Thermo Scientific TSQ 8000 Evo User Manual
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Thermo Scientific TSQ 8000 Evo User Manual

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TSQ 8000 Evo
Mass Spectrometer
AutoSRM User Guide
1R120586-0005 Revision B December 2015

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Summary of Contents for Thermo Scientific TSQ 8000 Evo

  • Page 1 TSQ 8000 Evo Mass Spectrometer AutoSRM User Guide 1R120586-0005 Revision B December 2015...
  • Page 2 © 2015 Thermo Fisher Scientific Inc. All rights reserved. TSQ, TRACE, TriPlus, and TraceFinder are trademarks, and Xcalibur is a registered trademark of Thermo Fisher Scientific in the United States. The following are registered trademarks in the United States and other countries: Microsoft, Windows, and Excel are registered trademarks of Microsoft.

  • Page 3: Table Of Contents

    Importing Transitions to the Method Editor......20 Thermo Scientific TSQ 8000 Evo AutoSRM User Guide...
  • Page 5 2); IEC 61010-2-010:2014 (ed. 3); IECEE CB SCHEME CERT NO. DE 3-30000 • TSQ 8000 Evo and TSQ Duo standards: EMC: EN 61326-1:2013. Safety: IEC 61010-1:2010 (ed. 3); IEC 61010-2-081:2015 (ed. 2); IEC 61010-2-010:2014 (ed. 3); IECEE CB SCHEME CERT NO. DE 3-30034...
  • Page 6 Notice on Lifting and Handling of Thermo Scientific Instruments For your safety, and in compliance with international regulations, the physical handling of this Thermo Fisher Scientific instrument requires a team effort to lift and/or move the instrument. This instrument is too heavy and/or bulky for one person alone to handle safely.

  • Page 7: Weee Compliance

    For manufacturing location, see the label on the instrument. WEEE Compliance This product is required to comply with the European Union’s Waste Electrical & Electronic Equipment (WEEE) Directive 2002/96/EC. It is marked with the following symbol: Thermo Fisher Scientific has contracted with one or more recycling or disposal companies in each European Union (EU) Member State, and these companies should dispose of or recycle this product.
  • Page 8 Conformité DEEE Ce produit doit être conforme à la directive européenne (2002/96/EC) des Déchets d'Equipements Electriques et Electroniques (DEEE). Il est marqué par le symbole suivant: Thermo Fisher Scientific s'est associé avec une ou plusieurs compagnies de recyclage dans chaque état membre de l’union européenne et ce produit devrait être collecté...

  • Page 9: Preface

    This guide contains detailed information about how to use the Thermo Scientific AutoSRM software application for the Thermo Scientific™ TSQ 8000™ Evo triple-quadrupole mass spectrometers. The TSQ 8000 Evo system provides the selectivity and sensitivity of a triple-quadrupole GC/MS while also functioning as a high-performance single quadrupole instrument.

  • Page 10: Related Documentation

    • TSQ 8000 Evo Hardware Manual, PN 1R120586-0003 • TSQ 8000 Evo Spare Parts Guide, PN 1R120586-0004 • TSQ 8000 Evo AutoSRM User Guide, PN 1R120586-0005 • Q Exactive GC, ISQ Series, and TSQ 8000 Evo Direct Probe System User Guide, PN 1R120505-0006 ...

  • Page 11: System Requirements

    Software • Microsoft™ Windows™ 7 SP1 Operating System (64-bit) • Microsoft Office™ 2013 • Thermo Foundation 3.1 SP1 (Thermo Scientific software) • Xcalibur™ 4.0 Safety and Special Notices Make sure you follow the precautionary statements presented in this guide. The safety and other special notices appear in boxes.
  • Page 12 MATERIAL AND EYE HAZARD: Indicates that eye damage could or might occur. RADIOACTIVE HAZARD: Indicates that exposure to radioactive material could or might occur. TSQ 8000 Evo AutoSRM User Guide Thermo Scientific...

  • Page 13: Hydrogen Safety Precautions

    You should also consider purging the hydrogen to further reduce hazards and ensure anyone who will be working with hydrogen has basic hydrogen safety training. Thermo Scientific TSQ 8000 Evo AutoSRM User Guide xiii...

  • Page 14: Using Hydrogen With The Mass Spectrometertsq 8000 Evo

    Using Hydrogen with the Mass SpectrometerTSQ 8000 Evo To use hydrogen with the TSQ 8000 Evo, you must always shut off the GC carrier gas before venting or turning off the TSQ 8000Evo. There are three hydrogen safety screws on the TSQ 8000 Evo that must be in place.

  • Page 15: Hydrogen Connection Guidelines

    Tubing connections should be clamped to barbed or press-fit type connections. Hose clamps or jubilee clamps must not be used. Thermo Scientific TSQ 8000 Evo AutoSRM User Guide...

  • Page 16: Purchasing Hydrogen

    There is a loss of flow to the ventilation system – A hydrogen detector alarms at 25% of the lower flammable limit of hydrogen in air. The oxygen exhausted by the electrolyzer should be vented to the outside as well. TSQ 8000 Evo AutoSRM User Guide Thermo Scientific...

  • Page 17: Properly Storing Hydrogen

    Bulk hydrogen systems represent a level of complexity again which is beyond the scope of this document; however some general guidelines are provided. Thermo Scientific TSQ 8000 Evo AutoSRM User Guide xvii...
  • Page 18 • As liquid hydrogen systems also have a cryogenic hazard, additional safety considerations for the use of cryogenic liquids might be necessary. xviii TSQ 8000 Evo AutoSRM User Guide Thermo Scientific...

  • Page 19: Hydrogen Safety Codes, Standards And References

    • NFPA 55, Standard for the Storage, Use, and Handling of Compressed Gases and Cryogenic Fluids in Portable and Stationary Containers, Cylinders, and Tanks, 2005 Edition • NFPA 68, Standard on Explosion Protection by Deflagration Venting • NFPA 70, National Electrical Code Thermo Scientific TSQ 8000 Evo AutoSRM User Guide...

  • Page 20: Hazardous Substances Precautions

    When working with biohazardous materials, you are responsible for fulfilling the following mandatory requirements: • Providing instructions on how to safely handle biohazardous material. • Training operators to be aware of potential hazards. TSQ 8000 Evo AutoSRM User Guide Thermo Scientific...

  • Page 21: Venting Toxic Gases

    Go to www.thermoscientific.com/en/support-landing/support.html.  To suggest changes to documentation or to Help • Fill out a reader survey online at www.surveymonkey.com/s/PQM6P62. • Send an e-mail message to the Technical Publications Editor at techpubs-austin@thermofisher.com. Thermo Scientific TSQ 8000 Evo AutoSRM User Guide...

  • Page 23: Chapter 1 Using Autosrm

    For precursor ion studies, along with the resulting chromatographic peaks and full-scan spectra, AutoSRM presents you with a table of the most intense product ion masses that you may select. If you wish, however, AutoSRM can automatically pick the product ion masses. Thermo Scientific TSQ 8000 Evo AutoSRM User Guide...
  • Page 24 1. Open the TSQ Series Dashboard. 2. Click AutoSRM. Figure 1. Accessing AutoSRM by the TSQ Series Dashboard 3. Click the Create a New Study icon on the left to create a new study. TSQ 8000 Evo AutoSRM User Guide Thermo Scientific...
  • Page 25 6. Select an instrument method file and click Open. 7. You may set the Mass Range, Start Time, and Stop Time. See Figure Any changes you make to your MS method here will override the method editor settings. Thermo Scientific TSQ 8000 Evo AutoSRM User Guide...
  • Page 26 Tip Create a folder for all files associated with your AutoSRM study. Otherwise, the study results files will be saved in the general instrument method folder and crowd it. See Figure Figure 5. Creating an AutoSRM Study Folder TSQ 8000 Evo AutoSRM User Guide Thermo Scientific...
  • Page 27 Acquiring Acquisition Data New Study Name Acquire Data Icon 15. (CI Only) If you are running a chemical ionization (CI) study, select Positive or Negative from the Ion Polarity pull-down menu. See Figure Thermo Scientific TSQ 8000 Evo AutoSRM User Guide...
  • Page 28 Note AutoSRM calculates the number of injections needed based on the compound list and vial positions you assigned. 17. The Submit Study for Acquisition window opens. See Figure Figure 9. Submitting a Study for Acquisition TSQ 8000 Evo AutoSRM User Guide Thermo Scientific...
  • Page 29 20. Select the check box next to the precursor ions you want to send to the working list or click the settings icon and choose Show Precursor Ion Settings to access additional settings for selecting precursor ions. See Figure Thermo Scientific TSQ 8000 Evo AutoSRM User Guide...
  • Page 30 22. By default, precursor ions are sorted by highest intensity. In the Precursor Ion Settings box, you may select precursor ions according to the following criteria. a. Number of Ions to Pick: Selects the number of precursor ions picked for each compound. TSQ 8000 Evo AutoSRM User Guide Thermo Scientific...
  • Page 31 Tip When selecting precursor ions, you often get better results by weighting m/z higher than intensity weight. 23. Click the green arrow icon to push the precursor ions you selected to the working list. See Figure Thermo Scientific TSQ 8000 Evo AutoSRM User Guide...
  • Page 32 25. When you have reviewed all the compounds and selected the precursor ions, click the Push icon in the working list (See Figure 14)to push the transitions in the working list to the Product Ion Study. TSQ 8000 Evo AutoSRM User Guide Thermo Scientific...

  • Page 33: Conducting The Product Ion Study

    Export Timed Transitions function.  To conduct a product ion study, use the following steps 1. The AutoSRM window displays the list of precursor ions you selected for the Product Ion study. Thermo Scientific TSQ 8000 Evo AutoSRM User Guide...
  • Page 34 Figure 15. Precursor Ions Selected for Product Ion Study 2. Click the Settings icon to access the product ion settings. See Figure Figure 16. Accessing Product Ion Settings 3. The Product Ion Settings box opens. See Figure TSQ 8000 Evo AutoSRM User Guide Thermo Scientific...
  • Page 35 Limit by m/z Range: Check this box and set the low m/z and high m/z to limit your product ion selection list to certain masses within the set scan range. Thermo Scientific TSQ 8000 Evo AutoSRM User Guide...
  • Page 36 During the Product Ion study, each product ion scans at 10, 20, and 30 eV collision energies to get a good collision energy range over which to search for the best product ions. TSQ 8000 Evo AutoSRM User Guide Thermo Scientific...
  • Page 37 Note AutoSRM lists product ions in order of highest energy intensity and at the optimal collision energy for each product ion. Tip AutoSRM automatically processes the data for you and suggests transitions if you push the purple wheel icon. Thermo Scientific TSQ 8000 Evo AutoSRM User Guide...

  • Page 38: Developing The Srm Optimization Study

    Tip You can import an SRM method directly into this step by clicking the Import icon. The import file must be in the same .csv format that the TSQ Series instrument method exports through its Export Timed Transitions function. TSQ 8000 Evo AutoSRM User Guide Thermo Scientific...
  • Page 39 This can be accomplished through the Create New Study from Existing Study function. Figure 21. Selecting SRM Energy Range 3. Save the study and submit the samples for analysis. See Figure Thermo Scientific TSQ 8000 Evo AutoSRM User Guide...
  • Page 40 Developing the SRM Optimization Study Figure 22. Submitting SRM Optimization Study for Analysis 4. Once the analysis is complete, the software displays the data for the user to perform a final review. See Figure TSQ 8000 Evo AutoSRM User Guide Thermo Scientific...
  • Page 41 6. Once you have reviewed the data and chosen the transitions you want to use, save the study and create a .csv file to transfer the transitions to your instrument method. See Figure Thermo Scientific TSQ 8000 Evo AutoSRM User Guide...

  • Page 42: Importing Transitions To The Method Editor

    2. Open your method in the TSQ Series method editor. See Figure Note If you have the desired method open in AutoSRM, click the link in the Instrument Method box to open your method in the TSQ Series method editor. TSQ 8000 Evo AutoSRM User Guide Thermo Scientific...
  • Page 43 4. Select Acquisition-Timed from the Method Type drop-down menu. 5. From the top menu, select TSQ Series | Import Timed Scans. See Figure Figure 26. Opening Timed Scans in the TSQ Series Method Editor Thermo Scientific TSQ 8000 Evo AutoSRM User Guide...
  • Page 44 Click Open to open the method in SIMBridge. d. If necessary, change the method headings in your original file to match those in the method editor. A green check mark appears when your method is validated. See Figure TSQ 8000 Evo AutoSRM User Guide Thermo Scientific...
  • Page 45 Figure Figure 30. Viewing the AutoSRM File in the Method Editor If you open an older model TSQ 8000 or a TSQ Duo (if you have a TSQ 8000 Evo system) method, the Instrument Model for Method box appears. g. Select your model from the drop-down menu in Instrument Model for Method in order to make the imported method compatible with your model.
  • Page 46 7. Adjust your scan settings as necessary. See the user guide for more information. Figure 31. Review Imported List 8. Once you are satisfied with your method, save it. 9. Run a set of samples to verify that the method meets your needs. TSQ 8000 Evo AutoSRM User Guide Thermo Scientific...

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