AB Sciex QTRAP 4500 LC/MS/MS system User manual

AB SCIEX 4500 Series of Instruments
System User Guide
Document Number: RUO-IDV-05-0264-A
Release Date: April 2013

AB Sciex Pte. Ltd.
Blk 33, #04-06
Marsiling Ind Estate Road 3
Woodlands Central Indus. Estate
SINGAPORE 739256
This document is provided to customers who have purchased AB SCIEX equipment to use in the
operation of such AB SCIEX equipment. This document is copyright protected and any
reproduction of this document or any part of this document is strictly prohibited, except as
AB SCIEX may authorize in writing.
Software that may be described in this document is furnished under a license agreement. It is
against the law to copy, modify, or distribute the software on any medium, except as specifically
allowed in the license agreement. Furthermore, the license agreement may prohibit the software
from being disassembled, reverse engineered, or decompiled for any purpose. Warranties are as
stated therein.
Portions of this document may make reference to other manufacturers and/or their products,
which may contain parts whose names are registered as trademarks and/or function as
trademarks of their respective owners. Any such use is intended only to designate those
manufacturers' products as supplied by AB SCIEX for incorporation into its equipment and does
not imply any right and/or license to use or permit others to use such manufacturers' and/or their
product names as trademarks.
AB SCIEX warranties are limited to those express warranties provided at the time of sale or
license of its products and are AB SCIEX’s sole and exclusive representations, warranties, and
obligations. AB SCIEX makes no other warranty of any kind whatsoever, expressed or implied,
including without limitation, warranties of merchantability or fitness for a particular purpose,
whether arising from a statute or otherwise in law or from a course of dealing or usage of trade,
all of which are expressly disclaimed, and assumes no responsibility or contingent liability,
including indirect or consequential damages, for any use by the purchaser or for any adverse
circumstances arising therefrom.
For research use only. Not for use in diagnostic procedures.
The trademarks mentioned herein are the property of AB Sciex Pte. Ltd. or their respective
owners.
AB SCIEX™ is being used under license.
© 2013 AB Sciex Pte. Ltd.
Printed in Canada.
4500 Series of Instruments System User Guide
2 of 138 RUO-IDV-05-0264-A

System User Guide 4500 Series of Instruments
RUO-IDV-05-0264-A 3 of 138
Revision Log
Revision Description Date
D5030863 A First release of document. March 2012
RUO-IDV-05-0264-A Assigned new document number. Updated template.
Applied new content model.
April 2013

Revision Log
4500 Series of Instruments System User Guide
4 of 138 RUO-IDV-05-0264-A

System User Guide 4500 Series of Instruments
RUO-IDV-05-0264-A 5 of 138
Contents
Chapter 1 Operational Precautions and Limitations . . . . . . . . . . . . . . . . . . . . . . 9
General Safety Information . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .9
Regulatory Compliance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .10
Australia and New Zealand . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .10
Canada . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .10
Europe . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .10
United States . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .10
International . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .11
Electrical Precautions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .11
AC Mains Supply . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .11
Protective Earth Conductor . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .11
Chemical Precautions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .11
System Safe Fluids . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .12
Ventilation Precautions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .13
Environmental Precautions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .13
Decommissioning and Disposal . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .14
Qualified Personnel . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .14
Equipment Use and Modification . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .14
Chapter 2 Hazards Symbols . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
Occupational Health and Safety Symbols . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .17
Symbols, Indicators, and Labels . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .18
Packaging . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .18
Mass Spectrometer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .19
Documentation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .20
Chapter 3 Principles of Operation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23
System Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .23
Panel Symbols . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .24
Connections . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .24
Theory of Operation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .26
Data Handling . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .26
Chapter 4 Operating Instructions — Hardware. . . . . . . . . . . . . . . . . . . . . . . . . . 27
Start Up the System . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .27
Reset the System . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .27
Shut Down the System . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .28
Adjust the Integrated Syringe Pump Position . . . . . . . . . . . . . . . . . . . . . . . . . . .28
Plumb the Diverter Valve . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .32
Plumb the Diverter Valve in Injector Mode . . . . . . . . . . . . . . . . . . . . . . . . . . .32
Plumb the Diverter Valve in Diverter Mode . . . . . . . . . . . . . . . . . . . . . . . . . . .34
Chapter 5 Operating Instructions — Sample Workflows . . . . . . . . . . . . . . . . . . 37
Chapter 6 Operating Instructions — Hardware Profiles and Projects . . . . . . . 39
Hardware Profiles . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .39

Contents
4500 Series of Instruments System User Guide
6 of 138 RUO-IDV-05-0264-A
Create a Hardware Profile . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .39
Add Devices to a Hardware Profile . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .43
Troubleshoot Hardware Profile Activation . . . . . . . . . . . . . . . . . . . . . . . . . . . .44
Projects and Subprojects . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .45
Create Projects and Subprojects . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .45
Create Subprojects . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .46
Copy Subprojects . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .46
Switch Between Projects and Subprojects . . . . . . . . . . . . . . . . . . . . . . . . . . .47
Installed Project Folders . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .48
Back Up the API Instrument Folder . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .48
Chapter 7 Operating Instructions — Tune and Calibrate. . . . . . . . . . . . . . . . . . 49
Optimize the Instrument . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .49
Verify or Adjust Performance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .50
Results Summary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .50
Chapter 8 Operating Instructions — Acquisition Methods . . . . . . . . . . . . . . . . 53
Create Acquisition Methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .53
Configure the Syringe Pump . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .53
Add an Experiment . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .53
Add a Period . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .54
Copy an Experiment into a Period . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .54
Copy an Experiment within a Period . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .54
Scan Techniques . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .54
Quadrupole-Mode Scan Types . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .54
LIT-Mode Scan Types . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .55
About Spectral Data Acquisition . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .56
Parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .56
Acquisition Method Editor Icons . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .62
Chapter 9 Operating Instructions — Batches . . . . . . . . . . . . . . . . . . . . . . . . . . . 63
Set Queue Options . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .63
Add Sets and Samples to a Batch . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .64
Submit a Sample or Set of Samples . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .66
Change Sample Order . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .66
Acquire Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .66
Set Sample Locations in the Batch Editor . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .67
Select Vial Positions using the Locations Tab (Optional) . . . . . . . . . . . . . . . . . .67
Stop Sample Acquisition . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .69
Batch and Acquisition Method Editor Tips . . . . . . . . . . . . . . . . . . . . . . . . . . . . .69
Batch Editor Right-Click Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .70
Queue States and Device Status . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .70
Queue States . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .71
View Instrument and Device Status Icons . . . . . . . . . . . . . . . . . . . . . . . . . . . .72
Queue Right-Click Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .73
Icon Quick Reference: Acquire Mode . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .74
Chapter 10 Operating Instructions — Analyze and
Process Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 77
Open Data Files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .77

Contents
System User Guide 4500 Series of Instruments
RUO-IDV-05-0264-A 7 of 138
Navigate Between Samples in a Data File . . . . . . . . . . . . . . . . . . . . . . . . . . . . .77
Show Experimental Conditions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .78
Show Data in Tables . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .79
Show ADC Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .80
Show Basic Quantitative Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .81
Chromatograms . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .81
Show TICs from a Spectrum . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .82
Show a Spectrum from a TIC . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .82
Generate XICs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .82
Generate BPCs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .84
Generate XWCs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .86
Show DAD Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .86
Generate TWCs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .87
Adjust the Threshold . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .87
Data Processing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .89
Graphs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .89
Zoom In on the Y-axis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .91
Zoom In on the X-axis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .91
Chapter 11 Operating Instructions — Analyze and
Process Quantitative Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 95
Quantitative Analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .95
Quantitation Methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .95
About Results Tables . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .96
Quantitation Methods and Results Tables . . . . . . . . . . . . . . . . . . . . . . . . . . . .96
Create a Method using the Quantitation Method Editor . . . . . . . . . . . . . . . . .96
Create a Results Table using the Quantitation Wizard . . . . . . . . . . . . . . . . . .97
Create a Standard Query . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .98
Results Table Right-Click Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .101
Peak Review and Manual Integration of Peaks . . . . . . . . . . . . . . . . . . . . . . . .102
Review Peaks . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .102
Manually Integrate Peaks . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .105
Peak Review Right-Click Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .107
Calibration Curves . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .107
View Calibration Curves . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .108
Overlay Calibration Curves . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .109
Calibration Curve Right-Click Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .109
Sample Statistics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .110
View the Statistics for Standards and QCs . . . . . . . . . . . . . . . . . . . . . . . . . .110
Compare Results Between Batches . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .111
Chapter 12 Reporter Software . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 115
Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .115
Reporter User Interface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .116
Generate Reports . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .117
Chapter 13 Service and Maintenance Information . . . . . . . . . . . . . . . . . . . . . . 119
Clean the Surfaces . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .120
Clean the Front-End . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .121
Best Practices . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .122

Contents
4500 Series of Instruments System User Guide
8 of 138 RUO-IDV-05-0264-A
Prepare for Cleaning . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .123
Clean the Curtain Plate . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .124
Clean the Front of the Orifice Plate . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .124
Put the System Back into Service . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .125
Empty the Source Exhaust Drain Bottle . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .125
Storage and Handling . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .127
Chapter 14 Troubleshooting . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 129
Appendix A Parameters for 4500 Series Instruments . . . . . . . . . . . . . . . . . . . .131
Appendix B Calibration Ions and Solutions . . . . . . . . . . . . . . . . . . . . . . . . . . . .137

1
System User Guide 4500 Series of Instruments
RUO-IDV-05-0264-A 9 of 138
Operational Precautions and Limitations
This section contains general safety-related information and provides regulatory compliance
information. It also describes potential hazards and associated warnings for the system, and the
precautions that should be taken to minimize the hazards.
In addition to this section, refer to Hazards Symbols on page 17 for information on the symbols
and conventions used in the laboratory environment, on the system, and in this documentation.
Refer to the Site Planning Guide for site requirements, including AC mains supply, source
exhaust, ventilation, compressed air, nitrogen, and roughing pump requirements.
General Safety Information
To prevent personal injury or system damage, read, understand, and obey all safety precautions,
warnings in this document, and labels on the mass spectrometer. These labels are shown with
international symbols. Failure to heed these warnings could result in serious injury.
This safety information is intended to supplement federal, state or provincial, and local
environmental health and safety (EHS) regulations. The information provided covers system-
related safety with regard to the operation of the mass spectrometer. It does not cover every
safety procedure that should be practised. Ultimately, the user and the organization are
responsible for compliance with federal, state or provincial, and local EHS regulations and for
maintaining a safe laboratory environment.
For more information, refer to the appropriate laboratory reference material and standard
operating procedures.

Operational Precautions and Limitations
4500 Series of Instruments System User Guide
10 of 138 RUO-IDV-05-0264-A
Regulatory Compliance
This system complies with the standards and regulations listed in this section. Applicable labels
have been affixed to the system.
Australia and New Zealand
•Electromagnetic Interference—AS/NZ CISPR 11 (Class A)
•Safety—AS/NZ 61010-1
Canada
•Electromagnetic Interference—CAN/CSA CISPR11. This ISM device complies
with Canadian ICES-001.
•Safety—CAN/CSA C22.2 No. 61010-1, and CAN/CSA C22.2 No. 61010-2-061
Europe
•Electromagnetic Compatibility—Electromagnetic Compatibility Directive
2004/108/EC, as implemented in these standards:
• EN 55011 (Class A)
• EN 61326-1
•Safety—Low Voltage Directives 2006/95/EC as implemented in these standards:
• EN 61010-1
• EN 61010-2-061
•WEEE—Waste, Electrical, and Electronic Equipment Directive 2002/96/EEC
United States
•Electromagnetic Interference, FCC Part 15, Class A—This equipment has been
tested and found to comply with the limits for a Class A digital device, pursuant to
Part 15 of the FCC (Federal Communications Commission) Compliance Rules.
These limits are designed to provide reasonable protection against harmful
interference when the equipment is operated in a commercial environment. This
equipment generates, uses, and can radiate radio frequency energy and, if not
installed and used in accordance with the operator’s manual, can cause harmful
interference to radio communications.
Operation of this equipment in a residential area is likely to cause harmful
interference in which case you will be required to correct the interference, at your
own expense. Changes or modifications not expressly approved by the
manufacturer could void your authority to operate the equipment.
•Safety—UL 61010-1, IEC 61010-2-061