Agilent Technologies 1100 Series User manual

Agilent Technologies
Agilent 1100 Series LC/MSD Trap
System Quick Start Guide
A guide to help you get started with the
LC/MSD Trap system
What is the Agilent 1100 Series LC/MSD Trap System? 2
Where to find additional system information 3
What is new in version 5.2 software? 4
Instructional overview 6
Step 1—Start the software 7
Step 1a—Become familiar with the software 10
Step 2—Prepare the instrument 21
Step 3—Set up and run an acquisition method 22
Step 4—Review data and identify compounds 28
Optional steps 34
Deconvolute and search protein spectra 34
Quantify compounds 35
Shut down or place the instrument in Standby 36
Agilent methods, data files and report layouts 38
Use this document to find help to install and troubleshoot
system hardware, to install the system software and to acquire
and analyze data with the LC/MSD Trap.

2 Agilent 1100 Series LC/MSD Trap System Quick Start Guide
What is the Agilent 1100 Series LC/MSD Trap System?
The LC/MSD Trap system consists of the Agilent 1100 Series LC, an atmospheric
pressure ion source and the MSD Trap mass spectrometer, which can be one of
several models: Classic, VL, SL, or XCT.
The LC/MSD Trap software controls the instrument and provides the tools to
acquire and analyze LC/MS data. The software consists of components to help you
with the following tasks:
•ChemStation A.10.02—LC control, LC method development and sequence setup
and execution
•MSD Trap Control 5.2—Trap control, MS method development, acquisition
monitoring
•DataAnalysis 3.2—compound-based data-mining and -browsing, search and
identification (LibraryEditor 3.2), report design (ReportDesigner 4.2) and
generation, analysis automation through Visual Basic Scripting
•QuantAnalysis 1.6—quantitation
You can also obtain licenses to add on or use the software below:
•G1981AA Deconvolution and Bioanalysis Software —
deconvolution of protein and peptide spectra and evaluation of MS and MS/MS
data from proteins and peptides
•G3310AA Security Pack 1.0—Help for compliance with 21 CFR Part 11
regulations, including user management, audit trail, access control, electronic
signatures and results revisioning
•G3311AA VL Upgrade Software — upgrade to MS(n) capabilities previously
available only on the SL and XCT products
To get started with any of the add-on software packages described above, see its
Quick Start Guide.

Agilent 1100 Series LC/MSD Trap System Quick Start Guide 3
Where to find additional system information
System information (hardware and software)
Printed
documents
Printed documents are also available on the CDs as files in Portable Document
Format (PDF).
System Installation Guide Guides you through hardware and software
installation, configuring the instrument, and verifying performance, if your
Agilent representative has not already done this.
System Concepts Guide Contains background information to help you
understand the hardware and software and how they work together.
System Quick Reference Guide Describes reasonable starting parameter values
to control the LC/MSD Trap hardware for all modes of operation. You obtain the
best performance by optimizing these settings.
Training Courses Visit www.chem.agilent.com to view a list of training courses for the Agilent
LC/MSD Trap system.
Hardware information
User’s Guide Describes the basic operation and maintenance of the MSD Trap
hardware.
Software information
Online help Use online help for in-depth information not given in this Quick Start Guide.
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 Help Topics, which includes task help,
reference help and manuals online.
Printed
documents
Software Familiarization Guide Provides exercises to help you learn all parts of
the LC/MSD Trap software. Use this guide if a training lab is not available.
Backup and Recovery Guide Presents instructions to back up and recover the PC,
including OS and application software, if there is a problem. Included with new
system bundles; also available on the CD as a PDF file.

4 Agilent 1100 Series LC/MSD Trap System Quick Start Guide
What is new in version 5.2 software?
New for overall software package
Data and methods
from previous
versions are
compatible with
5.2 software.
•Capacity to add on Security Pack 1.0 software for 21 CFR Part 11 compliance
•Supported on Windows 2000 SP4 and Windows XP SP1a only.
•Improved method structure for LC/MS systems including SOPs for LC, MS, and
processing parts of methods.
•SW Installation Qualification (IQ) report as text file.
New for individual programs with compliance software
ChemStation, Trap Control, DataAnalysis, QuantAnalysis
•Limited authorized access and authority checks
•User permissions and user roles
•Password policy
•Audit trails that track all operations for the system, method and sequence
setup, and analyses
•Audit trails that are time-stamped, secure, user-independent, readable,
automated and computer-generated
•Menu item ‘session locking’
•Menu item ‘User logon’ (to change user)
DataAnalysis, QuantAnalysis only
•Storage of multiple versions of electronic records (raw data, results, meta data,
etc.) with result revisioning
•Electronic signatures for results
•Reports with a listing of e-signatures and QuantAnalysis audit trail
New for individual programs with or without compliance software
LC/CE/Sequence control with ChemStation A.10.02
•Capacity to store methods in any location (recommended to use subdirectories
in the default method root)

Agilent 1100 Series LC/MSD Trap System Quick Start Guide 5
Trap control/data acquisition
•New isolation parameters
•New fragmentation parameters to eliminate isotopic discrimination effects
•New "Standby" mode (orange) to allow shutdown of the MSD Trap Control
software while maintaining MS in “Standby” state
DataAnalysis
Data files
acquired with the
5.2 software
cannot be
processed using
previous versions
of the software.
•Alternating polarity analyses to find compounds with spectra of both polarities.
Applies to Find Compounds - AutoMS(n), - Chromatogram, - Dissect.
•Subtraction of 2D spectral background to view chromatograms and spectra and
to calculate compound mass spectra.
•Charge deconvolution on line spectra and export of results to XML and MGF
•Time range argument for Find Compounds - AutoMS(n) and Find Compounds -
Dissect automation commands
•Ability to exclude MS/MS spectra for Find compounds - AutoMS(n) if they do
not exhibit characteristic mass differences (e.g., for amino acids)
•Improved Neutral Loss Chromatogram (capability to specify multiple losses;
also available with automation)
•Creation of “pseudo” Neutral Loss Spectra, where all mass signals in a MS/MS
spectrum are labeled as mass differences relative to the precursor ion
•Improved handling of Agilent data file format export (scaling, option to export
line or profile data in manual and automatic fashion)
•Manual deconvolution with Charge State Ruler
•Compound List Filter to enable/disable compounds based on Library Search or
Intensity Criteria
•Building Block Editor for automatic annotation of amino acids and nucleic
acids via ‘Difference Ruler’
•Improved Find Compounds - AutoMS(n) algorithm (limits algorithm to find the
x most intense compounds)
•Improved monoisotopic peak determination of precursor
•Library Search: Inclusion of the measured mass range with the spectrum
properties.
QuantAnalysis
•Improved weighted calibration

6 Agilent 1100 Series LC/MSD Trap System Quick Start Guide
Instructional overview
1Install the Trap System hardware
Use the instructions in the Agilent 1100 Series LC/MSD Trap System Installation
Guide to install the hardware.
2Install the Trap System software
Use the instructions in the Agilent 1100 Series LC/MSD Trap System Installation
Guide to install all the software components.
3Set 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.
Start
Here!
Set up and
run samples
3Set up and
run an
acquisition
method
1Start and
become
familiar with
the software
2Prepare the
instrument
4Review data
and find
compounds
(optional)
Deconvolute and
search protein
spectra
(optional)
Quantify
compounds
(optional) Shut
down or place
the instrument
in standby

Agilent 1100 Series LC/MSD Trap System Quick Start Guide 7
Step 1—Start the software
The instructions below include the following assumptions:
•The hardware and software are properly installed.
•The instrument is configured. Use instructions in the Agilent 1100 Series
LC/MSD Trap System Installation Guide to configure the instrument for the
first time.
To start the Trap software with the Security software installed, see the G3310AA
LC/MSD Trap Security Pack 1.0 Quick Start Guide.
Start the Trap software on an LC/MSD Trap Control PC
For an online installation, the desktop displays the following icons.
Start the Trap software
•Double-click the Instrument 1 Online icon.
This automatically opens ChemStation, MSD Trap Control and DataAnalysis in
that order.
You open the QuantAnalysis and ScriptStarter programs separately.
ChemStation Controls LC, lets you save and load LC/MS acquisition methods and lets you set up
and run sequences
MSD Trap Control Controls MSD Trap and lets you set up MS part of method
Data Analysis Lets you review qualitative data and search unknowns
QuantAnalysis Lets you set up calibration curves and quantify compounds
ScriptStarter Runs automated data processing for large sequences of data files, normally stored
in the same directory. Automation is possible because a DataAnalysis method,
containing a script, is initially stored with an acquisition method and then
transferred to the data file acquired by the acquisition method. See Chapter 3,
“How LC/MSD Trap Methods Work”, in the Concepts Guide for more information
on how methods are organized.
DataAnalysis ScriptStarter QuantAnalysis Trap Control Instrument 1 Online

8 Agilent 1100 Series LC/MSD Trap System Quick Start Guide
Switch between ChemStation, MSD Trap Control and DataAnalysis
You can switch between all three programs from the Windows taskbar. Refer to the
table below for instructions on how to switch to a program from within another
program.
Table 1 Switch between ChemStation, MSD Trap Control and DataAnalysis
If you want to switch
to this program:
From within this
program:
Do this:
MSD Trap Control ChemStation •Select Method > Edit MS Method
Part..., or
•Click the Trap Control
button, or
•Click the MS^n icon, and
select Settings.
DataAnalysis •Select Tools > ChemStation, or
•Click the Trap Control button
in DataAnalysis.
DataAnalysis ChemStation •Click the DataAnalysis
button in ChemStation.
MSD Trap Control •Click the DataAnalysis
button in MSD Trap Control.
ChemStation MSD Trap Control •Click the ChemStation
button in MSD Trap Control.
DataAnalysis •Select Tools > ChemStation, or
•Click the ChemStation
button in DataAnalysis.

Agilent 1100 Series LC/MSD Trap System Quick Start Guide 9
Start the Trap software for an offline installation
You use an offline installation, or standalone system, to analyze data. Therefore,
the ChemStation or MSD Trap Control programs are not installed.
For an offline installation the desktop displays the following icons.
•Double-click any button to start the program of choice.
Open the LibraryEditor or ReportDesigner programs
Included with the DataAnalysis software, for both online and offline installations,
are the LibraryEditor and ReportDesigner programs.
Open the LibraryEditor program
The LibraryEditor program lets you create spectral databases and search mass
spectra of unknown compounds against those databases.
•Select Start > Programs > LCMSD Trap > LibraryEditor,
or
1Open DataAnalysis.
2Click the LibraryEditor button.
Open the ReportDesigner program
The ReportDesigner program lets you create your own report layouts or modify the
existing ones.
•Select Start > Programs > LCMSD Trap > ReportDesigner,
or
1Open DataAnalysis.
2Select Print..., or Print Preview..., > ReportDesigner....
DataAnalysis ScriptStarter QuantAnalysis

10 Agilent 1100 Series LC/MSD Trap System Quick Start Guide
Step 1a—Become familiar with the software
ChemStation window
The ChemStation window is the first window that appears when you start an
online system for instrument control. You use the ChemStation software to
develop the LC part of LC-only or LC/MS methods, set up information for single
runs or sequences and acquire data. See the Agilent ChemStation document set
and ChemStation Online Help to familiarize yourself with this software.
Figure 1 ChemStation window

Agilent 1100 Series LC/MSD Trap System Quick Start Guide 11
MSD Trap Control window
The initial (default) MSD Trap Control window contains three panes, three areas
for acquisition parameter entry, and menus and a toolbar to set up and run MS
acquisition. (Figure 2).
Top Menu
Toolbar
Display Panes
Status Modes
Figure 2 Initial MSD Trap Control window
Line spectra displayed here
Profile spectra displayed here
Chromatograms displayed here
Tabs General Trap Parameters
Acquisition Method Editor

12 Agilent 1100 Series LC/MSD Trap System Quick Start Guide
Toolbar and Top Menu
The toolbar contains buttons that help you set up and run MS data acquisition.
Many of the actions accessed through the Top Menu and the toolbar are the same.
For menus and menu items not listed below, please refer to the Online Help.
Table 2 Actions that you can do through the MSD Trap Control toolbar and top menu
If you intend to do this: Click this toolbar button or select this
menu item from the top menu:
Additional information
Create a new MS method Method > New - MSD Trap
Control Method Part (Ctrl+N)
•Loads Def_MS.M
Open an existing MS method Method > Load - MSD Trap
Control Method Part (Ctrl+O)
Save the MS method Method > Save - MSD Trap
Control Method Part (Ctrl+S)
Start the acquisition Acquisition > Run Method (F5) •Acquires the data in the way
prescribed by the method that is
currently loaded.
•Note that when you are using MSD
Trap Control to acquire MS-only
data, Run Method acquires to the
file and directory specified by
Sample Info in the tab. If the MS
acquisition is part of an LC/MS
method run from ChemStation,
then the file name and directory
locations are prescribed in
ChemStation’s Sample Info.
Stop the acquisition Acquisition > Stop Run (F8)
Pause the acquisition Acquisition > Pause (Ctrl + F8)

Agilent 1100 Series LC/MSD Trap System Quick Start Guide 13
Continue the acquisition (after a
pause)
Acquisition > Continue (Ctrl+F5)
Save a single profile spectrum Acquisition > Save Profile Now
(F7)
•Acquires a single data point as
a Profile spectrum to a data file.
•The name of this data file and its
location are prescribed in the
Sample Info tab.
Zoom in View > Zoom in (F9) Lets you draw a rectangle with the
mouse around the area to zoom.
Select the mass with the maximum
abundance to the left of the mouse
cursor position.
View > Maximum Cursor (F10) Click this button, position the cursor
and click the mouse button to do this.
Show peak width in Profile spectrum View > Show peak width in
Profile Spectra (Ctrl+W)
Change the arrangement of the
graphics windows (panes). The first
arrangement is the default partition.
Use arrangement #5 for AutoMS(n)
acquisition to see the MS spectra
above and the MS/MS spectra in the
middle. Drag the border of the chroma-
togram upward to see the middle.
View > Arrange Spectrum Windows > 1-5
Maximize the active spectrum
window
View > Maximize Spectrum
Window
Tile the spectrum windows View > Tile Spectrum Windows
Show the LC program View > LC Program (Shift+F11)
Show DataAnalysis Program View > DataAnalysis (F11)
About MSD Trap Control Help > About...
If you intend to do this: Click this toolbar button or select this
menu item from the top menu:
Additional information

14 Agilent 1100 Series LC/MSD Trap System Quick Start Guide
Display panes
Line and Profile spectral panes Line spectra do not show peak widths because all
of the Profile peak intensities within a range determined by the Line spectrum
algorithm have been summed and grouped into a single Line spectrum peak.
•To compare Line and Profile spectra:
aClear the right-hand check boxes in the lower left corner of each spectral pane.
bTo adjust the frame border move the cursor to the edge and click and drag the
border until your screen appears as in Figure 3.
Lock all applications Help > Lock all Applications
(Ctrl+Alt+K)
•Available only after installation of
the LC/MSD Trap Security Pack
Print or preview the chromatogram
and spectrum panes
File > Print
File > Print Preview
Open an Analysis file and the method
from this file
File > Open Analysis File
(Ctrl+D)
If you intend to do this: Click this toolbar button or select this
menu item from the top menu:
Additional information
Figure 3 Comparison of a Line spectrum and Profile spectrum

Agilent 1100 Series LC/MSD Trap System Quick Start Guide 15
•To return to the normal view:
•Mark the right-hand check box at the lower left.
•To change the window axis range in the Profile spectrum view:
aMove the cursor over the axis until it changes into a bidirectional arrow
bClick and drag the axis to change the span of the range, or right-click and drag
the range to change the sensitivity of the span.
You cannot change the offset in the Line spectrum view.
•To enlarge different parts of the window:
•Click the Zoom-in button and draw a box around the area of interest.
Shortcut menus If you right-click a display pane, you can access shortcut
menus. These menus let you change the display properties of each display pane
and provide other useful features . The specific content of the line spectrum menus
depends upon the tab that is open. The content is the same for all the tabs except
for the MS(n) view and the Chromatogram view.
Acquisition Method Editor: Tabs
The MSD Trap Control window includes seven tabs that contain parameter fields
to control and monitor operation of the Trap during acquisition. To download
parameters to the Trap after you make changes, you click Apply.
Mode The Mode tab lets you select from three sets of parameters.
•Save Spectra—This feature lets you specify if and what data are acquired.
•Scan Mode—You can set the speed and resolution of a scan by selecting from
different scan modes. These selections are the scan modes available for your
particular instrument model (XCT, SL, VL or Classic).
•Divert Valve—When you are running an LC/MS method that elutes large
quantities of compounds that are not of interest, you may not want to acquire
MS data on them nor admit them into the ion source, which increases the
frequency of cleaning. Using the time segment feature of the software, you may
direct these compounds To Waste (as long as the LC is connected to the ion
source through the divert valve). Also, you may turn off the Save Spectra
feature in this tab for this segment, which saves disk space. See “Exercise
3.Change and run method to optimize peak height” on page 45 of the
Familiarization Guide to learn how to set up segments.

16 Agilent 1100 Series LC/MSD Trap System Quick Start Guide
Tune Tune tab provides two sets of parameters under the Smart Parameter Setting
(SPS) and the Expert Parameter Setting (EPS).
•Smart Parameter Setting—These settings let you control the ion optics and trap
accumulation as well as all supported sources. The default settings provide an
optimum signal for the positive ions of the ESI Tuning Mix (G2431A).
•Expert Parameter Setting—Because adjustments made to the Smart Parameter
Settings automatically adjust the Expert Parameter Settings, we recommend
that you complete most signal optimization procedures in the Smart view.
Optimize Use this tab to change values of the ion optics, trap drive or fragmentation voltage,
and mass product ion cutoff. For optimization beyond the SPS parameters, refer to
information on this view in the System Quick Reference Guide.
MS(n) This tab lets you enter parameters to isolate and fragment precursor ion(s), where
the number of MS levels (n) varies depending on the Trap model. AutoMS(n)
performs multiple iterations of MS/MS on a defined number of precursor ions
using generic parameters. ManualMS(n) lets you enter parameters for each
product ion. MRM (Multiple Reaction Monitoring) isolates and fragments multiple
precursor ions through one or two iterations.
Sample Info Enter information on the sample that you intend to run.
Chromatogram Use the Chromatogram tab to enter the information to monitor traces in the
Chromatogram pane. You can also enter the chromatographic trace information
when you click a line spectrum peak with the mouse maximum cursor activated.
Calibration There are two types of calibration: Automatic and manual. Automated lets you
execute algorithms to complete Scan (MS-only), Isolation, or Fragmentation
calibrations. To manually perform each calibration, you select a radio button.
Acquisition Method Editor: General Trap Parameters
Ion Charge Control (ICC) The ICC Target (or Smart Target for XCT) controls the
number of ions stored in the trap on a scan-to-scan basis. If too many ions are
stored in the trap, they interfere with each other's motions and are ejected from
the trap at the wrong instant during the scan. This results in a slight degradation
of mass assignment and resolution. Suggested values for the ICC Target are
provided with the default methods (e.g., DEF_LCMS.M).

Agilent 1100 Series LC/MSD Trap System Quick Start Guide 17
Figure 4 General MS parameters
Averages In general, the system averages and stores several scans together as
a single spectrum at a designated retention time. The number of scans is
controlled by Averages (field containing “5” in Figure 4). You can increase the
number of scans to obtain cleaner-looking spectra and an improved signal-to-noise
ratio. However, doing so reduces the number of data points (spectra) across the
chromatographic peak as the compound elutes. Usually, for quantitative analyses
the number of scans is chosen to yield 8-10 data points across the peak. For
qualitative analyses, you use fewer data points (a higher number for Averages).
Rolling Averaging Rolling Averaging is a different way of averaging. For example,
if Rolling Averaging is set to 2, all the scans in the previous spectrum and all the
scans in the current spectrum are combined, averaged, and stored as a single
spectrum at a designated retention time. This action improves the spectral quality
at the expense of chromatographic fidelity. Peaks appear skewed (rapid rise
followed by a longer tailing edge). Disable this feature for quantitative work.

18 Agilent 1100 Series LC/MSD Trap System Quick Start Guide
Status Modes
MSD Trap Control displays the current system status on the left side of the
window below the spectral panes.
Operate status
Green
•Ion trap is scanning and source gas settings are turned on.
Operate status
Blue
•Ion trap is scanning, source gas settings are turned on, and MS data
acquisition begins.
Standby status
Yello w
Standby status
Orange
•Yellow—Method Standby—Source gas settings are
still turned on, based on current method settings, but
the voltage to all ion optics is turned off. The ion trap
RF voltage is still on, but scanning is not in progress.
•Orange—Instrument Standby—Same as Standby
Yellow except that the gas settings are those you set
yourself for Standby mode, and settings are stored in the instrument so that
you can shut down the software without cooling the MS down.
Shutdown status
[You must shut
down the Trap
before you are able
to switch the ion
sources.]
•Source gas settings are switched off, and there is no
voltage to the ion optics and no scanning of the ion
trap. The Divert Valve is switched To Waste.

Agilent 1100 Series LC/MSD Trap System Quick Start Guide 19
DataAnalysis window
With the DataAnalysis window, you work with the raw data that you acquired with
acquisition methods set up through the ChemStation and MSD Trap Control
windows. In DataAnalysis, you can extract chromatograms, find unknown
compounds, extract averaged compound mass spectra, deconvolute mass spectra
and print reports.
Figure 5 DataAnalysis window
See “Step 1—Start the software” on page 7 to learn how to open this window.
See “Step 4—Review data and identify compounds” on page 28 and “Deconvolute
and search protein spectra” on page 34 for more information on how to to use this
window.

20 Agilent 1100 Series LC/MSD Trap System Quick Start Guide
QuantAnalysis window
For most of your analyses you probably want to review spectra and search
unknowns. You do this through the DataAnalysis window. If you intend to set up a
calibration curve and quantitate target compounds of interest, you start
QuantAnalysis and use the window shown below.
Figure 6 QuantAnalysis window
See “Step 1—Start the software” on page 7 to learn how to open this window.
See “Quantify compounds” on page 35 for more information on how to use this
window.