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