Agilent 6400 Familiarization Guide

Agilent MassHunter Workstation – Data
Acquisition for 6400 Series Triple
Quadrupole LC/MS

Familiarization Guide

Before you begin 3
Prepare your system 3
Prepare to acquire data 4
Exercise 1 – Develop an acquisition method 6
Task 1. Enter acquisition parameters and acquire data 6
Task 2. Determine precursor ion masses 11
Task 3. Find optimum fragmentor voltage for maximum response 14
Task 4. Determine product ion masses 24
Task 5. Find optimum collision energy for MRM acquisition 30
Exercise 2 – Develop a Dynamic MRM acquisition method from an MRM

acquisition data file or an MRM method 33
Task 1. Create a batch file from an existing MRM data file 33
Task 2. Print a report in the Quantitative Analysis program 36
Task 3. Create a Dynamic MRM method using Update dMRM 37
Task 4. Create a Dynamic MRM method from an MRM method 39
Exercise 3 – Create a Triggered Dynamic MRM acquisition method 40
Task 1. Create a Triggered Dynamic MRM method from a Dynamic MRM

method manually 40
Task 2. Add/Modify compounds in an existing database 42
Task 3. Create a Triggered Dynamic MRM method from an existing

database 52
Exercise 4 – Optimize Acquisition parameters 56
Task 1. Use the Optimizer Software to optimize acquisition

parameters 56
Task 2. Use the “Source and iFunnel Optimizer” program to optimize

acquisition parameters 63

Use the exercises in this guide to learn how to use the Agilent 6400 Series

NOTE

Triple Quad LC/MS. You can do these exercises with the demo data files,
SulfaDrugs, shipped with the system (in the Data folder of your Qualitative
Analysis installation disk), or with data you acquire.

In Exercise 1, you learn how to determine the best acquisition settings for
analyzing your compounds of interest. These instructions help you understand
not only how to set up a worklist to optimize instrument parameters for best
sensitivity in acquisition, but also how to use the Qualitative Analysis program
to identify parameter values producing optimum signal response. You can also
learn about the Qualitative Analysis program by using the Qualitative
Analysis Familiarization Guide or the Qualitative Analysis online Help.

In Exercise 2, you learn how to use either an acquired data file or the
Quantitative Analysis report results to update a dynamic MRM method. This
method allows you to easily set up a dynamic MRM method.

In Exercise 3, you learn how to create a triggered dynamic MRM method.

In Exercise 4, you learn how to use two programs to optimize parameters. The
Optimizer Software helps you optimize acquisition parameters. Specifically, it
automates the selection of the best precursor ion and the fragmentor voltage
for the most abundant precursor ion, selection of the best product ions, and
optimization of collision energy values for each transition for a list of
compounds you specify. The “Source and iFunnel Optimizer” program helps
you to find the optimal source and iFunnel parameters.

See the Concepts Guide to learn more about how the triple quadrupole mass spectrometer
works and why the fragmentor and collision energy voltages are important. For background
information, see Chapter 3, “Agilent Triple Quad MS and Sensitivity”, in the Concepts Guide.
See the online Help for detailed information on how the program works.

Each task is presented in a table with three columns:

• Steps – Use these general instructions to proceed on your own to explore
the program.

• Detailed Instructions – Use these if you need help or prefer to use a
step-by-step learning process.

• Comments – Read these to learn tips and additional information about each
step in the exercise.

2 Agilent 6400 Series Triple Quad LC/MS Familiarization Guide

Before you begin

NOTE

Before you begin, you need to check that your system is ready. If you plan to
acquire data, you also need to set up the instrument.

Prepare your system

1 Check that:

• The Data Acquisition program has been installed.

• The LC modules and the 6400 Series Triple Quad LC/MS have been

• The performance has been verified.

• The system has been turned on.

If these actions have not yet been done, see the Installation Guide for your
instrument.

2 Copy the data files to your PC.

Copy the folder named SulfaDrugs in the Data folder on your Qualitative
Analysis installation disk to any location on your hard disk. This folder
contains all the data files needed for this exercise.

Do not re-use the sulfa drug data files already on your system unless you know that you
copied them from the originals on the disk and you are the only one using them. Data files
that are already on the system may contain processed results, leading to different behavior
during the exercises in this guide.

Before you begin

Prepare your system

configured.

Agilent 6400 Series Triple Quad LC/MS Familiarization Guide 3

Before you begin

Prepare to acquire data

Prepare to acquire data

Parts List The exercise in this guide uses this equipment and materials:

If you do not intend to acquire data but want to learn how to use the
Qualitative Analysis program for method development, you can skip this step,
which tells you how to prepare the demo sample. You then do those tasks that
show you how to use the Qualitative Analysis program with the sulfa drug
data files shipped with the system.

• Agilent 1200, 1260 Infinity or 1290 Infinity LC modules: well-plate

sampler, binary pump, thermostatted column compartment, DAD

• Zorbax column (see Table 1 on page 4)

• A 1 ng/µL concentration of the sulfa mix sample (prepared in this step)

Tab l e 1 Zorbax columns

Triple Quadrupole Column Description Film

Thickness

6410B, 6420, 6430, 6460
and 6490

SB-C18 2.1mm x 50mm 1.8 µm 80Å 822700-902

Pore Size Part

Number

1 Prepare the LC solvent.

In 1-liter reservoirs of HPLC-grade water and acetonitrile (ACN), add 1 mL
of 5M ammonium formate each to make 5mM ammonium formate in water
and ACN and use for the A and B channels, respectively.

2 Prepare the sample.

a Add 10 µL of the sulfa mix from one of the ampoules (500 µL) to 990 µL

of solvent A in a 2 mL glass sample vial so that the final concentration is
1 ng/µL.

b Cap the vial and place in a sample location in the autosampler.

3 Set up the LC column.

Use the Agilent column from Table 1. Other columns and instrument
parameters may be used in these exercises, but some parameters may need
adjustment, and the results will differ.

4 Set the column temperature to 60

ο

C. Lower temperatures may be used;
however, the retention times will be longer, and the pump pressure may
exceed the limit of some LC systems.

4 Agilent 6400 Series Triple Quad LC/MS Familiarization Guide

Before you begin

Sulfamethizole Sulfamethazine Sulfachloropyridazine Sulfadimethoxine

NOTE

Prepare to acquire data

The Electrospray LC Demo Sample (P/N 59987-20033) contains five ampoules
with 100 ng/µL each of sulfamethizole (M+H)
279, sulfachloropyridazine (M+H)

+

= 285, and sulfadimethoxine (M+H)+ = 311.

+

= 271, sulfamethazine (M+H)+ =

Determining optimal parameter values for acquiring sample compound data requires that
the Agilent Triple Quad instrument already be tuned on the Tuning Mix calibrant ions.
Before proceeding with this exercise, make sure you have used Checktune or Autotune to
verify that calibrant ions each have the proper mass assignment, peak width, and signal
intensity.

See the Quick Start Guide, Installation Guide or online Help for instructions on tuning the
instrument.

Agilent 6400 Series Triple Quad LC/MS Familiarization Guide 5

Exercise 1 – Develop an acquisition method

Task 1. Enter acquisition parameters and acquire data

Exercise 1 – Develop an acquisition method

For this exercise you analyze a mixture of four sulfonamide compounds.

Task 1. Enter acquisition parameters and acquire data

In this exercise, you enter the conditions for the analysis of the sulfa drug mix.

l

Steps Detailed Instructions Comments

1 Enter LC parameters appropriate

for sulfa drug mix.

See Tab l e 2 .

a Double-click the Data Acquisition

icon.

b Make sure that Acquisition appears as

the selection in the Context text box.
If Tune is the selection, click
Acquisition from the Context
dropdown menu in the Combo bar.

c Enter the LC parameters listed in the

Tab l e 2.

• The Data Acquisition window
appears. See Figure 1.

Tab l e 2 LC parameters for sulfa drug mix

Parameter LC Parameter

PUMP

• Flowrate 800 µL/min

• Solvent A 5 mM ammonium formate in water

• Solvent B 5 mM ammonium formate in 90:10 acetonitrile:water

• Gradient (min - %B) 0 min - 13%

1.80 min - 60%
2 min - 60%

• Stop Time 2.5 min

• Post Time 3.0 min

INJECTOR

• Inj. Vol. 2.0 µL

6 Agilent 6400 Series Triple Quad LC/MS Familiarization Guide

Exercise 1 – Develop an acquisition method

Task 1. Enter acquisition parameters and acquire data

Tab l e 2 LC parameters for sulfa drug mix (continued)

Parameter LC Parameter

• Injection Standard

• Draw Position 0.0 mm

UV DETECTOR

• Ch A 254 nm (4 nm BW on DAD)

• REF A (DAD only) 400 nm (80 nm BW)

COL THERM

• Temp 60 °C for the 6460 and 6490 with Agilent Jet Stream Technology

40 °C for other instruments

Agilent 6400 Series Triple Quad LC/MS Familiarization Guide 7

Exercise 1 – Develop an acquisition method

Task 1. Enter acquisition parameters and acquire data

Figure 1

Steps Detailed Instructions Comments

2 Enter MS parameters appropriate

for sulfa drug mix and save the
method as iiiMS2Scantest.m,
where iii are your initials.

See Tab l e 3 .

Agilent MassHunter Workstation Software – Data Acquisition window

a Click the QQQ tab in the Method

Editor window.

b Select MS2Scan from the Scan Type

list in the Time Segments table.

c Enter the other MS parameters as

listed in Ta bl e 3 . These parameters are
in either the Acquisition or the Source
tabs.

d Save the method as

iiiMS2Scantest.m, where iii are your
initials.

8 Agilent 6400 Series Triple Quad LC/MS Familiarization Guide

Exercise 1 – Develop an acquisition method

If you have an Agilent 6490, you cannot edit the
Fragmentor column. The value for the Fragmentor
for a 6490 QQQ comes from the tune file, and for the
6490 it is typically closer to 380 V.

Task 1. Enter acquisition parameters and acquire data

Tab l e 3 MS parameters for sulfa drug mix

Parameter Value (ESI) Value (AJS ESI)

• Inlet ESI (positive polarity) AJS ESI (positive polarity)

• Scan Type MS2Scan MS2Scan

• Delta EMV pos 400 V 200 V

• Mass Range 100 to 400 100 to 400

• Cell Acceleration Voltage 7 V 7 V

• Gas Temp 350 °C

250 °C for Agilent 6490

• Gas Flow 12 L/min
14 L/min for Agilent 6490

• Nebulizer 50 psi 35 psi

• Sheath Gas Temperature not applicable 400 °C

• Sheath Gas Flow not applicable 12 L/min

• Nozzle Voltage not applicable 0 V

• Capillary Voltage positive 4000 V 4000 V

• Fragmentor 100 V (not adjustable on 6490, comes

from the Tune file)

350 °C
250 °C for Agilent 6490

10 L/min
14 L/min for Agilent 6490

100 V (not adjustable on 6490, comes
from the Tune file)

Figure 2 Select Scan Type of MS2 Scan in the QQQ tab

Agilent 6400 Series Triple Quad LC/MS Familiarization Guide 9

Exercise 1 – Develop an acquisition method

Task 1. Enter acquisition parameters and acquire data

Steps Detailed Instructions Comments

3 Acquire data (optional).

• Set up a one-line worklist with

the method you just created.

• Name the data file

iiisulfamix01.d, where iii are
your initials.

• Designate a directory path to

hold your data files and method.

a If necessary, click View > Worklist to

display the Worklist window.

b Click Worklist > Worklist Run

Parameters. Verify that the
parameters are set properly. Click OK.

c Click Worklist > Add Multiple

Samples.

d Ty p e iii

data file name

e Select iiiMS2Scantest.m as the

method name.

f Click the Sample Position tab.
g Select the Autosampler, Well-plate or

Vial Tray.

h In the graphic, select a single position.

Click OK.

i In the Worklist window, mark the

check box to the left of the sample.

j Click the Start Worklist Run icon in

the main toolbar, the Run Worklist
icon in the Worklist toolbar or click the
Worklist > Run command.

sulfamix01.d as the

• The Worklist window is tabbed with
the Method Editor window by
default. Click the Worklist tab to
show the Worklist window.

• The Number of samples is set to 1.

• You have just acquired a full scan

MS data file to see what ions are
being formed from the sample.

• This step is optional because you
can perform the next step with an
example data file that comes with
the program. If you prefer, you can
create your own data file as
described in this step.

10 Agilent 6400 Series Triple Quad LC/MS Familiarization Guide

Exercise 1 – Develop an acquisition method

Task 2. Determine precursor ion masses

Task 2. Determine precursor ion masses

In this exercise, you determine the precursor ions for each of the sulfa drugs
in the acquired data file.

Steps Detailed Instructions Comments

1 Open the acquired data file.

• In the Qualitative Analysis

program, open either the
example file, sulfamix01.d, or
the data file you created in “Task

1. Enter acquisition parameters
and acquire data” on page 6.

a Double-click the Qualitative Analysis

icon.

The program displays the “Open Data
File” dialog box.

• When you open the sulfa drug
directory after installation, the Load
result data (lower left corner) check
box is grayed out.

• If you see the check box marked,
this means that the data file(s)
already contains results. Clear this
check box before opening the file.

Agilent 6400 Series Triple Quad LC/MS Familiarization Guide 11

Exercise 1 – Develop an acquisition method

Before you begin, make sure that
all previous settings are returned
to their default values:

• Restore default layouts

• Click Configuration >

Window Layouts > Restore
Default Layout.

• Make sure the method is
default.m. (see title bar)

• Click Method > Open.

• Select default.m, and click

Open.

• Return display options to default
settings.

• In the Configuration menu,

click each of the Display
Options commands.

• Click Default, and then OK.

Or...

• Restore the General layout.

• Click Configuration >

Configure for Workflow >
General.

• Click OK.

• (optional) You may be asked to

save method changes.

• Return display options to default
settings.

• In the Configuration menu,

click each of the Display
Options commands.

Task 2. Determine precursor ion masses

Steps Detailed Instructions Comments

12 Agilent 6400 Series Triple Quad LC/MS Familiarization Guide

b Do one of the following:

• Select the example data file

sulfamix01.d, and click Open.

• Select the data file you created in

“Task 1. Enter acquisition
parameters and acquire data” on

page 6, and click Open.

By default, the system displays the
Total Ion Chromatogram (TIC).

• The figure below shows the default
layout.

• The Qualitative Analysis program
displays a newly opened data file
with the same layout and display
settings used for the previous data
file. Therefore, you MUST make
sure to return to the default settings
for this exercise.

Exercise 1 – Develop an acquisition method

Task 2. Determine precursor ion masses

Steps Detailed Instructions Comments

2 Determine precursor ion masses

for all four peaks.

• You have determined them

correctly if you find the values
are similar to those shown in
this table:

• If you acquired the data file using

the Agilent Jet Stream
Technology, the retention times
may be different.

• The sulfamix01.d data file was

acquired with a different column
so your retention times are
different.

• Close the data file after finding

the precursor ion masses.

a In the Chromatogram Results window,

make sure that the Range Select icon
in the toolbar is on.

b Click the left mouse button and drag

the cursor across the first peak to
produce a shaded region, as in the
figure below.

c Right-click the shaded area, and click

Extract MS Spectrum from the

shortcut menu.

.

• The system displays an averaged
spectrum across the peak in the MS
Spectrum Results window.

• The precursor mass of the first
compound, sulfamethizole, is
determined to be m/z 270.9.

• To obtain a single scan, double­click the apex of the peak.

d Repeat step a through step c for the

other compounds.
The precursor ion masses should
match those in the table in step 2.

e Click File > Close Data File.
f When asked if you want to save the

results, click No.

• Some compounds form sodium (Na)

and/or potassium (K) adducts as
well, corresponding to M + 23 and
M + 39 masses respectively. Seeing
these masses along with the M + H
can make for an easy confirmation
of which ion is the
pseudo-molecular ion (M + H)+.

Agilent 6400 Series Triple Quad LC/MS Familiarization Guide 13

Exercise 1 – Develop an acquisition method

Task 3. Find optimum fragmentor voltage for maximum response

Task 3. Find optimum fragmentor voltage for maximum response

Task 3 shows you how to carry out the optimization for fragmentor voltage by
creating selected ion-monitoring experiments for each compound within a
method and setting up multiple methods with varying fragmentor voltages.

The Fragmentor Voltage for the 6490 is set automatically during Autotune, and
it cannot be set in the Data Acquisition program. If your instrument is a 6490,
skip to “Task 4. Determine product ion masses”. You can do the Qualitative
Analysis part of this task by using the data files that were shipped with the
software.

Steps Detailed Instructions Comments

1 Set up six methods for six different

fragmentor voltages.

• Change to a SIM experiment.

• Use 60, 80, 100, 140, 180 and 220

volts as the fragmentor voltages
for the six methods.

• Save the methods as

iiiMS2SIMxxx.m, where iii are
your initials and xxx is the
voltage.

a In the Scan Type dropdown list, click

MS2 SIM.

14 Agilent 6400 Series Triple Quad LC/MS Familiarization Guide

Exercise 1 – Develop an acquisition method

Task 3. Find optimum fragmentor voltage for maximum response

Steps Detailed Instructions Comments

b In the Acquisition tab, enter the

Compound Name and Mass

(precursor ion mass) for
sulfadimethoxine.

c Right-click anywhere in the Scan

segments section, and click Add Row.

d Type the Compound Name and the

Mass for sulfachloropyridazine.

e Repeat steps c and d for

sulfamethazine and sulfamethizole.

f Save the method as iiiMS2SIM140.m,

where iii are your initials.

g Change the fragmentor voltage to 60,

and save the method as
iiiMS2SIM060, where iii are your
initials.

h Repeat step g for voltages 80, 100, 180

and 220, saving the methods as

iiiMS2SIM080, iiiMS2SIM100,
iiiMS2SIM180 and iiiMS2SIM220,
where iii are your initials.

• With the MS2SIM Scan Type set, a
different set of columns appears in
the Acquisition window.

• The Instrument Control and Data
Acquisition program creates a SIM
experiment for each compound
mass, starting with a default
fragmentor voltage of 140. See the
example below.

• The Fragmentor column is grayed
out if the instrument type is an
Agilent 6490.

Agilent 6400 Series Triple Quad LC/MS Familiarization Guide 15

Exercise 1 – Develop an acquisition method

Task 3. Find optimum fragmentor voltage for maximum response

Steps Detailed Instructions Comments

2 Set up and run the worklist

(optional).

• Set up six samples with Sample

Name SulfaDrugMix to inject 1ul
from vials 1-6 or the ones you
choose.

• Specify the data files as

iiiSulfaSIMxxx.d, where iii are
your initials and xxx is the
voltage.

a Click the Worklist icon if necessary to

make sure the worklist is visible.

b Click Worklist > New to start a new

worklist. You do not need to save the
last worklist.

c To set up the run, right-click the upper

left corner of the worklist, and click

Worklist Run Parameters.

d Type the paths for the method and data

files.

e Type the information for the 60 voltage

run.

f Click Worklist > Add Sample. Another

sample is added to the Worklist. Add
five samples to the worklist for
voltages 80-220.

g Mark the checkbox to the left of the

Sample Name for each of the six
samples.

• This step is optional because you
can use data files shipped with the
system to perform many of the
tasks in this exercise.

h Start the worklist.

• Click Worklist > Run.

• Click the icon in the main

toolbar.

• Click the icon in the worklist

toolbar.

• Note that the program only runs
those samples that are marked with
a checkmark.

• You can also run the worklist in
locked mode by clicking the

button in the main toolbar.

16 Agilent 6400 Series Triple Quad LC/MS Familiarization Guide

Exercise 1 – Develop an acquisition method

Task 3. Find optimum fragmentor voltage for maximum response

Steps Detailed Instructions Comments

3 Set up a qualitative method to view

the EIC data automatically.

• Open the data file

Sulfa_SIM60.d or your own

iiiSulfa_SIM60.d, where iii are
your initials.

• In the Method Editor, add in the

EICs corresponding to the
precursor ion masses of 271,
279, 285, and 311.

• Save the method as iiiExercise1,

where “iii” are your initials.

a Click File > Open Data File.

The system displays the Open Data
File dialog box

b Select either Sulfa_SIM60.d or

iiiSulfa_SIM60.d, and click Open.

c Click Method > Method Editor or

View > Method Editor.

The system displays the Method Editor
window.

• The Qualitative Analysis program
should be open. If not, see

“Double-click the Qualitative
Analysis icon.” on page 11.

Agilent 6400 Series Triple Quad LC/MS Familiarization Guide 17

Exercise 1 – Develop an acquisition method

Task 3. Find optimum fragmentor voltage for maximum response

Steps Detailed Instructions Comments

d If necessary, click Define

Chromatograms in the Chromatogram

section of the Method Explorer.

e To delete the BPC chromatogram, click

Delete.

f Select EIC for the Chromatogram

Definition Type,

g In the MS Chromatogram tab, make

sure MS Level is set to All and Scans
is set to All scan types.

h Clear the Do cycle sum check box.

271 as the m/z value.

i Ty p e
j Click Add.
k Repeat steps i and j for the other

precursor ions,

279, 285 and

311.

l Click Method > Save As. The system

opens the Save As dialog box

m Save the method as iiiExercise 1.m.
n Click Save.

• The default Method Editor list

selection after installation is

Integrate (MS).

• You can also select Define

Chromatograms from the Method
Items list in the Method Editor
window.

18 Agilent 6400 Series Triple Quad LC/MS Familiarization Guide

Exercise 1 – Develop an acquisition method

Task 3. Find optimum fragmentor voltage for maximum response

Steps Detailed Instructions Comments

4 Extract the chromatogram for the

data file and view the results.

• Make sure you can see all five

chromatograms, the TIC and four
EICs.

a Click the Run button on the Method

Editor toolbar.

b To see the TIC and four EICs, click the

arrow next to the Maximum Number of
List Panes icon in the Chromatogram
Results toolbar, as shown in the
example below.

c Select 5 to view five chromatograms

simultaneously.
The system displays chromatogram
results as shown below.

• You can also click the
Chromatograms > Extract Defined
Chromatograms command to

extract the defined chromatograms.

Agilent 6400 Series Triple Quad LC/MS Familiarization Guide 19

Exercise 1 – Develop an acquisition method

Task 3. Find optimum fragmentor voltage for maximum response

Steps Detailed Instructions Comments

5 Extract the remaining ion

chromatograms automatically.

• Extract Defined Chromatograms

should be the default action for
Assign File Open Actions.

• Open the remaining data files,

Sulfa_SIM80.d through
Sulfa_SIM220.d.

• Close the Method Explorer.

a Select File Open Actions from the

General section in the Method
Explorer.

b Make sure that Actions to be run list

only contains Extract Defined

Chromatograms.

• The Qualitative Analysis Method

Editor lets you define actions to be
performed automatically upon
opening a data file(s).

c Click File > Open Data File.

The system displays the Open Data
File dialog box.

d Select the data files to be opened,

Sulfa_SIM80.d through
Sulfa_SIM220.d.

e Mark the Run ‘File Open’ actions from

selected method check box. (lower left

corner)

20 Agilent 6400 Series Triple Quad LC/MS Familiarization Guide

Exercise 1 – Develop an acquisition method

Mark this check box.

Task 3. Find optimum fragmentor voltage for maximum response

Steps Detailed Instructions Comments

f Click Open.

The Qualitative Analysis program
displays all the EICs for all the data
files selected.

g To close the Method Explorer and

Method Editor, click the X in the upper
right corner of each window.

Agilent 6400 Series Triple Quad LC/MS Familiarization Guide 21

• You can also close the Method

Explorer and Method Editor
windows by clicking the View >

Method Explorer command and the
View > Method Editor command.

Exercise 1 – Develop an acquisition method

Task 3. Find optimum fragmentor voltage for maximum response

Steps Detailed Instructions Comments

22 Agilent 6400 Series Triple Quad LC/MS Familiarization Guide

Exercise 1 – Develop an acquisition method

You can overlay the
chromatograms by
clicking the Overlaid
mode icon in the
Chromatogram Results
toolbar.

Task 3. Find optimum fragmentor voltage for maximum response

Steps Detailed Instructions Comments

6 Select the fragmentor voltage that

produces the maximum response
for each of the precursor ions.

• Close the data files after you

determine the optimum voltage.

a In the Data Navigator window,

highlight the EICs for 271.0 m/z.

b Click the Show only the highlighted

items icon, .

Only the 271 m/z check boxes are now
marked.

c Look at the relative intensities of each

peak to determine which fragmentor
voltage setting will be best to use for
the 271 precursor.

• You press the Ctrl key to be able to
select multiple objects from the
Data Navigator window.

• You press the Shift key to be able to
select a group of objects.

• A fragmentor voltage of 100 should
be sufficient for each precursor ion.

• You can now determine the product
ions that are available for the
multiple-reaction monitoring
experiments to maximize sensitivity
for the analysis.

d Repeat step a through step c for the

other three base peaks or precursor
ions.

e Click File > Close Data File.
f Click Close when the Close Data File

dialog box appears.

•

• Click the different EICs in the Data

Navigator window to change which
chromatogram is labeled in the
Chromatogram Results window.
When the color of the label of the
chromatogram matches the color of
the chromatogram that has the
highest intensity, you use the
fragmentor voltage that was used
for that file.

Agilent 6400 Series Triple Quad LC/MS Familiarization Guide 23