Agilent 6400 Series Triple Quad LC/MS System
Quick Start Guide

Where to find information    4

Getting Started    7
Step 1. Start the Data Acquisition software    8
Step 2. Prepare the LC modules    14
Step 3. Prepare the Triple Quad LC/MS    18
Step 4. Set up and run an acquisition method    22
Step 5. Review results with the Qualitative Analysis program    30
Step 6. Analyze data with the Quantitative Analysis program    30

Use this guide for your first steps with the Agilent Triple Quad LC/MS, and as a 

road map for your user information.

What is the Agilent 6400 Series Triple Quad LC/MS?

The Agilent 6400 Series Triple Quad LC/MS is a liquid chromatograph triple 

quadrupole mass spectrometer that performs MS/MS using three sets of 

parallel rods (in this case, quadrupole, hexapole, quadrupole). The first 

quadrupole separates ions into precursor ions that are fragmented in the 

hexapole into product ions, which are separated by the second quadrupole. 

Often, two or more precursor ions and their product ions are monitored in 

sequence in MRM (multiple reaction monitoring) mode. You can monitor up to 

4000 MRM transitions by using Dynamic MRM.



What is the Agilent 6400 Series Triple Quad LC/MS?

2

Agilent 6400 Series Triple Quadrupole LC/MS Quick Start Guide

The Agilent 6490 and 6495 Triple Quad LC/MS includes the iFunnel Technology 

which provide more efficient sampling of ions into the mass spectrometer. The 

iFunnel Technology includes the Dual Offset Ion Funnel, the Agilent Jet Stream 

source, and a shorter desolvation assembly with Hexabore Capillary.
The Agilent 6495, 6490, 6470, and 6460 Triple Quad LC/MS are shipped by 

default with the Agilent Jet Stream source that uses a super-heated sheath gas 

to collimate the nebulizer spray, which dramatically increases the number of ions 

that enter the mass spectrometer. 
The Agilent 6495B Triple Quad LC/MS is equipped with a novel gate valve for 

replacing hexabore capillaries during routine maintenance without breaking 

vacuum.
You can set up a Triple Quad LC/MS with the Agilent 1100, 1200, 1260 or 1290 

Infinity, or 1260 Infinity II LC modules.
Also, the Triple Quad LC/MS comes with Agilent MassHunter Workstation 

Software that includes three major parts:
• Data Acquisition – From one program you can tune the mass spectrometer, 

control and monitor instrument parameters, set up acquisition methods and 

worklists containing multiple samples and monitor real-time run plots.

• Quantitative Analysis – From one program you can set up a batch of data files 

and quantify, evaluate and requantify the results. From this program you have 

access to the Method Editor for setting up and editing the quantitation 

methods. 

• Qualitative Analysis – From the Qualitative Analysis Navigator program you 

can extract and integrate chromatograms, subtract background, extract peak 

spectra, identify spectra, and compare data from different types of data files. 

From the Qualitative Analysis Workflows program, you can find compounds 

using a variety of algorithms and identify those compounds.



What’s New in Data Acquisition

Agilent 6400 Series Triple Quadrupole LC/MS Quick Start Guide

3

What’s New in Data Acquisition

The Data Acquisition program for the Triple Quad LC/MS has a few new features 

in this revision.

in B.09.00
• Spectral plots for different devices are shown in different tabs in the Spectrum 

Pane window.

• Version A.02.19 for the LC drivers  is supported.

in B.08.02
• The 6495B Triple Quad LC/MS is supported.
• Other supported models are 6410B, 6420A, 6430A, 6460A, 6460C, 6470A, 

6490A, and 6495A.

• The 1260 Infinity II LC system is supported.
• Qualitative Analysis software version B.08.00 is supported.
• Quantitative Analysis software version B.08.00 is supported.
• ECM 3.4.1 SP2 HF3 - HF4 is supported.
• A Resource App is available to access the eFamiliarization Guide, the updated 

animated Maintenance Guide (including Gate Valve instructions), and all user 

and installation guides.

• Microsoft Windows 10 and Microsoft Windows 7 are supported.
• Customizable, automatic data file name generation is available for a Worklist.

in B.08.01
• The supported models are 6410B, 6420A, 6430A, 6460A, 6460C, 6470A, 

6490A, and 6495A.

• Agilent Compliance (with ECM) is the only mode supported.

Where to find information

Help

4

Agilent 6400 Series Triple Quadrupole LC/MS Quick Start Guide

Where to find information 

Help

Press F1  To get more information about a pane, window or dialog box, place the 

cursor on the part of the pane, window or dialog box of interest and press F1. 

Help menu  From the Help menu, access “How-to” help and reference help. 

Installation and User Guides

You can access these guides from the TQ LC/MS Resource App or LCMS Data 

Analysis Resource App. Some of these guides are included with your system in 

printed format. They are also available at www.agilent.com.

MassHunter Workstation Software Installation Quick Start Guide  This guide 

provides instructions to install or upgrade MassHunter Workstation software.

MassHunter Workstation Data Acquisition Familiarization Guide  Do the exercises 

to learn to use the Triple Quad LC/MS and Data Acquisition program.

Agilent 6400 Series Triple Quad LC/MS Concepts Guide - The Big Picture  Learn 

the background information to help you understand operation of the hardware 

and software.

MassHunter Study Manager Quick Start Guide  Use this guide to learn to use the 

MassHunter Workstation Study Manager program.

MassHunter Optimizer Software Quick Start Guide  Use this guide to learn about 

the MassHunter Optimizer program. The MassHunter Optimizer program 

provides a way to automatically optimize the data acquisition parameters for 

MRM mode (multiple-reaction monitoring) on a Triple Quad LC/MS for each 

individual compound analyzed. 

Where to find information

Installation and User Guides

Agilent 6400 Series Triple Quadrupole LC/MS Quick Start Guide

5

MassHunter Workstation Qualitative Analysis Familiarization Guide  Do the 

exercises to learn to use the Qualitative Analysis programs.

MassHunter Workstation Quantitative Analysis Familiarization Guide  Do the 

exercises to learn to use the Quantitative Analysis program.

MassHunter Data Acquisition Compliance Mode Quick Start Guide  Use this guide 

to learn about the MassHunter Data Acquisition Compliance (with ECM) mode.

MassHunter Data Acquisition User Management and Audit Trail Quick Start Guide 

Use this guide to learn about the User Management and Audit Trail feature for the 

Data Acquisition program.

MassHunter Workstation Quantitative Analysis Audit Trail and Compliance Quick 

Start Guide  Use this guide to learn about the Compliance (with ECM) and User 

Management and Audit Trail modes for the Quantitative Analysis program.

MassHunter Workstation Data Acquisition eFamiliarization Guide  Use this 

interactive online guide to get to know the Data Acquisition program.

MassHunter Qualitative Analysis eFamiliarization  Use this interactive online 

guide to learn to use the Qualitative Analysis programs.

MassHunter Quantitative Analysis eFamiliarization  Use this interactive online 

guide to learn to use the Quantitative Analysis program.

Agilent 6000 Series LC/MS Hardware eFamiliarization  Use this interactive online 

guide to learn more about your Triple Quad LC/MS instrument.

Agilent 6200/6400/6500 Series Maintenance Guide (animated)  Use this 

animated guide to help maintain and troubleshoot your Triple Quad LC/MS.

MassHunter Workstation Administration Guide  This guide includes 

administration and troubleshooting tasks for your Triple Quad LC/MS.

Agilent 6000 Series LC/MS Safety Guide  This guide contains safety and 

conformity information for your Triple Quad LC/MS.

Where to find information

Training

6

Agilent 6400 Series Triple Quadrupole LC/MS Quick Start Guide

Training

Resource Apps  Use the material in the Resource Apps to learn to use your 

MassHunter Workstation software, to learn about the Triple Quad LC/MS 

instrument, and to maintain and troubleshoot your Triple Quad LC/MS.

Training Courses  Visit www.agilent.com to view a listing of training courses for 

the Triple Quad LC/MS.

Getting Started

Agilent 6400 Series Triple Quadrupole LC/MS Quick Start Guide

7

Getting Started

Set up, run, and analyze samples
The roadmap below shows you the steps to set up and run a batch of samples 

from start to finish. Follow the instructions on the next pages to get started and 

to learn where to find the information to help you with each step in this roadmap.

o

Getting Started

Step 1. Start the Data Acquisition software

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Agilent 6400 Series Triple Quadrupole LC/MS Quick Start Guide

Step 1. Start the Data Acquisition software

The instructions below include the following assumptions:
• The hardware and software are installed.
• The instrument is configured.
• The LC modules and the Triple Quad LC/MS are turned on, but the LC pump is 

not running.

After installation, you see all of the Agilent MassHunter Workstation Software 

icons on your Desktop. To start the Data Acquisition program, double-click the 

Data Acquisition icon. In Windows 7 you can instead click Start > Agilent > 

MassHunter Workstation > Data Acquisition. In Windows 10 you can instead 

click the click Start > Agilent > Data Acquisition.

The Data Acquisition window appears.

NOTE

When Data Acquisition opens, the software engines 

automatically start. If you need to restart them, right-click the 

Acq System Launcher icon in the system tray, and click Start 

Engines.
If you have recently changed LC modules, remember to 

configure the instrument again. See the Administration Guide 

for instructions.

Getting Started

Step 1. Start the Data Acquisition software

Agilent 6400 Series Triple Quadrupole LC/MS Quick Start Guide

9

Windows—where you do most of your work
When you first start the Data Acquisition program, the main window appears. 

You do almost all of your work within the eight windows of this main window. 

These windows provide the tools to set up acquisition methods, run samples 

interactively or automatically, monitor instrument status, monitor runs and tune 

the instrument.

Figure 1.

Main window of the Data Acquisition software program

Show/hide the windows  You can show one window at a time on the screen or up 

to seven windows. You can never hide all of the windows. To show or hide a 

window, you click the commands in the View menu. You can also hide a window 

by clicking the X icon in the upper right corner of the window.

Instrument 

Status window

Chromatogram 

Plot window

Method Editor 

window

Spectrum 

Pane window

Actuals 

window

The Sample Run and Worklist windows are tabs grouped together here. These three windows are “sharing” this 

space. You click the tab to switch to a different window.

Getting Started

Step 1. Start the Data Acquisition software

10

Agilent 6400 Series Triple Quadrupole LC/MS Quick Start Guide

When you click a window, the title of the active window changes to a different 

color. Press F1 to obtain help on the active window. You can also drag a window 

border to resize the window. If you double-click the title of the window, the 

window “floats” outside of the main window. You can double-click the title bar 

again to “dock” the window. 

Instrument Status window  With this window you view the status of each device 

configured with the instrument: Error, Not ready, Pre-run, Post-run, Running, 

Injecting, Idle, Offline, or Standby. You also set non-method control and 

configuration parameters for the LC devices and the MS instrument.
This window displays the current status of each device both as text and by its 

color-coding:

Actuals window  With this window you view the current value of selected 

instrument parameters. See “Set up to view real-time parameter values 

(actuals).” on page 15 for more information.

Getting Started

Step 1. Start the Data Acquisition software

Agilent 6400 Series Triple Quadrupole LC/MS Quick Start Guide

11

Chromatogram Plot window  With this window you monitor the chromatogram 

plots in real time. These plots can be user-defined signals and/or instrument 

parameters. You select the plots in the Chromatogram tab in the QQQ tab in the 

Method Editor window.

Spectrum Pane window  With this window you monitor the spectral plot in real 

time. A different tab is available for different devices.

Method Editor window   With this window you enter acquisition parameters for 

the method. If you click 

 in the QQQ tab, then you can see the tune values in 

the Tune Parameters dialog box.

Getting Started

Step 1. Start the Data Acquisition software

12

Agilent 6400 Series Triple Quadrupole LC/MS Quick Start Guide

Sample Run window   With this window you enter sample information to run 

individual samples interactively, and you can start a single sample run. You can 

also specify an Override DA Method and select either Both Acquisition and DA 

or DA Only for the Method Type, and then Data Analysis is run as part of the 

method. 

Worklist window  With this window you enter sample information for multiple 

samples. When you run the worklist, the samples are automatically run in the 

order listed in the worklist. You can select whether to run Acquisition Only, to run 

Both Acquisition and DA, or to run DA only by selecting one of these options for 

the Part of method to run in the Worklist Run Parameters dialog box.

Getting Started

Step 1. Start the Data Acquisition software

Agilent 6400 Series Triple Quadrupole LC/MS Quick Start Guide

13

Tune window  With this window you tune the mass spectrometer. You can use 

the automatic tuning algorithms that are provided, or you can manually tune the 

instrument. You have to switch to the Tune Context to see this window. 

This section 

shows the 

current progress 

in the Autotune 

or Checktune.

During an Autotune or Checktune, 

some of the parameters are 

ramped to determine the best 

If you make changes in the Manual Tune tab, you can print a 

Checktune and Autotune report when you click Create Tune Report.

Getting Started

Step 2. Prepare the LC modules

14

Agilent 6400 Series Triple Quadrupole LC/MS Quick Start Guide

Step 2. Prepare the LC modules

Read and follow the instructions in the online Help for each of the tasks in the 

checklist described on the following pages. While you condition or equilibrate the 

column, you can tune the Triple Quad LC/MS. 
1 Switch LC stream to Waste.
When you are not acquiring data, you switch the direction of the LC stream away 

from the MS ion source and to waste.
If you have the LC connected to a VWD or DAD, you can still monitor the 

fluctuations of the VWD or DAD real-time chromatogram before a run.

a Right-click the QQQ device in the Instrument Status window.

b Click LC > Waste.

2 Purge the LC pump.

Follow the directions for purging the pump in the User Guide for your pump.

3 Set up to condition or equilibrate the column.

a Type LC parameters, and click Apply in the toolbar to download them to 

the LC.

Getting Started

Step 2. Prepare the LC modules

Agilent 6400 Series Triple Quadrupole LC/MS Quick Start Guide

15

b Right-click an LC module in the Instrument Status window and click one of 

the commands to change any non-method control parameters, if needed.

c Monitor the baseline and adjust the plot to make sure the column is 

equilibrated and the baseline stable. (See step 4 and step 5 on page 15.)

4 Set up to view real-time parameter values (actuals).

As you prepare for a run and during a run, you want to see the actual values of 

the instrument parameters. You can do this in the Instrument Status window.
a Right-click the Actuals list to see the Setup command.

Getting Started

Step 2. Prepare the LC modules

16

Agilent 6400 Series Triple Quadrupole LC/MS Quick Start Guide

b Click Setup to open the list of Actuals available for monitoring.

c Add all the parameter values you intend to monitor, and click OK. 

Parameters that you may want to monitor include MS values (such as 

heater, and vacuum pressure) or LC values (such as binary pump, column, 

DAD, etc.) You can set the background and text color for each parameter. 

You can also set a range for the parameters which are numbers. If the 

value of the parameter is not within the limits which you entered, then the 

background of the parameter is set to red.

5 Set up real-time plot displays.

As you condition the column, you can set up the displays to monitor the 

effluent.
• Right-click the chromatogram plot, and click Change.

Getting Started

Step 2. Prepare the LC modules

Agilent 6400 Series Triple Quadrupole LC/MS Quick Start Guide

17

In the Edit Signal Plot dialog box, you can select the type of display signal.

Getting Started

Step 3. Prepare the Triple Quad LC/MS

18

Agilent 6400 Series Triple Quadrupole LC/MS Quick Start Guide

Step 3. Prepare the Triple Quad LC/MS

Do a Checktune, Autotune or Manual Tune
1 From the Context list, click Tune.

You can see the Instrument Status window, the Actuals window and the Tune 

window when you switch to the Tune context. Click Tune in the View menu if 

the Tune window is not visible.

2 Click Checktune to evaluate if the MS parameters are within the limits to 

produce the specified mass accuracy and resolution. Checktune can take 

approximately 45 minutes.
If the current tune file was last tuned with the Fast Scan Autotune, then the 

Checktune algorithm only checks MS2. If the current tune file was last tuned 

with Autotune, then the Checktune algorithm checks both MS1 and MS2. 
If the current tune file was last tuned with the Fast Scan Autotune, then the 

Fast Scan check box is marked on the Manual Tune tab.
Do a Checktune regularly.
You can run a Checktune with the following sources: ESI, AJS ESI, and MMI.
If Checktune passes, then skip to step .
If Checktune fails, then you can try using the Manual Tune tab to fix the 

problem. See the next step.

Getting Started

Step 3. Prepare the Triple Quad LC/MS

Agilent 6400 Series Triple Quadrupole LC/MS Quick Start Guide

19

3 Try the following quick changes to get Checktune to pass. 

a Click Manual Tune.
b If the failure occurred in MS1, click MS1. Select the Peak Width based on 

which resolution failed in Checktune. You can select Unit, Wide, or Widest. 

Then, click Adjust Gain & Offset.

c If the failure occurred in MS2, click the MS2 tab. Select the Peak Width 

based on which resolution failed in Checktune. Then, click Adjust Gain & 

Offset.

d If the Adjust Gain and Offset passes successfully, then save the autotune 

file. Click Manual Tune. Then, click Files, and click Save.

e Click Autotune.
f Click Checktune.
If Checktune fails again, you must run an Autotune, which is described next.

4 Click Autotune to tune the MS automatically (approximately 30 minutes for 

each ionization mode for all models except the 6490 and the 6495; for 6490 

and 6495, approximately 25 minutes per ionization mode). The system 

automatically changes different tune parameters to tune the MS. You only do 

an Autotune when needed.
For all instruments except the 6490 and the 6495, you can run an Autotune 

with the following sources: AJS ESI, and MMI. With the 6490 and 6495, you 

can run an Autotune with only the AJS source.
If Autotune fails, then you mark the Start from Factory Defaults check box. 

Then, if you click Autotune, the instrument is tuned starting from the factory 

defaults (approximately 30 minutes for each polarity for all models except the 

6490 and the 6495. The 6490 and 6495 take approximately 25 minutes per 

ionization mode.).

Getting Started

Step 3. Prepare the Triple Quad LC/MS

20

Agilent 6400 Series Triple Quadrupole LC/MS Quick Start Guide

Checktune and Autotune reports are automatically generated after Autotune 

completes successfully. If Autotune fails, no reports are printed. You can 

check the progress box in the lower right side of the Autotune tab to see the 

reasons why the tune failed. Then, you can either fix the problem, or call the 

Agilent service engineer and provide this information.
If Autotune fails or you assess that the Triple Quad LC/MS needs custom 

values entered for its tune parameters, you can manually tune the instrument. 

If you cannot get the instrument to tune successfully, then please call your 

Agilent service engineer.

5 Optional. Click Fast Scan Autotune Only if you want to tune for Fast Scan. You 

only do this step if the Autotune results are acceptable.
Fast scan acquisition is only supported on the 6490.
For Fast Scan acquisition you use one of these two scan types: MS2 Scan and 

Product Ion scan. Fast Scan autotune only tunes with the Wide (1.2) 

resolution, Samples set to 1 (on the Manual Tune > Acquisition tab), and the 

step size must be 0.2. The scan time in the Acquisition tab is generated 

automatically based on the step size and the mass range.
Fast Scan acquisition is not supported for the 6470 and 6495. Instead, you 

achieve the faster scan rate by increasing the step size to 0.3 m/z.

6 In the Context list, select Acquisition.

Switch LC stream to MS
• After you condition the column and tune the Triple Quad LC/MS, you switch 

the LC stream from Waste to MS. See “Switch LC stream to Waste.” on 

page 14 for how to do this.

Getting Started

Step 3. Prepare the Triple Quad LC/MS

Agilent 6400 Series Triple Quadrupole LC/MS Quick Start Guide

21

Monitor MS baseline and spectral displays
If you did not monitor the LC baseline with a VWD or DAD, make sure that the 

Triple Quad LC/MS baseline is stable, and no spectra of interfering intensity 

appear in the display.
If you did monitor the LC baseline with a VWD or DAD, you change back to the 

default Triple Quad LC/MS displays.
1 Right-click the chromatogram plot, and click Change.
2 Select the MS signal, and click OK.

View the system logbook for events and errors
As you prepare the instrument, you may run into an error that you want to 

troubleshoot. You do this through the System Logbook Viewer.
• Click Log (

) in the toolbar of the Data Acquisition window, and view the 

logged events.

• Or click Tools > System Logbook Viewer.
• Or right-click 

 in the system taskbar. First, click Enable Notification. Then, 

right-click LOG and click Configure. The system can notify you of new errors 

and warning by showing messages from the taskbar.

When the System Logbook Viewer is open, you can select the time period to keep 

System Logbook entries. You can set the value from 1 week to 1 year. To do this, 

you click Tools > Purge Settings. The System logbook purge dialog box opens.

Getting Started

Step 4. Set up and run an acquisition method

22

Agilent 6400 Series Triple Quadrupole LC/MS Quick Start Guide

Step 4. Set up and run an acquisition method

Read and follow the instructions in the online Help for each of the tasks described 

on the following pages.
Also, do Exercise 1 of the Data Acquisition Familiarization Guide to learn how to 

set up and run an acquisition method. 
1 Set up the method:

a Type the values and settings for each of the tabs below.
b Optional. If you want to download the settings to the instrument, click 

Apply.

c To save the method, click Method > Save As.
d Name the method and click OK.

2 Enter values for all of the LC modules configured for the instrument.

NOTE

Make sure when you type the MS parameters on the next page that the tune file 

is the one that you want to use with the acquisition.

Getting Started

Step 4. Set up and run an acquisition method

Agilent 6400 Series Triple Quadrupole LC/MS Quick Start Guide

23

3 Enter the QQQ parameter values.

a Select the Scan Type from the list in the Time segments table. The Scan 

segments table is cleared when you change the Scan Type. The 

parameters available on the right change depending on the Scan Type.

If you are changing the Scan Type from MRM to Dynamic MRM or to 

Triggered MRM, you can copy and paste the transitions from the original 

Scan segments table to the Clipboard and then to the new Scan segments 

table. See the online Help for more information.
b Type in any Acquisition values you want to change. You can enter multiple 

Scan segments.

You cannot set the fragmentor voltage in Acquisition if the instrument type is 

an Agilent 6490 or an Agilent 6495. It always uses the value in the tune file.

4 Set up to change Triple Quad LC/MS parameters with segments and scans:

a To add a segment, right-click anywhere in the Scan segments section to 

bring up the Scan Segments shortcut menu, and click Add Row.

b Type the parameters for each Scan segment.

Getting Started

Step 4. Set up and run an acquisition method

24

Agilent 6400 Series Triple Quadrupole LC/MS Quick Start Guide

5 Set up signals for the Chromatogram plot:

a Click Chromatogram.
b Select the Chromatogram Type, and type other plot values.

6 Set up the Stored instrument curves in the Instrument tab. In the Qualitative 

Analysis program, you can display these values in the MS Actuals window for 

the current spectrum. With the Triple Quad LC/MS, the values in the MS 

Actuals window in the Qualitative Analysis program are the values that you 

save in the Instrument tab.
a Click Instrument.
b Select the Stored instrument curves. These curves can be shown in the 

Chromatogram Results window in the Qualitative Analysis program. The 

values can be seen in the MS Actuals window.

Getting Started

Step 4. Set up and run an acquisition method

Agilent 6400 Series Triple Quadrupole LC/MS Quick Start Guide

25

7 Set up the data analysis (DA) parameters.

A method can contain BioConfirm parameters, Qualitative Analysis 

parameters, Quantitative Analysis parameters, or a combination. BioConfirm 

is a separate product that you can purchase. You can mark the BioConfirm 

Automation check box on the BioConfirm tab; the Qual Automation check box 

is marked on the Qual tab, and the Quant Automation check box is marked on 

the Quant tab.
a Click DA.
b Optional. Mark the Qual Automation check box. The name of the current 

Qualitative Analysis method is shown in the box. If you want to change the 

Qualitative Analysis method that is connected, click 

 to select a 

different method. When the Data Acquisition method is saved, the 

Qualitative Analysis method that you selected is copied or linked to the 

Data Acquisition method.

c Optional. Click Quant. Mark the Quant Automation check box. The name of 

the current Quantitative Analysis method is shown in the list. If you want to 

change the Quantitative Analysis method that is connected, click 

 to 

select a different method. When the Data Acquisition method is saved, the 

Quantitative Analysis method that you selected is copied or linked to the 

Data Acquisition method.

Getting Started

Step 4. Set up and run an acquisition method

26

Agilent 6400 Series Triple Quadrupole LC/MS Quick Start Guide

d Optional. Mark the Generate Report check box on the Quant tab. Then, you 

select the Method Path / Template File to use. If you want to print the 

report, mark the Print to default printer check box. You can also mark the 

Publish check box to create a CSV file, a TXT file, or a PDF file.

8 Set up the Properties for this method.

a Click Properties.
b Click 

 to select the Pre Run Script.

c Click 

 to select the Post Run Script.

d Type the Description for this method.

9 Save the method.

a Click Method > Save As or Method > Save.
b If User Management & Audit Trail or Compliance (with ECM) is enabled, 

enter the Reason for creating a new version of this method. Click OK.

c If necessary, name the method and click OK.

10 Set up and run interactive samples:

a Click the Sample Run window. By default, the tab is grouped with the 

Worklist and Method Editor windows.

b Enter the Sample Name, the Data File Name, the Path and other values. 
c Enter the Additional Information. You can change the value of the 

parameters in the Additional Information list.

Getting Started

Step 4. Set up and run an acquisition method

Agilent 6400 Series Triple Quadrupole LC/MS Quick Start Guide

27

You can run a Data Analysis method from this window by selecting Both 

Acquisition and DA or DA Only for the Method Type. In addition, you have 

to set Override DA method to indicate which Data Acquisition method 

contains the DA (Data Analysis) method to execute. You always have to do 

this.

d To start the single sample run, click Run (

) in the Sample Run window 

or Run (

) in the main toolbar. You can instead click Sample > Run.

You can run the single sample in either locked or unlocked mode. When the 

mode is locked, no one can change the method or sample parameters 

during a run. You also cannot overwrite this data file in the Data Acquisition 

program. The Lock button (

) in the main toolbar indicates that locked 

mode is on.

11 Set up and run worklists 

a Click Worklist to show the Worklist window. If the Worklist window is not 

visible, click View > Worklist.

b Right-click the upper left corner of the worklist.

Getting Started

Step 4. Set up and run an acquisition method

28

Agilent 6400 Series Triple Quadrupole LC/MS Quick Start Guide

c Click Add Multiple Samples. The Add Multiple Samples dialog box opens.
d Enter all the information on the Sample Information tab.
e Click Sample Position to specify the sample vial locations (make sure the 

specific sample tray type has been configured by right-clicking the 

autosampler device image).

f Specify the locations, and click OK.
g To set up the worklist run, right-click the upper left corner of the worklist, 

and click Worklist Run Parameters.

h On the Run Parameters tab, type the paths for the method.

Getting Started

Step 4. Set up and run an acquisition method

Agilent 6400 Series Triple Quadrupole LC/MS Quick Start Guide

29

i Click Data File Settings .
j Type or select the folders for the data files. Select the File Naming options.
k Click Additional Parameters.
l Review the information and click OK .
m To start the worklist, click Run Worklist (

) in the main toolbar or Run 

(

) in the Worklist window. You can also click Worklist > Run.

You run the worklist in locked or unlocked mode. When the mode is locked, no 

one can change the method or the worklist while the worklist is running.

NOTE

To use an acquisition method that has a different data analysis (DA) method 

than the method entered in the worklist, show the column called Override DA 

Method in the worklist by using the Show/Hide/Order Columns dialog box. In 

this column, type the name of another method containing the DA parameters you 

want to use for the sample. The DA part of this method is used instead of the DA 

part of the current method.
You can also type the name of this method in the Add Multiple Samples dialog 

box.

Getting Started

Step 5. Review results with the Qualitative Analysis program

30

Agilent 6400 Series Triple Quadrupole LC/MS Quick Start Guide

Step 5. Review results with the Qualitative Analysis 

program

Use the Qualitative Analysis programs to do these tasks and more:

• Review results for acquisition method development
• Select the most appropriate precursor and product ions for MRM analyses
• Find compounds
• Identify compounds
• Do molecular feature extraction

Do the exercises in the Qualitative Analysis Familiarization Guide to help you learn 

how to use the Qualitative Analysis program. View the Qualitative Analysis 

eFamiliarization Guide for TQ to get an overview of the software.
Do Exercise 1 of the Data Acquisition Familiarization Guide to help you learn how 

to use the Qualitative Analysis program to develop acquisition methods.
Also, refer to the online Help for the Qualitative Analysis software to learn how to 

do more operations to analyze your data.

Step 6. Analyze data with the Quantitative Analysis 

program

Another primary tool for analyzing and reporting Triple Quad LC/MS results is 

the Quantitative Analysis program. 
• Do the exercises in the Quantitative Analysis Familiarization Guide to learn how 

to quantitate the acquired data files:
• Set up a batch and a method to automatically quantitate a set of samples
• Review results by learning how to view and use the Batch-at-a-Glance 

results screen

• Identify and use outliers to change the method and requantitate the data 

using a better calibration curve fit or other more appropriate settings

Also, refer to the online Help for the Quantitative Analysis program to learn how to 

do more operations to analyze your data.

www.agilent.com
Agilent Technologies, Inc. 2018

May 2018

 
*G3335-90253*

G3335-90253 Revision 

A

In this book
This book contains brief instructions to help you 

get started with your Agilent Triple Quadrupole 

LC/MS. This book takes a quick look at using the 

Data Acquisition program to:
• Prepare the instrument for a run.
• Set up acquisition methods.
• Set up and run worklists.