution phase ionization

Ionization controlled by pH
Introduction of ions to MS requires removal of solvent
Can be applied to larger molecules and forms multiply charged ions
Must contain polar functional groups

Proteins have many suitable sites for protonation as all of the backbone amide nitrogen atoms could be
protonated theoretically, as well as certain amino acid side chains such as lysine and arginine which
contain primary amine functionalities. ESI can ionize peptides and proteins since they can take on
multiple charges. Since the mass spectrometer measures m/z, this brings the apparent mass down to
500 to 2000m/z.


APCI ionizes sample and solvent molecules by spraying the sample solution into a heater using nitrogen.
Solvent molecules are ionized by a corona discharge to generate stable reaction ions. Ions are produced
in the discharge and extracted to the mass spectrometer. Protons are transferred between these
reaction ions and sample molecules by either adding or removing a proton. APCI is used for analyzing
highly fat-soluble compounds or compounds that do not ionize in solution.

The solvent gas heated (from 300 to 500C) inside the APCI probe is ionized on the occurrence of corona
discharge due to the application of a high voltage (3 to 5kV) to the needle. The sample molecules are
ionized as a result of ion-molecular reactions (CI reactions) with the solvent ions. Nebulizer gas is used
to spray the liquid in the same way as with ESI.


Gas phase ionization

Transfer of charge from solvent ion in gas phase
Small molecules and forms singly charged ions
Suited for analysis of non-polar molecules


Dual Ion Source (DUIS) is an ionization method in which data can be obtained in both ESI and APCI
modes. High voltages are applied simultaneously to the nebulizer for ESI and the corona needle for APCI
and heated gas is used to assist ionization in the APCI mode. This probe is used as the nebulizer for ESI.

5. Triple Quadrupole

Quadrupole MS contains four parallel cylindrical metal rods inside a vacuum chamber, positioned
equidistant from the center axis, arranged in a square. The analyte ions are directed down the center of
the square. Voltages applied to the rods generate electromagnetic fields. The electromagnetic fields
determine which mass-to charge ratio of ions can past through the filter.

Quadrupole MS systems can separate ions at lower vacuum levels (10-2 to 10-3 Pa) than other mass
separation methods. Thus, when interfaced with LC unit, the drop in vacuum level caused by the
interface has minimum effect on mass separation performance. Quadrupole MS has a mass
measurement range of up to 2000m/z which enables qualitative analysis in a practical range of
molecular masses. High-speed switching enables simultaneously monitoring multiple selected ions (SIM)
for higher-sensitivity simultaneous quantitative analysis of multiple components.

Quadrupole MS can operate in two modes called scanning (scan) mode or selected ion monitoring (SIM)
mode. In scan mode, the mass analyzer will monitor for a range of mass-to-charge ratios. Scan mode is
good for qualitative and quantitative analysis. In SIM mode, it will monitor for only a few mass-to
charge ratios. SIM mode allows quantitative analysis.

The mechanism of analysis for the mass spectrometer is that samples are introduced from the liquid
chromatography. The sample is sprayed and ionized under atmospheric pressure by the atmospheric
pressure ionization probe. The ionized sample is introduced through the sample introduction unit or
desolvation line (DL), oriented 90 to the spray, into the first stage primary vacuum chamber, where it is
efficiently focused at the tip pf the skimmer by the Qarray where multi-stage high frequency ion guides
are arranged. The rear section of the skimmer [asses through the high frequency ion guides (multi-
poles) arranged in the second and third vacuum chambers. The ions are separated according to their
mass-to-charge ratio (m/z) by the quadrupole mass filter with pre-rod and the collision cell and are

detected by the detector. The detected ions signals are first amplified by the amplifier and then
processed by the LabSolutions data processing software.

The interface section introduces the ions generated by the ionization probe into a vacuum. The status
of the spray generated under atmospheric pressure can be observed through the source window at the
front of the unit.

The charged droplets that have been spray ionized are heated by the desolvation line (DL). This heating
serves to remove the solvent and introduce ions into the vacuum. The lens system is made up of the
Qarray, skimmer, multipole and entrance lens. The ions generated under atmospheric pressure are
efficiently focused, and then introduced into the quadrupole rods by the lens system.

The vacuum housing comprises the atmospheric pressure chamber and the first, second, third, and
fourth vacuum chambers. The rotary pump evacuates the first vacuum chamber and the rear part of the
triple inlet turbo molecular pump, while a single inlet turbo molecular pump evacuates the second,
third, and fourth vacuum chambers. The pressure is measured by the Pirani gauge fitted to the first
vacuum chamber and the ion gauge fitted to the fourth vacuum chamber.

The nitrogen gas supplies 3 types of gas: nebulizer gas, drying gas, and standard sample delivery gas.

A. Tandem Mass Spectrometry (MS/MS)

A mass spectrum tells us the molecular weight, however, we also want to see the fragment ions.
Fragments ions provide structural information for the compound of interest. The first mass
spectrometer is used to select a single(precursor) mass that is characteristic of a given analyte in a
mixture. The mass-selected ions pass through a CID where they are activated to cause them to fall apart
to produce fragment (product) ions. The second mass spectrometer is used to separate the fragment
ions according to mass. The resulting MS/MS spectrum consists only of product ions from the selected
1+= precursor ion
1 +
2 +
2+= product ion

= neutral loss

Product-ion scan (1+ specified)

If we perform an MS/MS experiment to find out all of the product ions, 2+ that result from the
decomposition of a specified parent ion 1+, and then this is a product-ion scan. It is used to determine
structurally significant fragment ions for a selected precursor ion.

Precursor-ion scan (2+ specified)

A precursor-ion scan experiment tells us all of the possible precursor ions, 1+ that decompose to
produce a specified product ion 2+. This is useful when you know that a particular product (fragment)
ion mass is characteristic of a class of compounds. You can identify the mixture components that belong
to that compound class.

Neutral-loss Scan ( N specified)

This is an MS/MS experiment that looks for all pairs of precursor ions and product ions that differ by a
constant neutral loss, N. This is useful when you know that a particular neutral loss mass is characteristic
of a class of compounds, and you would like to identify the mixture components that belong to that
class of compound.

B. Isotopes

A mass spectrometer has the ability to distinguish different isotopes. The presence of isotopes gives
each fragment a characteristic series of peaks with different intensities. These intensities can be
predicted based on the natural abundance of each isotope. An isotope has the same number to protons
but a different number of neutrons which results in a different overall mass. A lot of elements have a
variety of naturally occurring isotopes, like carbon, bromine and chlorine.

Most Abundant Secondary Abundance/100 atoms of Primary
Element Isotope Isotope Isotope
1 2
Hydrogen H H 0.015
1 13
Carbon 2C C 1.080
14 15
Nitrogen N N 0.370
16 17
Oxygen O O 0.040
O 0.200
32 33
Sulfur S S 0.800
S 4.400
35 37
Chlorine Cl Cl 32.50
79 81
Bromine Br Br 98.00
28 29
Silicon Si Si 5.100
Si 3.400

Each isotope will show up as a separate line in a mass spectrum. The Y-axis is relative intensity, so the
height of each peak will correspond to the relative abundance of each isotope in the sample. In the
example below, the compound contains a Bromine group. Its isotope of 81Br is two atomic mass units
more of the actual mass of the compound. Notice that the peak heights are nearly identical since each
isotope is almost 50% naturally occurring.

Another sample is a compound containing a 35Cl. It has a naturally occurring isotope of 37Cl which is two
atomic mass units more at 251amu.

Another compound is 12C which has a naturally occurring isotope of 13C. The sample below show the
exact mass of 325 m/z with a 13C isotope at 326m/z. The Base Peak of this spectrum is 325 and would be
labeled M+. and the 13C with an atomic mass of 1 greater would be labeled (M+1)+. The intensity of each
isotope peak is proportional to the abundance of the isotope.

6. Liquid Chromatography

LCMS API (atmospheric pressure ionization) is used to analyze organic compounds with low to medium
polarity or medium to high polarity. Reversed-phase LC mode is best for separating and ionizing these
types of compounds. API is used for ionizing compounds with relatively high polarity by spraying the
mobile phase into a strong electric field to form a fine aerosol of charged droplets. Therefore, the
mobile phase must be able to dissolve polar compounds (water and polar organic solvents) and readily
form charged droplets (solvents with low viscosity and volatile salts).

Mobile phase for API

Must be volatile
Must be a protic
Common choices
Ethyl Acetate

Mobile Phase

Must be MS grade
Be aware of source limitations on flow rates
For ESI from nano flow to 1ml/min
On our instrument never go above 1ml/min

Some fundamental mobile phases are listed below.

Ph/Additives for Mobile Phase

Use low concentration additives

Beware of
Ion pairing reagents
Strong acids/bases (TFA/TEA)

Mobile Phases Suitable for API

Fundamental Mobile Phase Solvents

Alcohols, such as methanol and ethanol
Water (pH adjusted, if necessary)

pH Adjusting Reagents (volatile, up to about 10 mM)

Acetic acid, formic acid, and TFA (trifluoroacetate) (acidic)
Aqueous ammonia (basic)
Ammonium acetate and ammonium formate (buffer solution)

Relatively Volatile Ion Pair Reagents *

Perfluorocarbonate (C2 to C8) (to retain basic compounds)
Dibutylamine, triethylamine, etc. (to retain acidic compounds)
* Requires particular care, as this can remain in system even after changing mobile phases

Usable Organic Solvents *

DMSO, DMF, THF, acetone, esters, chloroform, benzene, and hexane
* If a "fundamental mobile phase solvent" is present, it usually not a problem if the mobile
phase contains some of these organic solvents. (However, the ionization effect decreases as
the concentration increases.)

Solvents not to be used for LCMS are phosphate buffer solutions and non-polar solvents such as hexane.
Phosphate buffer solution can precipitate its non-volatile salts at the interface and potentially cause
mechanical damage. Non-polar solvents like hexane contribute very little to ionizing sample molecules
using APCI. Analytical conditions using this solvent would need modifications.

Since there are a limited number of mobile phases that are suitable for LCMS, one can change the
column as another option. C18(octadecyl) is the standard reverse-phase column, but one could try a
C30 to increase retention or a C8 to reduce retention. A phenyl column could increase separation
selectivity. Other options for better LC methods are to try isocratic or a different gradient elution.

ESI ionization extracts compounds existing as ions in solution via a pas phase by spraying the solution
into a high voltage electric field. To achieve high sensitivity with ESI, it is important to liberate the ions
from the droplets efficiently, such as by obtaining droplets that are as fine as possible, reducing droplet
surface tension, and optimizing droplet pH. Mobile phase pH affects sensitivity.

If a basic compound is detected as positive ions, adding an acidic reagent (AH) shifts the equilibrium in
the following equation to the right, which in turn increases sensitivity.

M-NH2 + AH {M-NH3]+ + A-

For acidic compounds, add a basic reagent (B) or use a mobile phase which has a pH value1 or 2 lower
than the pKa value.

M-COOH + B [M-COO]- + BH+

In the case of neutral compounds without an ionic group, adding a volatile salt like ammonium acetate
can sometimes increase ionization efficiency as adduct ions.

M + BH+ [M+BH] + M + A- [M+A]-

TIC -Total Ion current chromatogram is a chromatogram this is displayed using all of the detected ions.

MC- Mass chromatogram shows the change in the intensity of m/z over time for a selected ion with a
specific mass.

7. Analysis Modes
a. MS Analysis
1) MS Analysis is possible using either Q1 or Q3 in the MS analysis mode. Scan analysis
and SIM analysis are also possible. High speed scanning at 15,000/sec can be
performed in Q3 MS mode.

b. MS Scan Mode
1) Scan measurement is performed while scanning the mass ranges once every fixed
interval. This method is mainly used for qualitative analysis.
c. SIM Mode
1) In scan mode, a mass spectrum is obtained continually. In SIM mode, only ions with
the target mass are selectively detected. This enables high-sensitivity analysis with
no detection time wasted on the detection of ions with masses that are not
required. Since the peak height and area are stable, SIM is normally used for
quantitative analysis.
d. MS/MS Analysis Mode
1) Specific ions are selected in the first quadrupole mass filter (Q1). These selected
ions are referred to as precursor ions. The precursor ions are collided with inert gas
in the collision cell (collision-induced dissociation, CID) to generate product ions. By
measuring the product ions in the second quadrupole mass filter (Q3), we can
obtain information regarding the structure of the precursor ions. This analysis
method is referred to as MS/MS. Four types of analysis are possible by configuring
either scan or SIM analysis for Q1 and Q3.

e. Precursor Ion Scan Mode

1) This mode involves performing scanning in Q1, fixing Q3 to a specific m/z, and
selectively analyzing the ions generated in the CID. This allows examination of
precursor ions with common product ions, and it is suitable for screening ions with
common substructures.

f. Product Ion Scan Mode
1) This mode involves fixing Q1 to a specific m/z and performing selective analysis on
precursor ions selected in Q3 that were generated in the CID. As product ion
spectra can be obtained, this mode is suitable for examining the structure of ions
selected in Q1. This mode would be good for determining the amino- acid sequence
of peptides and proteins.

g. Neutral Loss Scan Mode

1) This mode involves maintaining the difference in the m/z for analysis in Q1 and Q3
while performing scan analysis. This allows the scanning of ions desorbed from
common neutral fragments. As with the precursor ion scan mode, this mode is
good for screening ions with common substructures (neutral fragments).

h. MRM Scan Mode

1) This mode involves fixing both Q1 and Q3 to a specific m/z and selectively analyzing
ions. Precursor ions are selected in the Q1 and product ions that contain structural
information generated in the CID are selected in Q3. As both precursor and product
ions are specified and monitored, highly selective quantitative analysis that is low in
unwanted substances can be achieved compared to SIM measurement. This means
this mode is effective in determining the quantities of trace constituents contained
in large matrix samples.

8. Sample Preparation-Very Important
a) TFA suppresses ionization. Remove TFA by lyophilization or vacuum.
b) Dissolve sample in MeOH or H2O-MeOH or CH3CN-H2O.
c) No DMSO, DMF, THF, or hexane
d) Centrifuge your samples before loading them into vials. Particulates can clog column.
Recommended to double centrifuge.
e) Filter through 0.22m filter.

Mass Spectrometer Important Facts

a. m/z maximum of 2000 Da

b. CID gas 230
c. PG vacuum 80-140Pa (96)
d. Neb gas 2 or 3(higher flow rate)
e. DL-250-300(for higher flow rates)
f. Drying gas 15 or 20 (higher flow rate)

Liquid Chromatography Important facts:

a) Never use 100% water for C18 column bad for column
b) Solvent A is always Water (Acid or base)
c) Solvent B is always Organic ( MeOH, Acetonitrile)
d) Water has 0.1% v/v solution of acid or base
a. Example: 1ml formic acid in 1 liter of H2O.
e) Use H2O from wall unit or LC/MS grade
f) Store column in 50/50 mixture of MeOH/H2O (no acid or base)
g) Read about your particular column.
h) Never use a flow rate above 1mL/min.

9. Data Acquisition
1) Check lights on MS. There should be a total of three lights lit by LED. One of them is blinking.




2) Check level of solvents A and B on top of instrument. Be sure there is sufficient solvent
volume for your run. Bottle A is aqueous and Bottle B is organic.
3) Check the waste can.
4) If changing solvents:
5) Hit Purge button on Autosampler. This is set to purge for 25 minutes.
6) Turn black knob on LC-20AD Pump A 90 counterclockwise towards open. Press purge on LC-
20AD Pump A.

90 counter-

7) Turn black knob on LC-20AD Pump B 90 counterclockwise towards open. Press purge on LC-
20AD Pump B.
8) Turn black knob back to closed on LC-20AD Pump A 90 clockwise when purge is complete (5
9) Turn black knob back to closed on LC-20AD Pump B 90 clockwise when purge is complete (5

10) Double click on Lab Solutions icon on computer Desktop.

11) Logon as Admin. No password needed. Just hit OK.

12) The Lab solutions windows will open. Click on the Instruments icon

13) Select and Double-click on the LCMS icon

14) Click the Data Acquisition icon in the Main assistant toolbar

15) Create a New Method File. Under File, choose Save Method File as. Choose name for your
method and be sure to save in your data folder. Hit Save.
16) Set Data Acquisition parameters.
A. Enter the LC Stop Time as time from one sample to the next.
B. Click Apply to All acquisition time to set end time for each detector to the same time
as the LC detector.
17) Under Pump, keep as binary gradient, even if running isocratic.
a. Set Pump Flow rate. Max is 1mL/min!
b. Set initial concentration for gradient systems, Pump B conc (never 100% H2O or A).
c. Set Pressure Max for your column ( i.e 6000).
18) Set Oven Temperature. Want slightly above room temperature. Usually set at 40C. Hit icon

to start warming column

19) Click on Download when complete.


20) Click on the LC Time Prog. tab to enter gradient conditions.

A. Set Time, Module to Pumps, Command is Pump B Concentration, and Value is
percentage of B concentration.

B. Click on Draw Curve.

21) Click on the MS Instrument On/Off icon on the top toolbar to start DL heater and
heat block temperature control.

22) Click on the Pump ON/Off icon on the top toolbar. Pump Solvent delivery is
23) Set Interface parameters.
i. ESI and/or APCI mode.
ii. Nebulizing Gas flow 2 L/min. (3 L/min for higher flow rates)
iii. DL temp =250 (300 for higher flow rates)
iv. Heat Block temp =400C.
v. Check off drying gas flow 15 L/min.

24) Click on the MS Instrument On/Off icon on the top toolbar to start DL heater and
heat block temperature control.
i. CID gas should be 230.
ii. PG vacuum should be 1.0 e02 (80-120).
iii. IG vacuum should 1.8 e-03

25) Set the MS Instrument Parameters. Click on MS tab.
A. Each individual MS condition is called an event and polarity can be set for each event. The
system can be scanned in positive and negative modes simultaneously. This can be
accomplished by setting events. Each event has its own parameters.

a) Select polarity of the event to set; Positive or Negative.

b) Click the button for the datas acquisition mode; MRM(), Product Ion Scan(), Precursor
Ion Scan (), or Neutral Loss Scan (), SIM () or scan ().
c) The event is now added to the Event Table.

26) Set detailed parameters for events.
A. MRM-Q1 and Q3 are both parameters for the SIM Measurement mode

B. Product Ion Scanning- Q1 and Q3 are parameters for SIM and scan measurement modes

C. Precursor Ion Scanning- Q1 and Q3 are parameters for SIM and scan measurement modes

27) Set the Same Measurement Time for all events.
Right click on the events in the Event Table, then click Set Same Measurement Time.

28) Under File, choose Save Method File As..

29) Enter the File name and click Save.

30) Click the Realtime Batch icon
31) A realtime batch table will open.

32) Under File, choose New Batch File.

a) Enter Vial #,
b) Tray name =1
c) Sample Name
d) Sample ID
e) Sample Type-unknown, standard
f) Method File set up previously
g) For Data File see step 28
h) Injection volume 0.1ul to 1.0ml.
33) Under File, choose Save Batch method as...

34) Right click on screen and choose Settings or click on Settings icon
35) Click on the Data File tab. Check
i. Check Create Filenames Automatically.
ii. Move Sample Name and Sample ID with Add.

Create Filename automatically

Add Sample Name and Sample ID

36) Go to Shutdown tab under Settings. Enter conditions for automatic shutdown with a cooling
time of longer than the running time. Be sure all instruments are checked off to shutdown after

Shutdown is checked

Cool down time

longer than run time

All instruments
checked off

37) Select the rows and numbers to be analyzed.

38) Click on Start Realtime Batch icon .

35. Select All Rows or Selected Rows.

10.Data Analysis

1) Click on the Postrun icon or the Data Analysis icon .

2) Double-click on Postrun.

3) Drag and drop a file into the window. Or Double-click on file.

4) Average MS Spectrum-
a. Click on Average Spectrum on toolbar.

b. Use mouse to select the time range to be averaged.

5) Subtract MS Spectrum
a. Click (Subtract Spectrum on MS Data Analysis toolbar.

b. Use mouse to select time range to be subtracted.

6) Add spectra to Spectrum Process Table

a. The spectrum displayed can be entered in the Spectrum Process Table.
b. Click on Register to Spectrum Process table in MS Analysis Toolbar.

c. Click OK.

d. The Spectrum is registered to the Spectrum Processed Table.

1) Save screen as seen
a. Under File, choose Print Graph Image, then PDF Output.
b. Save on USB drive.

2) Data Report
a. Click on Data Report icon under Main.
b. Click on MS Spectrum icon
i. Click on box under Chromatogram
ii. Expend box

c. Save as PDF Output

12. After 5pm Batch Runs

It is possible to program batch runs to run after 5pm when the BCl is closed.

A. Create a batch file.

B. Right click and choose Settings or use the Settings icon

C. Go under the Startup tab
D. Place a check mark next to the Startup box.
E. Add the Start Date & Time.
F. Check off the box next to Set start date and time when starting batch.
G. In Pumping Period, put the time you want to flow the beginning mobile phase before
starting your first sample.
H. Hit OK to close out the Startup window.

I. Save batch file.

J. Start RealBatch run, and it will begin a timer until the batch will run.

Check Startup box

Enter Start Date and Time.

Check Set start date and time

when starting batch box.

You can add the Method file if you

are using one method otherwise
leave unchecked.

Pumping Period runs at initial

conditions before starting batch

1. Close Lab Solutions by going under File and choosing Exit.

2. A shutdown sub-window opens. Be sure everything is checked off.

3. Under File, choose Exit Lab Solutions.