Agilent Technologies 1100 Series Manuel utilisateur

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,

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,

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

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