Agilent 6210 TOF LC/MS System

Quick Start Guide

Use this guide for your first steps with the Agilent 6210 LC/MS TOF Sys-
tem, and as a roadmap for your user information.

What is the Agilent 6210 TOF LC/MS system?

The Agilent TOF is an orthogonal-axis time-of-flight mass
spectrometer (oa-TOF). That is, the ions reaching the time-of-flight
chamber are impelled in a direction perpendicular to their original
path.
You can set up an Agilent time-of-flight mass spectrometer system
(TOF) in several configurations:
ESI – Electrospray Ionization • For normal flow LC/MS with a binary pump, quaternary pump,
APCI – Atmospheric Pressure well-plate sampler (or autosampler) and ESI , APCI, APPI or
Chemical Ionization MMI ion sources
APPI – Atmospheric Pressure • For microflow LC/MS with a capillary pump, micro well-plate
Photo Ionization sampler and ESI, APCI or MMI ion source
MALDI – Matrix-Assisted Laser
• For nanoflow LC/MS with a nanopump, micro well-plate
Desorption Ionization
sampler and nanospray source or dual nanospray source
MMI - Multimode Ionization
• TOF system with an AP-MALDI source
Each Agilent system has advantages for drug discovery — high
throughput sample screening with highly sensitive detection and
accurate mass assignment.
Each system uses the same Agilent MassHunter Software to enable
these advantages, although the AP-MALDI TOF system uses only
the TOF portion of the software.

Agilent Technologies
 You use the Agilent MassHunter Software for setting up and running data
acquisition. For data analysis, you have two choices. You can use the PE Sciex
Analyst QS 1.1 software package which Agilent provides which is especially
modified for the Agilent 6210 LC/MS TOF system.
You can also use the Agilent MassHunter Workstation Qualitative Analysis
program and the Agilent MassHunter Workstation Quantitative Analysis program.
Both of these programs are included. Before using either of these programs, you
need to translate your data files from the WIFF format to the format used by these
Agilent programs using the Translator program. You can run this program
interactively or directly from a worklist. The translator program is included in the
Agilent MassHunter Workstation Qualitative Analysis program’s installation.

What’s New in A.02.02

Agilent MassHunter Software has many new features in this revision.
• Priming of the flush pump for WPS is now supported.
• Seal Wash for Pumps is now supported.
• Minimum Carryover Reduction for WPS is now supported.
• G1315D DAD is now supported.
• G1329B ALS is now supported.
• Device Reorder Utility is now available.
• WIFF files can be translated when running a Data Analysis method into the
data format used by the Agilent MassHunter Workstation Qualitative Analysis
program and the Agilent MassHunter Workstation Quantitative Analysis
program. Both Analyst and Agilent MassHunter Workstation Qualitative
Analysis programs must be installed for this feature to work.
• Saturation limit has been removed from both the EFC and Mass List reports.
This guide is valid for A.02.xx revisions of the Agilent 6210 MassHunter Software,
where xx refers to minor revisions of the software that do not affect the technical
accuracy of this guide.

2 Agilent 6210 TOF LC/MS System Quick Start Guide

Where to find information

Online Help
Press F1 To get more information about a pane or dialog box, place the cursor on
the part of the pane or dialog box of interest and press F1.

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

PE-Sciex Analyst online help Refer to Analyst online help to learn how to view,
quantitate and report on Agilent 6210 LC/MS TOF results.

Documents
You can find these manuals delivered with the TOF hardware or software. You can
also find a PDF version on the installation CD-ROM, in the Manuals folder.

TOF User’s Guide Use this guide to install and set up the TOF hardware. This
guide also contains background information to help you operate, maintain and
troubleshoot the TOF.

6210 LC/MS TOF System Installation Guide This guide is used by the Agilent
customer engineer to install the 6210 LC/MS TOF hardware and MassHunter
Software, configure the instrument, and verify performance.
You can find these manuals on the installation CD-ROM, in the Manuals folder.

Concepts Guide - The Big Picture Learn the background information to help you
make selections in the software.

Familiarization Guide Do the exercises to learn to use the MassHunter Software.

Training
Familiarization Guide Use this guide as a training lab.

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

for the Agilent 6210 LC/MS TOF system.

Agilent 6210 TOF LC/MS System Quick Start Guide 3

Instructional overview

1 Install the TOF hardware

Use the Agilent G1969 LC/MSD TOF User’s Guide to install the hardware.

2 Install the software

Use the instructions in the Agilent 6210 Time-of-Flight LC/MS System Installation
Guide to install both the MassHunter Software and the Analyst software. The
sequence in which you install the software is listed below:
a Install Analyst QS 1.1.
b Install the Agilent MassHunter Software.
c Configure the instrument for the first time.
d Start the software and verify performance.

3 Set up and run samples

The roadmap below shows you the steps to set up and run a sample 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.
Read the
Concepts Guide
for background on
these steps.
Start 1 Start the 2 Prepare the
software instrument
Here!

3 Set up an
Set up and acquisition
run samples method

5 Analyze data 4 Acquire data

4 Agilent 6210 TOF LC/MS System Quick Start Guide

Step 1—Start the 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.
• The LC modules and the TOF are turned on, but the pump is not running.

Start software/check configuration

1 Double-click the
Agilent TOF group
on your desktop.

2 Double-click the
TOF icon to start
the software
engines.

Figure 1 Agilent TOF group window

Agilent 6210 TOF LC/MS System Quick Start Guide 5

3 Click Start.

4 When all of the

engines say
“Running”, click
Close.

5 Double-click the
TOF icon in the
Agilent TOF
group (Figure 1).

The main window appears. See Figure 2 on page 7. 6 Make sure that the LC modules are the
The top pane of this window is the Instrument Status ones that you want configured with
pane. (Figure below) the instrument. (See below.)

• Select File >

Print >
Instrument
Configuration,
OR

• Check the
headers of the LC
modules labeled
in the Instrument
Status pane.
If LC modules other than those you intend to use appear in the
Instrument Status pane or the Configuration report, use the Online
Help to access instructions to reconfigure the instrument.

6 Agilent 6210 TOF LC/MS System Quick Start Guide

 Four panes—where you do most of your work
When you first start the MassHunter Software, the main window appears. You do
almost all of your work within the four panes of this main window. These panes
provide the tools to set up acquisition methods, run samples interactively or
automatically, monitor instrument status and monitor runs.

Click a button to
Instrument Status pane Real-time Plot pane Method pane Worklist pane
see the pane you
want to use.

Figure 2 Main window of the TOF application

Agilent 6210 TOF LC/MS System Quick Start Guide 7

 Show/hide the panes
You can show one pane at a time on the screen or up to four panes. You can never
hide all four panes. To show or hide a pane, you click on the icons in the main
window toolbar.
When you click on a pane, the active pane is outlined in blue. Press F1 to obtain
help on the active pane. You can also drag a pane border to resize the pane.

S–Instrument Status; R–Real-time Plot

M–Method; W–Worklist

Instrument Status pane

You may have several different LC modules in your LC stack, for example, both a
well-plate sampler and micro well-plate sampler. With this pane you can make
sure that the correct LC module is configured.
You also set non-method control and configuration parameters for the LC devices
and TOF and monitor the status of the device parameters during a run.

Real-time Plot pane

With this pane you monitor the plot of chromatograms and spectra in real time.

8 Agilent 6210 TOF LC/MS System Quick Start Guide

 Method pane
With this pane you enter instrument settings for acquisition methods and sample
information to run individual samples interactively.

Worklist pane
With this pane you enter sample information for individual samples and
information for batch samples. When you run the worklist, the samples and
batches are automatically run in the order listed in the worklist.

Agilent 6210 TOF LC/MS System Quick Start Guide 9

Step 2—Prepare the instrument
Read and follow the steps in the user information listed below to learn how to
prepare the instrument for a run.
• The steps on the next pages that take you through the roadmap below.
• Chapter 2 of the Concepts Guide, Instrument Preparation, for background
information that you may need to prepare the 6210 LC/MS TOF.
• Chapter 1, Prepare the instrument, in the Familiarization Guide to learn to
prepare the LC and TOF to run an ESdemo sample.
• Online Help under Master Task List, LC Startup and TOF optimization and
calibration.

1 Prepare the 2 Set up

Start LC modules parameters
here! display
(actuals)

3 Set up DAD
Prepare the real-time
instrument plot displays
(optional)

5 View and
4 Prepare the
work with
TOF
the system
logbook

10 Agilent 6210 TOF LC/MS System Quick Start Guide

 Prepare LC modules

Switch LC stream to Waste

While you purge the LC pump and condition or equilibrate the column, you can
tune and calibrate the TOF. During this time you do not want effluent streaming
into the TOF.
If you specify that the LC stream goes to Waste and not to the TOF, the stream
passes through the DAD. You can then monitor the fluctuations of the DAD
real-time chromatogram and spectra before a run.
1 Click the Method pane icon to view the Method pane.

Figure 3 Data tab of the MS-TOF tab in the Method pane

2 Click the MS-TOF tab of the Method pane.

3 Click the Data tab within the MS-TOF tab.
4 Select Waste if not already selected.
5 Click Apply.

Agilent 6210 TOF LC/MS System Quick Start Guide 11

 Purge the LC pump

Purge the binary pump You purge the binary pump manually.

1 Right-click the
binary pump
status box in the
Instrument
Status pane.

2 Select Standby
in the shortcut
menu.

3 Turn the black valve on the front of the pump

counter-clockwise two turns.

4 Click the Bin

Pump tab in the
Method pane.

5 Enter a Flow of
5 ml/min, and
click Apply.

6 Select On in the
binary pump
shortcut menu.

7 After purging,
enter the flow 8 Close the black Purge for about 9 minutes to pass about
you use to valve. 45 mL or 3X the volume for the binary
equilibrate the pump.
column, and
click Apply.

12 Agilent 6210 TOF LC/MS System Quick Start Guide

 Purge the capillary or nano pump

1 Right-click
pump device in
the Instrument
Status pane to
bring up pump
device menu. 2 Select Purge to
bring up the Pump
Purge System
dialog box.

3 Start the purge

with this dialog
box and bring
up the
monitoring
dialog box.

4 Monitor the
purge with this
dialog box and
click Cancel
after the purge
is complete.

Agilent 6210 TOF LC/MS System Quick Start Guide 13

 Condition or equilibrate the column
After you purge the pump, you set up to condition or equilibrate the column.
• Enter and download LC parameters, OR open a conditioning method.
• Change any non-method control parameters, if necessary.
• Monitor the baseline and adjust the plot to make sure the column is equilibrated
and the baseline stable. (See “Set up to view real-time parameter values
(actuals)” on page 16 and “Set up DAD chromatographic and spectral displays
(optional)” on page 17.)

Enter and download LC parameters or open a conditioning method

1 Select Open from

the File menu to
open a method,
OR enter LC
parameters in the
Method pane.

2 Click Apply to
send the
parameters to the
LC.

You can also load a method using the Methods

selection box in the Combo bar.

14 Agilent 6210 TOF LC/MS System Quick Start Guide

 Change non-method control/configuration parameters, if necessary. With these
menus, you can set the time to automatically turn the module on or off, you can set
maximum values or you can configure the autosampler.

Right-click the LC
module in the
Instrument Status
pane to bring up
the control menu
for that module.

Agilent 6210 TOF LC/MS System Quick Start Guide 15

 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 pane.

1 Right-click the
Actuals box to
bring up Setup
item.

2 Click Setup to
bring up the tool
to select
instrument
actuals.

3 Select actuals
to set up to view
the actual
conditions in
the Instrument
Status pane.

16 Agilent 6210 TOF LC/MS System Quick Start Guide

 Set up DAD chromatographic and spectral displays (optional)
As you condition the column, you set up the displays to monitor the effluent.

Set up chromatographic display

1 Right-click the
signal plot to
bring up the
signal shortcut
menu.
2 Select Change to
bring up the tool
for selecting the The default display is of a TIC chromatogram.
signal and its plot
parameters.

3 Select a DAD
signal that you
intend to monitor,
and click Add.

4 Highlight a
Selected Signal.

5 Set the y and x

axis ranges, and
click OK.

The real-time plot

now displays the
DAD signal. (See
next page.)

Agilent 6210 TOF LC/MS System Quick Start Guide 17

Adjust the plot with
these arrows.

Set up spectral display

The default spectral display is a TOF line

spectrum above the chromatogram and a profile Profile spectrum
Line spectrum spectrum to the right of the chromatogram.

1 Right-click the
line or profile
spectral plot to
bring up the
spectra shortcut
menu.
2 If you clicked the
line spectral plot,
select the DAD
spectrum as the
spectrum to Or, if you right-clicked the
view. profile spectral plot, select
Line first, then select the
DAD spectrum.

18 Agilent 6210 TOF LC/MS System Quick Start Guide

 Prepare the TOF

Calibrate the TOF

You calibrate the TOF more frequently than you tune the TOF. Agilent
recommends that you do a 10 mass calibration. Make sure that you open the
method corresponding to your ion source before you calibrate or tune the TOF to
set default TOF acquisition parameters.
• ESIautotune.m for ESI
• nanoESIautotune.m for nanospray or dual nanospray
• APPIautotune.m for APPI
• APCIautotune.m for APCI
• MMIautotune.m for MMI
You cannot calibrate the TOF with a MALDI source installed.
If the method loaded does not match the current ion source, then a warning is
given.

Polarity Switching
If you are using Polarity Switching, you need to use a different autotune method.
For each source, there is a positive and a negative method for Polarity Switching.
The name of the autotune method has either “PolaritySWPos” or “PolaritySWNeg”
appended to it.
• ESIautotunePolaritySWPos.m for ESI
• ESIautotunePolaritySWNeg.m for ESI
• nanoESIautotunePolaritySWPos.m for nanospray or dual nanospray
• nanoESIautotunePolaritySWNeg.m for nanospray or dual nanospray
• APPIautotunePolaritySWPos.m for APPI
• APPIautotunePolaritySWNeg.m for APPI
• APCIautotunePolaritySWPos.m for APCI
• APCIautotunePolaritySWNeg.m for APCI
• MMIautotunePolaritySWPos.m for MMI
• MMIautotunePolaritySWNeg.m for MMI
You will need to perform four autotunes to correctly tune the TOF system when
using Polarity Switching. First, you need to tune in both positive and negative
modes. Then, you need to tune using the Polarity Switching methods in both
positive and negative modes.

Agilent 6210 TOF LC/MS System Quick Start Guide 19

 Check and do a tune

1 Click the MSTOF

tab in the
Method pane When you click Calibrate, the Click to use the default
and select ion valve to Calibration solution A coefficients for the
polarity. opens. calibration.

3 Click Calibrate if you 4 Click to make sure

have already chosen that the calibration is
2 Enter calibration the ten masses. satisfactory.
parameters.

5 If you want to
select a different
set of masses or
you want to use a
different
calibration
standard, click
Show Extended.

6 Select masses to
use for
calibration, OR
load another
mass list.

7 Then calibrate
again.

20 Agilent 6210 TOF LC/MS System Quick Start Guide

1 Click the Tune You do an initial autotune after repair or installation.
tab under the
MSTOF tab.

2 Check to see if
the TOF needs
tuning.
4 Or click Show
Extended to do a
3 Click Autotune manual tune on the
for a tune that parameters that need
takes 15-20 adjusting.
minutes or
Quicktune for a
tune that takes
1-3 minutes.

1 Select the
masses for the
ramp.

2 Select the
parameter to
vary.
3 Select the
variable to
optimize, and
click Ramp.

If you do a manual
tune, you must also
do a calibration.
Autotune and
Quicktune include
mass calibration
with one mass.
After you do a tune,
the optimized
parameters appear
in the Parameters
panel.

Agilent 6210 TOF LC/MS System Quick Start Guide 21

 Switch LC stream to MS
After you condition the column and calibrate and tune the TOF, you switch the LC
stream from Waste to MS.
1 Click the Method pane icon to view the Method pane.

Figure 4 Data tab of the MS-TOF tab in the Method pane

2 Click the MS-TOF tab of the Method pane.

3 Click the Data tab within the MS-TOF tab.
4 Select MS in the LC Stream (Seg.) section.
5 Click Apply.

Monitor TOF baseline and spectral displays

If you did not monitor the LC baseline with a DAD, skip this module. Make sure
that the TOF baseline is stable and no spectra of interfering intensity appear in the
display.
If you did monitor the LC baseline with a DAD, follow these steps.
1 Right-click the chromatogram display.
2 Select Change.
3 Highlight the TIC signal in the list of Selected Signals.
4 Set the x and y axis ranges.
5 Click OK.
6 Right-click the spectral displays.
7 Select TOF spectra >Line or Profile.
8 Monitor the baseline and spectra.

22 Agilent 6210 TOF LC/MS System Quick Start Guide

 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.

Select System
OR, click the Log Select Columns
Logbook Viewer from
icon.
the Tools menu. Find

Filter Events

Click icon to find or

filter an event, or to
show or hide a
column.

Export the logbook to

print the logbook.

Agilent 6210 TOF LC/MS System Quick Start Guide 23

Step 3—Set up acquisition methods
Read and follow the steps in the user information listed below to learn how to set
up methods.
• The steps on the next pages that take you through the roadmap below.
• Chapter 3 of the Concepts Guide, Acquisition Methods, to learn background
information to help you set up methods.
• Exercise 2, Set up an Acquisition Method, in the Familiarization Guide
• Online Help for the tasks that correspond to the roadmap steps and the tasks
listed on the next pages.

Start 1 Enter LC 2 Select polarity

parameters and enter TOF
Here! parameters

3 Set up to
Set up change TOF
acquisition parameters
methods during run

6 Save and 5 Set up TOF 4 Enable

print the signals for the reference
acquisition real-time plot mass
method correction

24 Agilent 6210 TOF LC/MS System Quick Start Guide

 Enter LC parameter values

You can also enter

pre-run/
post-run scripts in
the Properties tab.

If you click Apply,

Enter LC parameters
the parameters are
in the LC module
sent to the
tabs. instrument but are
NOT saved to the
method.

Do not modify scripts provided by Agilent because these scripts may be

overwritten the next time you upgrade the Agilent software.

Enter TOF parameter values

1 Select ion
polarity.

2 Enter TOF
parameters in
the Data, and
Acquisition tabs.

You enter these values for the initial Right-click each field to All entries in the Tune,
time 0.0 min and the whole run and for find the maximum and Calibration and Parameters tabs
one scan, unless you add other time minimum values. are not saved with the method.
segments and scans. See the next page.

Agilent 6210 TOF LC/MS System Quick Start Guide 25

 Set up to change TOF parameters with segments and scans

1 For the initial

run time of 0.0
and 1 scan, enter
TOF values.

2 Enter the next

time for which
you want to
change
segment values
and click Add.

You can also change Note that Ion Polarity can Note the values you Note the values you
3 Add up to four scans values on the Data be changed for each time can change with can change with
for each time tab for each time segment. The label for that each time segment. each scan.
segment, including segment. section will be “Ion
the initial time. Polarity (Seg.)” if there are
4 For each scan, more than one time
change a value segments.
or values.

26 Agilent 6210 TOF LC/MS System Quick Start Guide

 Enable reference mass correction
You enable for mass correction during a run to obtain the specified mass accuracy.

Set up for mass correction

1 Enable
reference mass
correction.

2 Mark Bottle A
to use the
Agilent
reference std.

3 Set the auto

recalibration
parameters.
4 Mark the
masses that you
If the list is blank or you want a different If you want to create a new mass list or
want to use for
list for another standard, click the Select modify the existing default lists, click Edit
the correction.
Masses button. Mass Lists. See next page.

Agilent 6210 TOF LC/MS System Quick Start Guide 27

 Edit mass list

1 Select the
default mass
list for your ion
source and
polarity.

2 Enter a new
name into the
Name field.

3 Click Save As The Save As New List

New List. button appears when you
enter a new Name.

All the other grayed out

buttons appear when you
click Save As New List.

4 Add or delete
masses to the
new list.

5 Click Save List.

28 Agilent 6210 TOF LC/MS System Quick Start Guide

 Set up signals for the real-time plot

Select the signal

that you want to see
in the real-time
plot.

You can also select

different time
segments and scans
to monitor.

Save and print the method

Select Save in the

File menu to save
the currently
Or, click the Save icon for the method.
opened method, OR
select Save As in
the File menu to
save a new method.

Select Print >

Acquisition Method
in the File menu to
set up to print a
method.

Agilent 6210 TOF LC/MS System Quick Start Guide 29

Step 4—Acquire data
Read and follow the steps in the user information listed below to learn how to
acquire data.
• The steps on the next pages that take you through the roadmap below.
• Chapter 4 of the Concepts Guide, Data Acquisition, to learn background
information to help you acquire data.
• Chapters 3 and 4 of the Familiarization Guide
• Online Help for the tasks that correspond to the roadmap steps and the tasks
listed on the next pages.

1 Set up and 2 Set up and

Start run an run a
Here! interactive worklist
sample.

3 Print a
Acquire real-time
data plot report

5 Print a 4 Modify a
worklist worklist in
report progress

30 Agilent 6210 TOF LC/MS System Quick Start Guide

 Set up and run interactive samples

1 Open a method 6 Click this Start to

using the menu run interactive
item or the single samples.
Combo bar.
5 Select Acquisition
Only.

2 Click the Sample

tab in the Method
pane.

3 Enter the sample

name and custom
variables.

4 Select a project
and enter the data
file name.
You can only create projects in Even though Both Acquisition and DA is a selection
Analyst. See “Step 5—Analyze data” in the “Part of method to run” list, it is not available
on page 35. for single samples in this version of software.

Agilent 6210 TOF LC/MS System Quick Start Guide 31

 Set up and run worklists (e.g., empirical formula confirmation)

1 Right-click here to
bring up the worklist
shortcut menu.

2 Select Add Multiple

Samples to add a
series of samples to
the worklist.

3 Select Add
column(s) to add a
column for the You must select
empirical formula. default.anm to
produce an empirical
formula confirmation
4 Enter the generic report.
name (Formula_x)
and formula for an
EFC column.

You can also add

batches of samples
whose information and
data you may want to
keep together.
You can see an
example of the You can also select Show/Hide
resulting worklist on columns to hide unnecessary
the next page. columns.

32 Agilent 6210 TOF LC/MS System Quick Start Guide

This is an example of
the resulting
worklist.

Click this Start to

run a worklist.

If Track Worklist is
On (Worklist menu),
the row that is
running is
highlighted blue.

Print a real-time plot report

• To print a
real-time plot
report during the
run, select Print
> Real-Time Plot.

Agilent 6210 TOF LC/MS System Quick Start Guide 33

 Modify the worklist in progress

You can modify any

row below the row
located under the
running row (shaded
blue).
If the last selected
row is executing,
then all rows are
locked.

When you place the

cursor on the row to be
edited, tracking is
automatically turned
off. To turn tracking
back on, you must
check the worklist
menu item, Track
Worklist Run.

Print the worklist

Select Print >

Worklist to print the
worklist report.

34 Agilent 6210 TOF LC/MS System Quick Start Guide

Step 5—Analyze data
The primary tool for analyzing and reporting on results is PE-Sciex Analyst QS.
PE-Sciex has modified their software specifically to accommodate the Agilent TOF
system requirements.
Read and follow the steps in the user information listed below to learn how to
review TOF data and customize the data analysis method, default.anm, used to
confirm empirical formulas.
• The steps on the next pages that take you through the roadmap below.
• Chapter 5 of the Concepts Guide, Data Analysis, to learn background
information to help you analyze data.
• Chapters 3 and 4 of the Familiarization Guide
• Online Help for the tasks that correspond to the roadmap steps and the tasks
listed on the next pages.
• Consult the PE-Sciex Analyst User’s Guide and online help to learn how to
perform other analysis operations not associated with the Agilent system.

Start 1 Start software 2 Review

and open data signals/
Here! file chromatograms

3 Review
Analyze spectra and
data sample
information

4 Set up and
5 Customize the generate a
data analysis
parameter
method,
optimization
default.anm
report

Agilent 6210 TOF LC/MS System Quick Start Guide 35

 Start the Analyst QS software and open a data file

1 Double-click the
Analyst QS icon
in the Agilent TOF
Software group
window.

2 Select the project

that contains the
data file.

3 Click to open .wiff

files.

36 Agilent 6210 TOF LC/MS System Quick Start Guide

 Review signals/chromatograms

1 Right-click on
chromatogram to See the next page to learn about
bring up the spectral operations with Analyst.
shortcut menu.

2 Do any of the • Drag the cursor across a

bulleted tasks on peak and select Show
this page in any Spectrum from the shortcut
order that you menu to see the mass
want. spectra in the peak

• Select List Data

from the shortcut • To zoom into a
menu to see the peak, draw a
results of rectangle under
integration. the peak
baseline.

• Select Script > Agilent Peak • Select Extract Ion from

Finder Parameters.dll to the shortcut menu to
change integration produce an XIC (EIC)
parameters. chromatogram.

Method Setpoints by default are saved with the

data file. Use the tool TOFSystemConfig to change
whether Method Setpoints are saved. See the
installation guide for more information.

Agilent 6210 TOF LC/MS System Quick Start Guide 37

 Review spectra and sample information

1 Right-click on
spectrum to bring
up the shortcut
menu.

• Select View
Actuals from the
shortcut menu to
see the real-time
TOF parameter
values.

• Select
Re-Calibrate TOF
to recalibrate the
TOF from Analyst.

• Click the sample

information icon
in the Analyst
toolbar to view
method and
sample
information on
the data file.

38 Agilent 6210 TOF LC/MS System Quick Start Guide

 Set up and generate a parameter optimization report

1 Select Script >

Parameter
Optimization.dll
in the Analyst
main window.

2 Select the
samples for
the report.

3 Continue
through the
wizard, then
click Finish.

Agilent 6210 TOF LC/MS System Quick Start Guide 39

 Customize the data analysis method for empirical formula confirmation

1 Click the Data Analysis

Editor icon in the TOF
Software program
folder.
2 Click the Formula
Confirmation tab in the
Data Analysis Method
Editor window.
3 Enter values in the
Formula Confirmation
tabs to modify the
default.anm method. Enter
values in the Report
Options tab to select
which of the graphs to
include. Enter values in
the Screening tab to
enable the database
search.

4 Save the method.

5 Regenerate the report by
rerunning the worklist in
Data Analysis Only mode.

The EFC report can now also include a backward database search
(called an EFC Database Screening Report). Based upon a formula, a
mass is determined and then XICs are extracted for that mass to see
if the compound can be found. You can limit the search of the
database to formulas with a certain retention time tolerance. A value
of -1 in the Retention time tolerance field indicates to not limit the
search based upon retention time.

40 Agilent 6210 TOF LC/MS System Quick Start Guide

 Create a data analysis method for Mass List Report

1 Click the Data Analysis

Editor icon in the
Agilent TOF Software
program folder.
2 Select Select DA
Operations menu item
from the Edit menu in the
Data Analysis Method
Editor window.
3 Click Mass List in the
Available Operations list
and click the Add button.
If any other option
appears in the Selected
Operations list, click on it
and click the Remove
button.
4 Click OK to close the
Select DA Operations
dialog box.
5 Select the Report Type
“Mass list report only”.
6 Enter values in the Mass
List tabs to modify the
method.
7 Save the method with a
new name, using the
File>Save As menu item.
8 To generate a mass list
report, create a worklist
that specifies the data
analysis method created
in the steps above. The
report will be generated
for each sample when you
run the worklist.

Agilent 6210 TOF LC/MS System Quick Start Guide 41

 Create a DA method for Mass List Report type Empirical Formula Generation

1 Click the Data Analysis

Editor icon in the
Agilent TOF Software
program folder.
2 Select Select DA
Operations menu item
from the Edit menu in the
Data Analysis Method
Editor window.
3 Click Mass List in the
Available Operations list
and click the Add button.
If any other option
appears in the Selected
Operations list, click on it
and click the Remove
button.
4 Click OK to close the
Select DA Operations
dialog box.
5 Select the Report Type
“Include generation of
empirical formulae”.
6 Enter values in the Mass
List tabs to modify the
method including the
“Formula Generation”
tab.
7 Save the method with a
new name, using the
File>Save As menu item.
8 To generate a mass list
report, create a worklist
that specifies the data
analysis method created
The Mass List Report including Empirical Formula
in the steps above. The
Generation identifies valid molecular formulas that
report will be generated
for each sample when you
match the masses found in your sample based upon
run the worklist. the values entered in this tab.

42 Agilent 6210 TOF LC/MS System Quick Start Guide

 Create a DA method for Mass List Report type Confirmation Screening
1 Click the Data Analysis
Editor icon in the
Agilent TOF Software
program folder.
2 Select Select DA
Operations item from the
Edit menu in the Data
Analysis Method Editor
window.
3 Click Mass List in the
Available Operations list
and click the Add button.
If any other option
appears in the Selected
Operations list, click on it
and click the Remove
button.
4 Click OK to close the
Select DA Operations
dialog box.
5 Select the Report Type
“Include confirmation
screening by database
search”.
6 Enter values in the Mass
List tabs to modify the
method including the
“Confirmation Screening”
tab.
7 Save the method with a
new name, using the
File>Save As menu item.
8 To generate a mass list
report, create a worklist
that specifies the data
analysis method created The Mass List Report including Confirmation Screening is a
in the steps above. The forward screening report. After determining the mass, the
report will be generated database is searched for formulas with the corresponding
for each sample when you mass.
run the worklist.

Agilent 6210 TOF LC/MS System Quick Start Guide 43

 Create a DA method for Molecular Features Extraction report
1 Click the Data Analysis
Editor icon in the
Agilent TOF Software
program folder.
2 Select Select DA
Operations item from the
Edit menu in the Data
Analysis Method Editor
window.
3 Click Molecular Features
Extraction in the
Available Operations list
and click the Add button.
If any other option
appears in the Selected
Operations list, click on it
and click the Remove
button.
4 Click OK to close the
Select DA Operations
dialog box.
5 Select the Report Type
“Molecular Feature
Extraction only”.
6 Enter values in the
Molecular Feature
Extraction tabs to modify
the method.
7 Save the method with a
new name, using the
File>Save As menu item.
8 To generate a molecular
feature extraction report,
create a worklist that
specifies the data
analysis method created The Molecular Feature Extraction Report lists out masses of
in the steps above. The chemical compounds and a list of isotopes of a compound
report will be generated found in the sample. The MFE report shows isotopes in the
for each sample when you form of multiple isotope cluster based on adducts used in the
run the worklist. ionization.

44 Agilent 6210 TOF LC/MS System Quick Start Guide

 Create a DA method for MFE Report including Confirmation Screening
1 Click the Data Analysis
Editor icon in the
Agilent TOF Software
program folder.
2 Select Select DA
Operations item from the
Edit menu in the Data
Analysis Method Editor
window.
3 Click Molecular Feature
Extraction in the
Available Operations list
and click the Add button.
If any other option
appears in the Selected
Operations list, click on it
and click the Remove
button.
4 Click OK to close the
Select DA Operations
dialog box.
5 Select the Report Type
“Include confirmation
screening by database
search”.
6 Enter values in the MFE
tabs to modify the method
including the
“Confirmation Screening”
tab.
7 Save the method with a
new name, using the
File>Save As menu item.
8 To generate a mass list
report, create a worklist
that specifies the data The Molecular Feature Extraction Report including
analysis method created Confirmation Screening is a forward screening report. After
in the steps above. The determining the mass, the database is searched for formulas
report will be generated with the corresponding mass.
for each sample when you
run the worklist.

Agilent 6210 TOF LC/MS System Quick Start Guide 45

46 Agilent 6210 TOF LC/MS System Quick Start Guide
Agilent 6210 TOF LC/MS System Quick Start Guide 47
www.agilent.com

In this book
This book contains brief
instructions to help you get
started with your Agilent 6210
Time-of-Flight TOF LC/MS
system. This books shows you
how to:
• Prepare the instrument for a
run
• Set up acquisition methods
• Set up and run an
interactive sample and
worklists
• Review data
To submit comments about this
guide, send an e-mail to
[email protected].

© Agilent Technologies, Inc. 2003 - 2007

Printed in USA
Fifth Edition, March 2007

*G3300-90016*
G3300-90016

Agilent Technologies