Agilent Technologies 6400 Series User manual

Agilent 6400 Series Triple Quadrupole
LC/MS System
Quick Start Guide
Where to find information 3
Getting Started 5
Step 1. Start the Data Acquisition software 6
Step 2. Prepare the LC modules 12
Step 3. Prepare the Triple Quad instrument 16
Step 4. Set up and run an acquisition method 20
Step 5. Review results with the Qualitative Analysis program 27
Step 6. Analyze data with the Quantitative Analysis program 27
Use this guide for your first steps with the Agilent 6400 Series Triple Quad LC/MS, and as a
road map for your user information.
What is the Agilent 6400 Series Triple Quad LC/MS system?
The Agilent Triple Quadrupole 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.
The Agilent 6490 and 6495 Triple Quadrupoles contain the iFunnel Technology
which provide more efficient sampling of ions into the mass spectrometer. The
iFunnel Technology includes the Dual Offset Ion Funnel and these other
technologies: the Agilent Jet Stream Technology, and shorter desolvation assembly
with Hexabore Capillary.

What’s New in Data Acquisition
2 Agilent 6400 Series Triple Quadrupole LC/MS Quick Start Guide
The Agilent 6495, 6490 and 6460 Triple Quad LC/MS are shipped by default with
the Agilent Jet Stream Technology that utilizes a super-heated sheath gas to
collimate the nebulizer spray which dramatically increases the number of ions that
enter the mass spectrometer.
You can set up an Agilent Triple Quad LC/MS with the Agilent 1100, 1200, 1260 or
1290 Infinity LC modules.
Also, the Agilent Triple Quad LC/MS comes with Agilent MassHunter Workstation
Software that includes three major programs:
•Data Acquisition – From one screen 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 screen you can set up a batch of data files and
quantify, evaluate and requantify the results. From this screen you have access
to the Method Editor for setting up and editing the quantitation methods.
•Qualitative Analysis – From one screen you can extract and integrate
chromatograms, subtract background, extract peak spectra, and compare data
from different types of data files.
What’s New in Data Acquisition
The Data Acquisition program for the 6400 Series Triple Quadrupole has many
new features in this revision.
in B.07.00
•The supported models are 6420A, 6430A, 6460A, 6460C, 6490A, and 6495A.
•The supported LC models are 1100, 1200, 1260, 1290, HTS, and HTC.
•You can autotune the 6495 with the Agilent Jet Stream.
•Autotune is faster for the 6490 and the 6495 than in previous versions.
•The 6495 supports Unit, Wide, and Widest resolutions.
•Fast scan autotune is not supported for the 6495.
•Optimizer allows you to set the injection volume for a compound.
•Optimizer allows you to set the number of transitions to find during
optimization.
•Optimizer allows you to open a different database from the File menu in
Optimizer.

Where to find information
Help
Agilent 6400 Series Triple Quadrupole LC/MS Quick Start Guide 3
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.
Documents
You can find these manuals delivered with the Triple Quad hardware or software.
You can also find a PDF version on the installation disk, in the Manuals folder.
Many of these manuals are also available at www.chem.agilent.com.
Installation Guide This guide is used to install the hardware and software,
configure the instrument, and verify performance.
Upgrade Guide This guide is used to upgrade your MassHunter Workstation
software from a previous version.
Maintenance Guide Use this guide to help maintain and troubleshoot your
Agilent Triple Quad LC/MS.
Concepts Guide - The Big Picture Learn the background information to help you
understand operation of the hardware and software.
Data Acquisition for 6400 Series Triple Quad Familiarization Guide Do the
exercises to learn to use the Triple Quad LC/MS hardware and Data Acquisition
program for 6400 Series Triple Quad.
Study Manager Quick Start Guide Use this guide to learn to use the MassHunter
Study Manager software.
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 instrument for each individual
compound analyzed.

Where to find information
Training
4 Agilent 6400 Series Triple Quadrupole LC/MS Quick Start Guide
MassHunter QQQ Compliance Quick Start Guide Use this guide to learn about the
MassHunter QQQ Compliance program.
MassHunter Quant Compliance Quick Start Guide Use this guide to learn about
the MassHunter Quant Compliance program. (This guide is on the Quantitative
Analysis disk.)
Qualitative Analysis Familiarization Guide Do the exercises to learn to use the
Qualitative Analysis program. (This guide is on the Qualitative Analysis disk.)
For information on what is new in the Qualitative Analysis program, refer to the
Qualitative Analysis Familiarization Guide.
Quantitative Analysis Familiarization Guide Do the exercises to learn to use the
Quantitative Analysis program. (This guide is on the Quantitative Analysis disk.)
For information on what is new in the Quantitative Analysis program, refer to the
Quantitative Analysis Familiarization Guide.
Training
Familiarization Guide Use all three familiarization guides to get to know the
software.
Quick Start Guide Use the quick start guides for Study Manager, Optimizer and
Compliance to get to know these programs.
Training Courses Visit www.chem.agilent.com to view a listing of training courses
for the Agilent Triple Quad LC/MS.

Getting Started
Agilent 6400 Series Triple Quadrupole LC/MS Quick Start Guide 5
Getting Started
Install the Triple Quadrupole LC/MS hardware and software
Use the Installation Guide to install the hardware and software and verify
performance.
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.
Start
Here!
Set up, run
and analyze
samples
3Prepare the
Triple Quad
instrument.
1Start the
Data
Acquisition
software.
2Prepare the
LC modules.
4Set up and
run an
acquisition
method.
5Review
results with
Qualitative
Analysis.
6Analyze data
with
Quantitative
Analysis.

Getting Started
Step 1. Start the Data Acquisition software
6 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.
Use instructions in the Installation Guide to configure the instrument for the
first time and any time you change the LC configuration.
The LC modules and the Triple Quad 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.
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 Installation Guide for instructions.

Getting Started
Step 1. Start the Data Acquisition software
Agilent 6400 Series Triple Quadrupole LC/MS Quick Start Guide 7
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
Instrument Status
window
Chromatogram Plot
window
Method Editor
window
Spectrum Plot
window
Actuals
window
The Sample Run and Worklist windows are tabbed 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
8 Agilent 6400 Series Triple Quadrupole LC/MS Quick Start Guide
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.
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. You can also float and dock the
window when you right-click the title of the window and click Floating.
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:
Table 1 Color Coding in the Instrument Status Window
Color Status
Red Error
Yellow Not ready
Purple Pre-run, post-run, Waiting
Blue Running, injecting
Green Idle
Dark gray Offline
Light gray Standby (for example, lamps off)

Getting Started
Step 1. Start the Data Acquisition software
Agilent 6400 Series Triple Quadrupole LC/MS Quick Start Guide 9
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 14 for more information.
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 Plot window With this window you monitor the spectral plot in real
time.

Getting Started
Step 1. Start the Data Acquisition software
10 Agilent 6400 Series Triple Quadrupole LC/MS Quick Start Guide
Method Editor window With this window you enter acquisition parameters for
the method. If you click the button, then you can see the tune values in the
Tune Parameters dialog box.
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.