SCIEX TripleTOF 5600 Plus User manual

TripleTOF®5600/5600+ System
System User Guide
January 2018RUO-IDV-05-7040-B

This document is provided to customers who have purchased SCIEX equipment to use in the operation of such SCIEX
equipment. This document is copyright protected and any reproduction of this document or any part of this document is
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Software that may be described in this document is furnished under a license agreement. It is against the law to copy, modify,
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are as stated therein.
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For research use only. Not for use in diagnostic procedures.
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AB SCIEX™is being used under license.
©2018 AB Sciex
AB Sciex Pte. Ltd.
Blk 33, #04-06
Marsiling Ind Estate Road 3
Woodlands Central Indus. Estate.
SINGAPORE 739256
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1 Operational Precautions and Limitations...............................................................................................7
General Safety Information................................................................................................................................................7
Regulatory Compliance......................................................................................................................................................7
Australia and New Zealand..........................................................................................................................................7
Canada........................................................................................................................................................................8
Europe.........................................................................................................................................................................8
United States...............................................................................................................................................................8
International................................................................................................................................................................9
Electrical Precautions.........................................................................................................................................................9
AC Mains Supply..........................................................................................................................................................9
Protective Earth Conductor........................................................................................................................................10
Chemical Precautions.......................................................................................................................................................10
Ventilation Precautions....................................................................................................................................................11
Environmental Precautions..............................................................................................................................................12
Electromagnetic Environment....................................................................................................................................13
Decommissioning and Disposal..................................................................................................................................14
Qualified Personnel..........................................................................................................................................................14
Laboratory Conditions......................................................................................................................................................14
Operating Conditions.................................................................................................................................................14
Performance Specifications........................................................................................................................................15
Equipment Use and Modification.....................................................................................................................................15
Contact Us.......................................................................................................................................................................16
Technical Support............................................................................................................................................................16
Documentation Symbols and Conventions.......................................................................................................................16
Related Documentation...................................................................................................................................................17
2 Principles of Operation..........................................................................................................................18
System Overview..............................................................................................................................................................18
Hardware Overview...................................................................................................................................................18
Panel Symbols............................................................................................................................................................21
Theory of Operation.........................................................................................................................................................22
Data Handling............................................................................................................................................................23
3 Operating Instructions—Hardware......................................................................................................24
Start Up the System.........................................................................................................................................................24
Shut Down the System.....................................................................................................................................................25
Adjust the Integrated Syringe Pump Position...................................................................................................................26
Reset the Syringe Pump...................................................................................................................................................29
4 Operating Instructions —Sample Workflows.....................................................................................31
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Contents

5 Operating Instructions —Hardware Profiles and Projects.................................................................34
Hardware Profiles............................................................................................................................................................34
Create a Hardware Profile..........................................................................................................................................34
Add Devices to a Hardware Profile............................................................................................................................39
Troubleshoot Hardware Profile Activation.................................................................................................................41
Projects and Subprojects..................................................................................................................................................42
Create Projects and Subprojects.................................................................................................................................42
Create Subprojects.....................................................................................................................................................44
Copy Subprojects.......................................................................................................................................................44
Switch Between Projects and Subprojects..................................................................................................................44
Installed Project Folders.............................................................................................................................................45
Back Up the API Instrument Folder............................................................................................................................46
Recover the API Instrument Folder.............................................................................................................................46
6 Tune and Calibrate.................................................................................................................................47
Optimize the Mass Spectrometer.....................................................................................................................................47
About the Verifying or Adjusting Performance Dialog.....................................................................................................48
Results Summary..............................................................................................................................................................48
7 Operating Instructions —Acquisition Methods..................................................................................50
Create an Acquisition Method Using the Acquisition Method Editor...............................................................................50
Add an Experiment....................................................................................................................................................51
Add a Period..............................................................................................................................................................51
Copy an Experiment into a Period..............................................................................................................................52
Copy an Experiment within a Period..........................................................................................................................52
Create an Acquisition Method using the Method Wizard................................................................................................52
Scan Techniques..............................................................................................................................................................53
Single Mass Spectrometry................................................................................................................................................53
Quadrupole-Based Single Mass Spectrometry............................................................................................................53
Time-of-Flight Single Mass Spectrometry...................................................................................................................54
Tandem Mass Spectrometry.............................................................................................................................................54
Product Ion Mass Spectrometry.................................................................................................................................54
Precursor Ion Mass Spectrometry...............................................................................................................................54
About Spectral Data Acquisition................................................................................................................................54
Parameters.......................................................................................................................................................................55
8 Operating Instructions —Batches........................................................................................................60
Set Queue Options...........................................................................................................................................................60
Add Sets and Samples to a Batch....................................................................................................................................62
Submit a Sample or Set of Samples..................................................................................................................................65
Set Up Sample Calibration...............................................................................................................................................65
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..................................................................................................................................................68
Batch Editor Right-click Menu..........................................................................................................................................69
Queue States and Device Status......................................................................................................................................70
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Contents

Queue States..............................................................................................................................................................70
View Instrument and Device Status Icons..................................................................................................................71
Queue Right-click Menu.............................................................................................................................................72
9 Operating Instructions —Analyze and Explore Data.........................................................................74
Open Data Files................................................................................................................................................................74
Navigate Between Samples in a Data File........................................................................................................................75
View Experimental Conditions.........................................................................................................................................75
Show Data in Tables........................................................................................................................................................76
Show ADC Data...............................................................................................................................................................78
Show Basic Quantitative Data..........................................................................................................................................79
Chromatograms...............................................................................................................................................................79
Show TICs from a Spectrum.............................................................................................................................................80
Show a Spectrum from a TIC............................................................................................................................................81
About Generating XICs....................................................................................................................................................82
Generate an XIC Using a Selected Range...................................................................................................................82
Generate an XIC Using the Maximum Peak...............................................................................................................83
Generate an XIC Using Base Peak Masses.................................................................................................................83
Extract Ion by Selecting Masses.................................................................................................................................83
Generate BPCs.................................................................................................................................................................84
Generate XWCs................................................................................................................................................................86
DAD Data.........................................................................................................................................................................86
Generate TWCs................................................................................................................................................................87
Adjust the Threshold........................................................................................................................................................87
Chromatogram Panes......................................................................................................................................................88
Spectra Panes..................................................................................................................................................................89
Graphical Data Processing.........................................................................................................................................89
Graphs.............................................................................................................................................................................90
Manage Data.............................................................................................................................................................90
Zoom In on the Y-axis................................................................................................................................................92
Zoom In on the X-axis................................................................................................................................................92
10 Service and Maintenance Information...............................................................................................93
Recommended Maintenance Schedule............................................................................................................................93
Clean the Surfaces...........................................................................................................................................................95
Clean the Front-End.........................................................................................................................................................95
Symptoms of Contamination......................................................................................................................................96
Required Materials ....................................................................................................................................................96
Cleaning Best Practices..............................................................................................................................................97
Prepare the Mass Spectrometer.................................................................................................................................98
Clean the Curtain Plate..............................................................................................................................................99
Clean the Front of the Orifice Plate..........................................................................................................................101
Put the Mass Spectrometer Back in Service.............................................................................................................101
Empty the Source Exhaust Drain Bottle..........................................................................................................................101
Inspect the Roughing Pump Oil Level............................................................................................................................103
Replace the Mass Spectrometer Cooling Fans Filter.......................................................................................................104
Storage and Handling....................................................................................................................................................106
11 Mass Spectrometer Troubleshooting...............................................................................................107
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A Recommended Calibration Ions..........................................................................................................110
B Exact Masses and Chemical Formulas................................................................................................113
C Toolbar Icons........................................................................................................................................116
D Glossary of Symbols............................................................................................................................125
E Glossary of Warnings...........................................................................................................................130
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Contents

Note: Before operating the system, carefully read all of the sections of this guide.
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 Glossary of Symbols on page 125 for information about 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 of the safety precautions and warnings
in this document, the manufacturer chemical safety data sheet (SDS), and product label information. These labels
are shown with internationally recognized symbols. Failure to heed these warnings could result in serious injury.
This safety information is intended to supplement federal, state, provincial, and local environmental health and
safety (EHS) regulations. The information provided covers system-related safety information applicable to the
operation of the system. It does not cover every safety procedure that should be practised. Ultimately, the user
and the organization are responsible for compliance with federal, state, provincial, and local EHS regulations and
for maintaining a safe laboratory environment.
Refer to the appropriate laboratory reference material and standard operating procedures.
Regulatory Compliance
This system complies with the regulations and standards listed in this section. Refer to the Declaration of Conformity
included with the system and the individual system components for dated references. Applicable labels have been
affixed to the system.
Australia and New Zealand
•Electromagnetic Compatibility (EMC): Radio Communications Act 1992 as implemented in these
standards:
•Electromagnetic Interference—AS/NZS CISPR 11/ EN 55011/ CISPR 11 (Class A). Refer to Electromagnetic
Interference on page 13.
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Operational Precautions and
Limitations

•Safety: AS/NZ 61010-1 and IEC 61010-2-061
Canada
•Electromagnetic Interference (EMI): CAN/CSA CISPR11. This ISM device complies with Canadian
ICES-001. Refer to Electromagnetic Interference on page 13.
•Safety:
•CAN/CSA C22.2 No. 61010-1
•CAN/CSA C22.2 No 61010-2-061
Europe
•Electromagnetic Compatibility (EMC): Electromagnetic Compatibility directive 2014/30/EU as
implemented in these standards:
•EN 61326-1
•EN 55011 (Class A)
Refer to Electromagnetic Compatibility on page 13.
•Safety: Low Voltage Directives 2014/35/EU as implemented in these standards:
•EN 61010-1
•EN 61010-2-061
•Waste Electrical and Electronic Equipment (WEEE): Waste Electrical and Electronic Equipment 2012/
96/EEC, as implemented in EN 40519. Refer to Waste Electrical and Electronic Equipment on page 14.
•Packaging and Packaging Waste (PPW): Packaging and Packaging Waste Directive 94/62/EC
•RoHS Restriction of Hazardous Substances: RoHS Directive 2011/65/EU
United States
•Radio Emissions Interference Regulations: 47 CFR 15, as implemented in FCC Part 15 (Class A)
•Safety: Occupational Safety and Health Regulations, 29 CFR 1910, as implemented in these standards:
•UL 61010-1
•IEC 61010-2-061
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Operational Precautions and Limitations

International
•Electromagnetic Compatibility (EMC):
•IEC 61326-1
•IEC CISPR 11 (Class A)
•IEC 61000-3-2
•IEC 61000-3-3
Refer to Electromagnetic Compatibility on page 13.
•Safety:
•IEC 61010-1
•IEC 61010-2-061
Electrical Precautions
WARNING! Electrical Shock Hazard. Do not remove the covers. Removing the
covers might cause injury or malfunctioning of the system. The covers need
not be removed for routine maintenance, inspection, or adjustment. Contact
a SCIEX Field Service Employee (FSE) for repairs that require the covers to be
removed.
•Follow required electrical safe work practices.
•Use cable management practices to control electrical cables. This will reduce the chance of a tripping hazard.
For information about system electrical specifications, refer to the Site Planning Guide.
AC Mains Supply
Connect the system to a compatible AC mains supply as instructed in this guide.
WARNING! Electrical Shock Hazard. Use only qualified personnel for the
installation of all of the electrical supplies and fixtures, and make sure that
all of the installations adhere to local regulations and safety standards.
WARNING! Electrical Shock Hazard. Make sure that the system can be
disconnected from the mains supply outlet in an emergency. Do not block
the mains supply outlet.
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Operational Precautions and Limitations

WARNING! Electrical Shock Hazard. Use only the power cables supplied with
the system. Do not use power cables that are not properly rated for the
operation of this system.
An external line transformer is not needed for the mass spectrometer or roughing pump.
Protective Earth Conductor
The mains supply must include a correctly installed protective earth conductor. The protective earth conductor
must be installed or checked by a qualified electrician before the system is connected.
WARNING! Electrical Shock Hazard. Do not intentionally interrupt the
protective earth conductor. Any interruption of the protective earth conductor
creates an electrical shock hazard.
WARNING! Electrical Shock Hazard. Make sure that a protective earth
conductor (grounding cable) is connected between the sample loop and an
appropriate grounding point at the ion source. This supplementary grounding
will reinforce the safety configuration specified by SCIEX.
Chemical Precautions
WARNING! Ionizing Radiation Hazard, Biohazard, or Toxic Chemical Hazard.
Determine whether decontamination is required prior to cleaning or
maintenance. The customer must decontaminate the system prior to cleaning
or maintenance if radioactive materials, biological agents, or toxic chemicals
have been used with the system.
WARNING! Environmental Hazard. Do not dispose of system components in municipal
waste. Follow local regulations when disposing of components.
WARNING! Biohazard, Toxic Chemical Hazard. Connect the drain tubing to
the mass spectrometer and the source exhaust drain bottle properly, to
prevent leaks.
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Operational Precautions and Limitations