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  • Agilent InfinityLab LC/MSD Series and 6100 Series LC/MS

    Concepts Guide

  • Agilent InfinityLab LC/MSD Series and 6100 Series LC/MS Concepts

    Notices © Agilent Technologies, Inc. 2017 No part of this manual may be reproduced in any form or by any means (including electronic storage and retrieval or transla- tion into a foreign language) without prior agreement and written consent from Agi- lent Technologies, Inc. as governed by United States and international copyright laws.

    Manual Part Number G1960-90104

    Edition Revision A, May 2017 Agilent Technologies, Inc. 5301 Stevens Creek Blvd. Santa Clara, CA 95051

    Warranty The material contained in this docu- ment is provided “as is,” and is sub- ject to being changed, without notice, in future editions. Further, to the max- imum extent permitted by applicable law, Agilent disclaims all warranties, either express or implied, with regard to this manual and any information contained herein, including but not limited to the implied warranties of merchantability and fitness for a par- ticular purpose. Agilent shall not be liable for errors or for incidental or consequential damages in connection with the furnishing, use, or perfor- mance of this document or of any information contained herein. Should Agilent and the user have a separate written agreement with warranty terms covering the material in this document that conflict with these terms, the warranty terms in the sep- arate agreement shall control.

    Technology Licenses The hardware and/or software described in this document are furnished under a license and may be used or copied only in accordance with the terms of such license.

    Restricted Rights Legend U.S. Government Restricted Rights. Soft- ware and technical data rights granted to the federal government include only those rights customarily provided to end user cus- tomers. Agilent provides this customary commercial license in Software and techni- cal data pursuant to FAR 12.211 (Technical Data) and 12.212 (Computer Software) and, for the Department of Defense, DFARS 252.227-7015 (Technical Data - Commercial Items) and DFARS 227.7202-3 (Rights in Commercial Computer Software or Com- puter Software Documentation).

    Safety Notices

    CAUTION A CAUTION notice denotes a haz- ard. It calls attention to an operat- ing procedure, practice, or the like that, if not correctly performed or adhered to, could result in damage to the product or loss of important data. Do not proceed beyond a CAUTION notice until the indi- cated conditions are fully under- stood and met.

    WARNING A WARNING notice denotes a hazard. It calls attention to an operating procedure, practice, or the like that, if not correctly per- formed or adhered to, could result in personal injury or death. Do not proceed beyond a WARNING notice until the indicated condi- tions are fully understood and met.

    Software Revision This guide is valid for the C.01.07 SR3 or later revision of the Agilent OpenLAB CDS ChemStation Edition software for the Infini- tyLab LC/MSD Series and 6100 Series LC/MS until superseded.

  • Agilent InfinityLab LC/MSD Series and 6100 Series LC/MS Concepts Guide 3

    In This Guide... The Concepts Guide presents an overview of the InfinityLab LC/MSD Series and 6100 Series LC/MS mass selective detector, to help you understand how the hardware and software work.

    1 Overview of Hardware and Software Learn how the hardware works in the InfinityLab LC/MSD Series and 6100 Series LC/MS instrument, and get a brief introduction to the OpenLAB CDS ChemStation Edition program.

    2 Instrument Preparation Learn the concepts you need to prepare the LC and column for an analysis, and to tune the MS.

    3 Data Acquisition Learn about setting up methods and running samples.

    4 Data Analysis Learn the concepts you need for qualitative and quantitative data analysis with the ChemStation Edition program.

    5 Reports Learn about predefined results reports and about setting up custom reports.

    6 Verification of Performance Learn the concepts for Operational Qualification/ Performance Verification (OQ/PV) and system verification with the ChemStation Edition program.

    7 Maintenance and Troubleshooting Learn about tools that are proved in the ChemStation Edition program to help you maintain your system and diagnose and fix problems.

  • 4 Agilent InfinityLab LC/MSD Series and 6100 Series LC/MS Concepts

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  • Content

    1 Overview of Hardware and Software 9

    How the Agilent mass selective detectors work 10 Overview 10 Details 11

    Types of data you can acquire 15 Scan versus selected ion monitoring (SIM) 15 Generation of fragment ions: low versus high fragmentor 16 Positive versus negative ions 18 Multiple signal acquisition 19

    Ion sources 21 Electrospray ionization (ESI) 21 Agilent Jet Stream 25 Atmospheric pressure chemical ionization (APCI) 27 Atmospheric pressure photoionization (APPI) 29 Multimode ionization (MMI) 30

    Introduction to the ChemStation Edition program 31 Overview 31 Reviewing data remotely 33

    2 Instrument Preparation 35

    Preparation of the LC system 36 Purpose 36 Summary of procedures 36 Setting parameters for LC modules 38 Column conditioning and equilibration 39 Monitoring the stability of flow and pressure 41

    Preparation of the MS – tuning 42 Overview 42

    Agilent InfinityLab LC/MSD Series and 6100 Series LC/MS Concepts Guide 5

  • Contents

    Ways to tune 44 When to tune – Check Tune 45 Autotune 47 Manual tuning 49 Tune reports 51 Gain calibration 52

    3 Data Acquisition 55

    Working with methods 56 Method and Run Control View 56 Loading, editing, saving and printing methods 58 More on editing methods 59

    Running samples 62 Running a single sample 63 Running a sequence 64 Flow injection analysis 67

    Monitoring analyses 70 Online signal plots 70 Logbooks 71 Instrument shutdown 72

    4 Data Analysis 73

    The Data Analysis View 74

    Loading and manipulating chromatograms 76 Loading signals 77 Removing signals from the chromatogram display 81 Changing how chromatograms are displayed 81

    Working with spectra 83 Displaying spectra 84 Peak purity 85

    Performing quantification 86

    6 Agilent InfinityLab LC/MSD Series and 6100 Series LC/MS Concepts Guide

  • Contents

    Integrating peaks 86 Calibration 88

    Data review and sequence reprocessing 90 The Navigation Table 90 Batch review 91

    5 Reports 93

    Using predefined reports 94 Generating reports 94 Report styles 95

    Defining custom reports 96 Summary of process 96 Example report templates 96 The Report Layout View 97

    6 Verification of Performance 99

    The Verification (OQ/PV) View 100

    Instrument verification 101 Setting up and running instrument verification 102 Available OQ/PV tests 104 Verification logbook 105

    System verification 106 Overview 106 Setting up and running system verification 107

    7 Maintenance and Troubleshooting 109

    The Diagnosis View 110 Overview 110 Instrument panel 111 Logbooks 113

    Maintenance 114

    Agilent InfinityLab LC/MSD Series and 6100 Series LC/MS Concepts Guide 7

  • Contents

    Early maintenance feedback 114 Maintenance logbook 115 Maintenance procedures 115 Venting and pumping down the MS 116

    Diagnosing and fixing problems 117 Symptoms and causes 117 Diagnostic tests for the MS 118 Fixing problems 120

    8 Agilent InfinityLab LC/MSD Series and 6100 Series LC/MS Concepts Guide

  • InfinityLab LC/MSD Series and 6100 Series LC/MS Concepts Guide

    1 Overview of Hardware and Software How the Agilent mass selective detectors work 10

    Overview 10 Details 11

    Types of data you can acquire 15 Scan versus selected ion monitoring (SIM) 15 Generation of fragment ions: low versus high fragmentor 16 Positive versus negative ions 18 Multiple signal acquisition 19

    Ion sources 21 Electrospray ionization (ESI) 21 Atmospheric pressure chemical ionization (APCI) 27 Atmospheric pressure photoionization (APPI) 29 Multimode ionization (MMI) 30

    Introduction to the ChemStation Edition program 31 Overview 31 Reviewing data remotely 33

    This chapter provides an overview of the hardware and ChemStation Edition program that comprises the InfinityLab LC/MSD Series and 6100 Series LC/MS systems. The InfinityLab LC/MSD Series consists of two models: LC/MSD XT and LC/MSD. The 6100 Series LC/MS family consists of three models: 6120B, 6130B, and 6150B.

    9

  • 1 Overview of Hardware and Software How the Agilent mass selective detectors work

    How the Agilent mass selective detectors work

    Overview Mass selective detectors (MSD) analyze ions moving through a vacuum to produce mass spectra. Mass spectra provide valuable information about the molecular weight, structure, identity, quantity, and purity of a sample. MSDs add specificity to both qualitative and quantitative analyses.

    A quadrupole mass a