Name: Thermo Scientific TSQ Quantis
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Acquiring Sample Data

Using the Xcalibur Data System to Acquire Sample Data

Thermo Scientific TSQ Altis, Quantis, and Fortis Hardware Manual 85

3. If a check mark appears in the Start Instrument column for the MS or if you need to

change the start instrument to another device, click Change Instruments to open the

Change Instruments In Use dialog box (Figure 44).

Figure 44. Change Instrument in Use dialog box

a. In the Instrument column, click the arrow in the column on the left of the

instrument and select the device.

b. Click OK.

4. In the Run Sequence dialog box, complete the remaining selections.

5. Click OK.

This completes the start instrument setup.

Acquiring Data Files with the Xcalibur Data System

For instructions, refer to the Instrument Setup and Sequence Setup topics in the Xcalibur

Help.

Default Chapter7
- Default Chapter7
  - Table of Contents7
- Preface15
Chapter 1 Introduction19
- Mass Spectrometry Models19
- MS Mass-To-Charge Ratio Ranges21
- Principles of Operation23
  - Overview of the MS System23
  - Figure 1. Block Diagram of MS Hardware Components23
Chapter 2 Principles of Operation23
- Overview of Ion Optics and Mass Analyzer25
- Figure 2. Ion Optics and Mass Analyzer Assemblies25
Chapter 3 Vacuum System27
- Vacuum Pumps27
- Vacuum Manifold28
- Figure 3. Placement of the Turbomolecular Pump Next to the Vacuum Manifold28
- Vacuum System Block Diagram30
- Figure 4. Functional Block Diagram of the Altis Vacuum System30
- Vacuum Gauges31
Chapter 4 Internal Gas Supply33
- Figure 5. Gas Inlets and Vacuum (Foreline) Port (Left Side of the MS)34
Chapter 5 Atmospheric Source Interface35
- API Source Interface Overview36
- Figure 6. API Source Interface for the TSQ Altis MS (Cross Section)36
- Ion Transfer Tube37
- Figure 7. Altis Ion Transfer Tube37
- Figure 8. Quantis Ion Transfer Tube37
- Figure 9. Fortis Ion Transfer Tube37
- RF and Exit Lens38
- Figure 10. Altis RF Lens and Exit Lens38
- Figure 11. Quantis RF Lens38
- Figure 12. Fortis Exit Lens39
Chapter 6 Ion Optics and Detector Components41
- MP00 Ion Optics41
- Figure 13. MP00 Lens (Left) and Lens L0 (Right)41
- MP0 Ion Optics and Beam Blocker42
- Dual-Mode, Discrete-Dynode Ion Detection System42
- Figure 14. MP0 Multipole with Neutral Beam Blocker (1)42
- Figure 15. EL11 (Left) and EL12 (Right) Lenses42
Chapter 7 Controls and Indicators43
- Leds43
- Figure 16. Leds on the Instrument Front Panel43
- Power Entry Module44
- Communications Panel45
- Figure 18. Communication Connectors (Right Side of the MS)46
- Cooling Fans48
Chapter 8 Using the MS Power Options49
- Turning the MS on49
- Placing the MS in Standby Mode49
- Shutting down the MS System in an Emergency50
- Figure 19. Main Power Switch on the Power Module50
Chapter 9 Shutting the MS System down Completely51
- Shutting the MS down Completely51
- Turning off the LC, Gases, Data System, and Autosampler52
- Figure 20. Electronic Service Switch and Main Power Switch52
Chapter 10 Restarting the MS System after a Shutdown53
- Restarting the Data System53
  - Restarting the Data System Using Windows53
  - Restarting the Data System Using the Power Button53
- Resetting the Mass Spectrometer54
- Figure 21. Reset Button (1) on the Communication Panel54
- Pumping the MS down55
- Figure 22. Electronic Service Switch and Main Power Switch55
- Resetting Calibration Parameters56
- Starting the LC, Gases, and Autosampler57
Chapter 11 MS Components On/Off Status59
Chapter 12 Maintaining the MS on a Daily Basis61
- Before Operating the Mass Spectrometer61
- After Operating the Mass Spectrometer65
Chapter 13 Recommended Inlet and Flow Rates67
- Guidelines for LC/H-ESI/MS Parameters67
- Guidelines for LC/APCI/MS Parameters67
- Guidelines for LC/NSI/MS Parameters68
Chapter 14 Connecting the Sample Flow to the Source69
- Connecting the Sample Flow to the H-ESI Source69
- Connecting the Sample Flow to the APCI Source70
- Figure 23. Connection to the H-ESI or the Low-Flow H-ESI Source70
- Figure 24. Connection to the APCI Spray Insert71
- Calibrating the MS73
  - Preparing the Syringe Pump for Calibration73
Chapter 15 Calibrating the MS73
- Preparing the MS for Calibration74
- Determining the Initial API Source Settings75
- Figure 25. Syringe Pump Settings Box75
- Evaluating the Spray Stability76
- Figure 26. Define Scan Parameters76
- Figure 27. Plot Chromatogram Dialog Box77
- Calibration Parameters78
- Calibrating and Tuning the MS78
Chapter 16 Optimizing the Compound Signal85
- Performing Compound Optimization Animation85
- Setting up for Compound Optimization85
- Optimizing Parameters in the Optimization Pane86
- Figure 34. Optimizing the Source Parameters in the Optimization Pane87
- Figure 35. Example Optimization of the RF Lens (SRIG RF) Tuning for M/Z 997.5588
- Figure 36. Examples of the Optimization Results Tables88
Chapter 17 Scan Types89
- Quadrupole Capacities90
- Summary of Scan Types90
- Full Scan Q1 and Q3 Scan Types91
- Selected Ion Monitoring Scan Type91
- Product Scan Type92
- Figure 37. Illustration of Product Scan Type92
- Precursor Scan Type93
- Neutral Loss Scan Type93
- Figure 38. Illustration of the Precursor Scan Type93
- Figure 39. Illustration of the Neutral Loss Scan Type94
- Selected Reaction Monitoring Scan Type95
- Figure 40. Examples of Compounds with a Common Fragment95
Chapter 18 Data Types97
- Profile and Centroid Data97
- Figure 41. Examples of Profile (Left) and Centroid (Right) Data97
- Ion Polarity Modes98
Chapter 19 Acquiring Sample Data99
- Creating an SRM Method Animation99
- Using Tune to Acquire Sample Data100
- Figure 42. Data Acquisition Pane in the Tune Window101
- Using the Xcalibur Data System to Acquire Sample Data102
- Using Templates in Thermo Xcalibur Instrument Setup104
- Figure 45. Templates in Method Editor104
Chapter 20 Maintenance Schedule and Supplies105
- MS Parts105
- Maintenance Schedule106
- Guidelines107
- Tools and Supplies107
Chapter 21 Maintaining the API Source and Replacing the H-ESI Needle111
- Cleaning the API Source Housing111
- Replacing the H-ESI Needle111
Chapter 22 Maintaining the RF Lens, Exit Lens, MP00 RF Lens, and Lens L0113
- Removing the API Source Interface113
- Figure 46. API Source Interface Removed from the Vacuum Manifold114
- Removing the RF Lens, Exit Lens, MP00 RF Lens, and Lens L0 (Altis/Quantis)115
- Figure 47. Removing the Multipole MP00 and Lens L0 Assembly (TSQ Altis MS)115
- Figure 48. Removing the RF Lens and Exit Lens (TSQ Quantis MS)116
- Figure 49. Removing the Lens L0 and Multipole MP00 from the MP00-L0 Mount Cage116
- Removing the Exit Lens, MP00, and Lens L0 (Fortis)117
- Figure 50. Removing the Multipole MP00 and Lens L0 Assembly (TSQ Fortis)117
- Cleaning the RF Lens, Exit Lens, MP00, and Lens L0118
- Figure 51. Removing the Exit Lens (TSQ Fortis)118
- Figure 52. Removing the Lens L0 and Multipole MP00 from the MP00-L0 Mount Cage118
- Reinstalling the API Source Interface119
Chapter 23 Maintaining the API Source Interface121
- Performing Source Maintenance Animation121
- Removing the Ion Sweep Cone and the Ion Transfer Tube122
- Figure 53. Ion Sweep Cone Removed from the MS Mount Assembly122
- Figure 54. Ion Transfer Tube Removal Tool (TSQ Altis MS)123
- Figure 55. Ion Transfer Tube Removal Tool (TSQ Quantis MS)124
- Figure 56. Ion Transfer Tube Removal Tool (TSQ Fortis MS)124
- Cleaning the Spray Cone and O-Ring125
- Figure 57. Spray Cone, O-Ring, Ion Transfer Tube, and Ion Sweep Cone125
- Cleaning the Ion Transfer Tube126
- Cleaning the Ion Sweep Cone126
Chapter 24 Maintaining the Forepumps and the Air Filter129
- Maintaining the Forepumps129
- Maintaining the Air Filter129
- Figure 58. Air Filter Location in the MS with the Front Cover Removed130
Appendix A Using Basic Tune Functions131
- Performing Compound Optimization Animation131
- Opening the Tune Window132
- Figure 59. Tune Window Showing the Define Scan Pane132
- Setting the Instrument System Controls133
- Setting the Instrument Power Mode134
- Checking the Instrument Readback Status135
- Setting the Tune Preferences136
- Figure 60. Tune Preferences Dialog Box136
- Using the Mass List Table in the Define Scan Pane137
- Using the History Pane139
- Using the Favorites Pane to Save System Settings139
- Figure 62. Favorites Pane140
- Figure 63. State Name Box140
Appendix B Setting up the Syringe with the Syringe Pump143
- Connecting the Syringe Union to the Syringe143
- Figure 64. PEEK Tubing Connection to Syringe Union143
- Setting up the Syringe Pump144
- Figure 65. Syringe Pump with Syringe145
Appendix C Divert/Inject Valve147
- About the Divert/Inject Valve147
- Divert/Inject Valve Configurations148
- Divert/Inject Valve Controls149
- Figure 67. Divert/Inject Valve Plumbed as a Divert Valve149
- Figure 68. Divert/Inject Valve (Front View)150
Appendix D Setting up Sample Introduction Techniques151
- Setting up H-ESI or Low Flow H-ESI Direct Infusion151
- Setting up High-Flow Infusion Without an Autosampler155
- Setting up Loop Injections for Flow-Injection Analysis156
- Figure 71. HPLC Infusion Tee Valve156
- Setting up Injections Using the Autosampler157
- Figure 72. Injector Valve Set up157
- Figure 73. Divert/Inject Valve Plumbed as a Divert Valve158
Appendix E Replaceable Parts159
- Chemical Kit159
- Calibration Kit160
- MS Setup Kit161
- Performance Specification Kit161
- Single Mechanical Pump Kit162
- Dual Mechanical Pumps Kit162
- TSQ Source Installation Kit163
- API Source Interface163
- Miscellaneous Parts163
- Glossary165
- Index173

Thermo Scientific TSQ Quantis User Manual

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Thermo Scientific TSQ Quantis Specifications

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Brand	Thermo Scientific
Model	TSQ Quantis
Category	Laboratory Equipment
Language	English