SCIEX TripleTOF 5600 Plus User manual

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

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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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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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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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