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Thermo Scientific TSQ 8000 Evo User Manual

Thermo Scientific TSQ 8000 Evo User Manual

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TSQ 8000 Evo
Mass Spectrometer
User Guide
1R120586-0002 Revision C December 2015

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  • Page 1 TSQ 8000 Evo Mass Spectrometer User Guide 1R120586-0002 Revision C December 2015...
  • Page 2 © 2015 Thermo Fisher Scientific Inc. All rights reserved. TSQ, TRACE 1300, TRACE 1310, 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

    Accessing Auto Tune ..........31 Thermo Scientific TSQ 8000 Evo User Guide...

  • Page 4: Table Of Contents

    Index ............. . .127 TSQ 8000 Evo 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 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 your Thermo Scientific TSQ 8000™ Evo triple-quadrupole GC/MS system. 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. The system is designed to stay cleaner longer to maximize your instrument’s uptime and improve your lab’s productivity.
  • Page 10 • TSQ 8000 Evo Hardware Manual, PN 1R120586-0003 • TSQ 8000 Evo Spare Parts Guide, PN 1R120586-0004 • TSQ 8000 Evo Auto SRM User Guide, PN 1R120586-0005 • Q Exactive GC, ISQ Series and TSQ 8000 Evo Direct Probe System User Guide, PN 1R120505-0006 ...
  • Page 11 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 User Guide Thermo Scientific...
  • Page 13 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 User Guide xiii...
  • Page 14 These are attached to your instrument at the factory. Figure 1. Hydrogen Safety Screws on the Mass Spectrometer Left Top Right Top Cover Screw Cover Screw Front Panel Screw Before powering on the GC-MS/MS system, ensure that: TSQ 8000 Evo User Guide Thermo Scientific...
  • Page 15 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 User Guide...
  • Page 16 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 User Guide Thermo Scientific...
  • Page 17 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 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 User Guide Thermo Scientific...
  • Page 19 • 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 User Guide...
  • Page 20 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 User Guide Thermo Scientific...
  • Page 21 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 User Guide...

  • Page 23: Chapter 1 Introduction

    Checking Power to the System To confirm that the TSQ 8000 Evo system is powered on, check that the power light on the front panel is lit and solid green. See Figure 1.

  • Page 24: Verifying The Carrier Gas Flow Rate

    Introduction Confirming Your Instrument is Working  To power on the TSQ 8000 Evo instrument Lift up the power switch located on the upper left side panel of the instrument near the back. Figure 1. Front Panel of the TSQ 8000 Evo Instrument ...
  • Page 25 4. The TRACE 1300 status pane opens. Figure 2. Status Pane in TraceFinder Software Real Time Status Real Time Status Pane 5. Verify the column flow rate under the Flow tab in the Real Time Status pane. Thermo Scientific TSQ 8000 Evo User Guide...

  • Page 26: Checking Your Carrier Gas Tank Pressure

    60 ± 1 psig. Checking the Vacuum and Temperature Use the lights on the front of your TSQ 8000 Evo system to check the vacuum and temperature of the instrument. To check the vacuum, look at the Vacuum light. See Figure 3.
  • Page 27 Introduction Confirming Your Instrument is Working Figure 3. Using the Lights on the TSQ 8000 Evo Instrument Vacuum Heaters Power Busy Evacuate Ready to Open To check the temperature, look at the Heaters light. When the Heaters light is a solid green, the GC-MS/MS system is at temperature.

  • Page 28: Cleaning The Exterior Of Your Instrument

    When the exterior of your instrument gets dirty, wipe it with a clean, dry, lint-free cloth. Configuring Your Instrument Initially, the field service engineer will configure your TSQ 8000 Evo instrument. However, if you have reinstalled Xcalibur or you have a new computer or device, follow these instructions to reconfigure it.
  • Page 29 4. Select the TSQ Series icon in the Available Devices column and click Add to move it into the Configured Devices column. Figure 5. Finding Available Devices 5. Select the icon for each instrument you want to configure (See Figure 6) and click Add. Thermo Scientific TSQ 8000 Evo User Guide...
  • Page 30 Configuring a Device 6. Select the TSQ Series from the list of configured devices. 7. Click Configure to open the TSQ Series Configuration dialog box. 8. On the General page, set the pressure units. TSQ 8000 Evo User Guide Thermo Scientific...
  • Page 31 9. Set the remote start, which tells the TSQ 8000 Evo system when the GC has started a run. When you configure the GC, you can tell it what to send out to the instrument.
  • Page 32 Enabling Method Portability 11. Click Communications to reset the network IP address and assign a TCP port. See Figure 10. This tells the instrument method how to find the TSQ 8000 Evo system if you TSQ 8000 Evo User Guide Thermo Scientific...
  • Page 33 14. Select the Filament 1 check box to enable the maintenance reminder. In a leak-free system, expect the filament to last between 30-360 days, depending on usage. Thermo Scientific TSQ 8000 Evo User Guide...
  • Page 34 Figure 12. Main Instrument Configuration Window 19. Select the TRACE 1300 or TRACE 1310 icon to configure the GC handshaking parameters. 20. Under the General tab, set the handshaking parameters as shown in Table TSQ 8000 Evo User Guide Thermo Scientific...
  • Page 35 TRACE 1310 Series GC User Guide. Refer to your autosampler user documentation for the correct autosampler configuration settings. Note If you are running samples with a Direct Probe System, you do not have to configure the GC. Thermo Scientific TSQ 8000 Evo User Guide...
  • Page 36 22. Click Done to close the Instrument Configuration window. 23. Check the status of the configured instruments in the Status Pane of the TSQ Series Dashboard. Figure 14. TSQ Series Dashboard Status Pane TSQ 8000 Evo User Guide Thermo Scientific...

  • Page 37: Chapter 2 Changing The Column

    Changing the Column The TSQ 8000 Evo GC-MS/MS system ships with a factory-tested 15 m × 0.25 mm ID TR-SQC column, which the field service engineer uses to qualify the instrument. However, once it gets dirty, you cannot purchase a new one, so you must install a column that accommodates the type and quantity of samples that you will be running.

  • Page 38: Replacing The Factory Installed Column

    Very short columns (2.5, 5, and 10 m) are also available. Note Contact your local sales representative to order a Thermo Scientific column. You can also refer to our catalog or visit our Web site at www.thermoscientific.com/columns.
  • Page 39 TSQ 8000 Evo system. 3. On the left side of the instrument, push down on the power switch to power-off the TSQ 8000 Evo system. Figure 15. Powering Off the TSQ 8000 Evo Instrument Vacuum Interlock Shield Power Switch Vent Valve Knob 4.
  • Page 40 Allow the column to purge for at least 10 minutes. If you used methanol to detect column flow, remove column from methanol during purge time. Insert the column into the fitting of the column flowmeter connector that blocks the column flow. TSQ 8000 Evo User Guide Thermo Scientific...
  • Page 41 If you have a TRACE 1310, select the Back or Front Column icon in the Configuration menu. Otherwise, perform the column evaluation through the Chromatography Data System. See the TRACE 1300 and TRACE 1310 User Guide for instructions. Thermo Scientific TSQ 8000 Evo User Guide...
  • Page 42 WARNING FIRE HAZARD: Do not use hydrogen as the carrier gas for conditioning your column. It could vent into the oven and present an explosion hazard. TSQ 8000 Evo User Guide Thermo Scientific...

  • Page 43: Connecting The Column To The Transfer Line

    1. Lower the oven temperature and allow it to cool. 2. If the TSQ 8000 Evo system is running, shut down and vent it. See the instrument’s hardware manual for instructions. CAUTION BURN HAZARD: The injector, detectors, oven, and transfer line may be hot.
  • Page 44 12. Turn the spring loaded transfer line nut 1 flat backward so the column is able to move in the ferrule with slight resistance. 13. Line up the outlet of the column with the arrows on the end of the column measuring tool. TSQ 8000 Evo User Guide Thermo Scientific...
  • Page 45 15. Pull the column back from the spring loaded transfer line nut. Do not move the septum from its position on the column. Figure 21. Pulling the Column Back from the Spring Loaded Transfer Line Nut Spring Loaded Column Transfer Line Nut Septum Thermo Scientific TSQ 8000 Evo User Guide...
  • Page 46 20. Loosen the nut by turning it exactly 1 flat backward. 21. Position the column in the transfer line using the cut septum to measure the correct length you should insert the column. TSQ 8000 Evo User Guide Thermo Scientific...
  • Page 47 27. Restore working conditions. a. Raise the oven temperature to the initial temperature that you will use. b. Turn on vacuum compensation on the GC. 28. Power on the TSQ 8000 Evo instrument. See Chapter 1, “Introduction,” instructions. 29. Once the instrument is pumped down and able to scan, view air water spectra and look for evidence of leaks with a large m/z 28 signal.
  • Page 48 1. Lower the oven temperature and allow it to cool. 2. If the TSQ 8000 Evo system is running, shut down and vent it. See the instrument’s hardware manual for instructions. CAUTION BURN HAZARD: The injector, detectors, oven, and transfer line may be hot.
  • Page 49 Figure 26. Lining Up the Column in the Column Measuring Tool Column Outlet 13. Place a septum with a notch cut into it behind the transfer line nut. The septum marks the place on the column where it should exit the nut. Thermo Scientific TSQ 8000 Evo User Guide...
  • Page 50 16. Remove the column, transfer line nut and ferrule from the column measuring tool, making sure not to move the septum from its location on the column. 17. Insert the column into the transfer line. TSQ 8000 Evo User Guide Thermo Scientific...
  • Page 51 21. Tighten the nut 1 flat forward—back to where it is secure enough in the transfer line that you cannot move it. 22. Tighten the nut 1 additional quarter turn. 23. Remove the cut septum. Thermo Scientific TSQ 8000 Evo User Guide...
  • Page 52 Chapter 1, “Introduction,” instructions. d. Once the TSQ 8000 Evo instrument is pumped own and able to scan, view air water spectra and look for evidence of leaks with a large m/z 28 signal. If you observe a leak, stop scanning and gently tighten the nut in small increments until no leaks appear when scanning.

  • Page 53: Chapter 3 Tuning

    Tuning Tuning will improve the performance of your TSQ 8000 Evo system. For optimum stability, you must wait until the power, vacuum, and heaters lights on the front of the instrument are a solid green. These lights indicate that the instrument has reached vacuum and that it is at the last set temperature.

  • Page 54: Tuning The Mass Spectrometer

    Tuning the Mass Spectrometer  To tune your mass spectrometer 1. In the Tune Types field, select EI, CI, or Both, depending upon which ionization mode you are using. 2. Select a tuning category. See Figure TSQ 8000 Evo User Guide Thermo Scientific...
  • Page 55 219 ion with an intensity of 20,000,000 counts. Unless your SOP requires it, this is not the best tune to use on a daily basis because of the length of time required to run it. Thermo Scientific TSQ 8000 Evo User Guide...
  • Page 56 EI standard tune. This tune starts with the tune file stored in the instrument at the factory. It then performs a mass calibration and leak check, sets the repeller to 0 V, and tunes the lenses. The quadrupole offset TSQ 8000 Evo User Guide Thermo Scientific...
  • Page 57 Note To add a tune type to the list, see Modifying an Automatic Tune. 4. Select the Display Report When Complete check box so that you can view the tune report after running the tune. Thermo Scientific TSQ 8000 Evo User Guide...
  • Page 58 Once the tune completes, your tune report opens in the Tune Results Viewer. If you did not select the Display Report When Complete check box, you can click View Tune Report on the dashboard and view the report. TSQ 8000 Evo User Guide Thermo Scientific...
  • Page 59 69. Some masses may have over 100% abundance. If you do not wish to have a relative abundance above 100%, select Base Peak. This option will select the reference mass as the highest abundance mass in the tune. 9. Click OK. Thermo Scientific TSQ 8000 Evo User Guide...
  • Page 60 Tuning Tuning the Mass Spectrometer Figure 36. Tune Report Options 10. To print your tune report, click Print Report to open a print dialog box and print your report. TSQ 8000 Evo User Guide Thermo Scientific...
  • Page 61 Some changes in peak height are normal, but if the difference is significant, see Troubleshooting. 12. To browse to another tune report on your computer, click Open Tune Results in the top of the window. 13. Click Open to open a previously saved tune report. Thermo Scientific TSQ 8000 Evo User Guide...

  • Page 62: Updating Tunes For New Rf Lens

    Manual Tune utility and retune your instrument.  To update the ion guide frequency using the Manual Tune utility 1. Open the TSQ Series Dashboard. 2. Click Manual Tune on the dashboard. See Figure TSQ 8000 Evo User Guide Thermo Scientific...
  • Page 63 3. The Manual Tune utility opens. 4. Select Frequency Tune on the top menu. See Figure Figure 40. Accessing Frequency Tune Frequency Tune 5. From the Device drop-down menu, select Ion Guide. See Figure Thermo Scientific TSQ 8000 Evo User Guide...
  • Page 64 Figure 42. Saving the New Ion Guide Frequency to the Instrument 8. To confirm that the intensities are still correct, select Mass & Resolution Tune on the top menu to go back to the Manual Tune home page. TSQ 8000 Evo User Guide Thermo Scientific...
  • Page 65 Figure 44. Setting the Calibration Gas Level to EI 11. Click Start Scan. Check the intensities for the masses 69, 219, and 502. Set the masses using the Mass drop-down menu below each spectrum. See Figure Thermo Scientific TSQ 8000 Evo User Guide...
  • Page 66 Note The intensities might be lower than they were at the previous frequency set for the ion guide until the lenses are tuned in AutoTune. 12. Once you have confirmed the intensities are sufficient for tuning, retune the system. TSQ 8000 Evo User Guide Thermo Scientific...

  • Page 67: Chapter 4 Creating A Method

    Creating a Method Once you have tuned the TSQ 8000 Evo system, you can create a method for each of its components. Use these methods to indicate to the GC/MS system how to collect your data. Contents • Accessing the Method Editor •...
  • Page 68 The current instrument name also appears in the main menu. Figure 46. Method Editor Window Instrument Name Icon Arrow TSQ 8000 Evo User Guide Thermo Scientific...

  • Page 69: Creating An Autosampler Method

    Injectors—Enter the injection ID into the corresponding injector port. b. Syringes—Enter the syringe ID information. c. Wash Station—Enter the wash station ID information. d. (Optional) Internal Standard/Solvent Stations—Enter ID information for your solvent station or interval standard station. Thermo Scientific TSQ 8000 Evo User Guide...
  • Page 70 Plunger Strokes—Select the number of plunger strokes to use when drawing up the sample. Air bubbles in the syringe change the amount of sample injected, which can cause signal variation in different runs. To prevent this from occurring, increase the TSQ 8000 Evo User Guide Thermo Scientific...
  • Page 71 Post-inj Dwell Time(s)—Use this field to enter the time (in seconds) that the needle will be in the injection port after the plunger injects the sample. 6. Configure the settings under the Washes tab (see Figure 49): Figure 49. GC Liquids Washes Settings Thermo Scientific TSQ 8000 Evo User Guide...

  • Page 72: Creating A Ms Instrument Method

    TSQ 8000 Evo mass spectrometer.  To create a method for the TSQ 8000 Evo mass spectrometer 1. Click the TSQ Series icon in the left pane to open the method view for this instrument. 2. From the Method Type list, select Acquisition-General or Acquisition-Timed. See Figure 50.
  • Page 73 3. Use the Method Setup pane to set the temperatures and acquisition threshold in General Acquisition mode. See Figure 51 page Thermo Scientific TSQ 8000 Evo User Guide...
  • Page 74 GC oven and enters the TSQ 8000 Evo system. The maximum allowable temperature is 350 °C. CAUTION You will damage the column and contaminate the TSQ 8000 Evo instrument if you set the transfer line temperature above the maximum allowed temperature for the column.
  • Page 75 MS with the method. See Figure e. To assign gases to the CI gas ports, open the TSQ 8000 Evo Dashboard and click Instrument Control in the Status tab. Set CI Gas Port A or CI Gas Port B to the appropriate CI gas attached to that port.
  • Page 76 Fisher Scientific recommends that you select this option to save burn time on the filament. b. In the Scans pane, click a scan row to enter scan information under each column. See Figure TSQ 8000 Evo User Guide Thermo Scientific...
  • Page 77 You will get a complete set of scans every 0.108 seconds. Note The faster the MS scans, the more data points across a peak it will acquire. However, the precision of individual scans may be reduced. Thermo Scientific TSQ 8000 Evo User Guide...
  • Page 78 If you want to perform a precursor ion scan, enter the mass of the target precursor ion into this column. Note Entering a product ion mass changes a scan to SRM. TSQ 8000 Evo User Guide Thermo Scientific...
  • Page 79 Use the SIM Widths column to set the width range of the SIM window. The range of values can be between 0.01 and 10. The default is 1 amu, which means the MS will collect all the ions from your SIM mass ±0.5 amu. Thermo Scientific TSQ 8000 Evo User Guide...
  • Page 80 Note By default not all columns are displayed in the Groups pane. Right-click a heading to display them. You can also reorganize the columns by clicking the heading of a column and dragging it to the left or right. TSQ 8000 Evo User Guide Thermo Scientific...
  • Page 81 GC run, the scanning completely changes. Now the scans will repeat every 0.108 seconds until the GC run is complete. As the total scan time is a calculated value, it is not editable. Thermo Scientific TSQ 8000 Evo User Guide...
  • Page 82 Tune or saved to the instrument in Manual Tune, then you can set the gain manually. Higher gains give larger signals, but may shorten the lifetime of the detector when concentrated samples are detected. TSQ 8000 Evo User Guide Thermo Scientific...
  • Page 83 SIM scan on the precursor ion. If you enter a specific gain, the MS will use that gain for the SRM scan without the multiplier. 5. The following settings apply to Acquisition-Timed methods only. Thermo Scientific TSQ 8000 Evo User Guide...
  • Page 84 Link to External File. You may link to a .csv or .xml method file. Note In order to edit the scans within the TSQ 8000 Evo method editor, clear the Link to External File.
  • Page 85 Click Open to open the method in SIMBridge. e. 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 Thermo Scientific TSQ 8000 Evo User Guide...
  • Page 86 Figure Figure 63. Viewing a Linked File in the Method Editor g. 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.
  • Page 87 By varying the collision energy, a single precursor ion can be fragmented into several product ions. An SRM transition is defined by a precursor ion being fragmented into a particular product ion mass using a certain collision energy. Thermo Scientific TSQ 8000 Evo User Guide...
  • Page 88 65) to validate your method. A chart appears with all your analytes by name and in order of their retention times. See Figure Figure 65. Accessing the Show Analysis Feature Show Analysis Button TSQ 8000 Evo User Guide Thermo Scientific...
  • Page 89 Click the ladder icon again to stop the process at any time. Open the options menu to select the information you want made available in the analytes window. Thermo Scientific TSQ 8000 Evo User Guide...
  • Page 90 6. Use the right-side panel in Acquisition-Timed mode to make the following adjustments to your method. a. Use the Scan Settings panel to adjust the following settings. See Figure 68 page TSQ 8000 Evo User Guide Thermo Scientific...
  • Page 91 Desired Scans Per Peak, increase the Min Baseline Peak Width, or reduce the number of transitions contained in your method before you will be allowed to save your method (see Chapter 7, “Troubleshooting.” Thermo Scientific TSQ 8000 Evo User Guide...
  • Page 92 The SIM/SRM time is the total length of all SIM or SRM scans for each compound in your list. This will match the total scan time unless the method also has a full scan event. TSQ 8000 Evo User Guide Thermo Scientific...
  • Page 93 Post-width columns are no longer available in the compound list editor. If your method is linked to a file or imported from a file with values in these columns, the values are stored in memory and can be recovered by deactivating the window optimizer. Thermo Scientific TSQ 8000 Evo User Guide...
  • Page 94 The margin of error is ± 0.5 μA. TSQ 8000 Evo User Guide Thermo Scientific...
  • Page 95 Figure 69. Acquisition-Timed Instrument Settings Instrument Settings 7. To import a Thermo Scientific™ ISQ™ Series or TSQ Quantum™ Series MS method, choose TSQ Series | Import MS Method. See Figure Note This will only import the MS part of the method. You must set the GC and autosampler parameters.
  • Page 96 TraceFinder application. a. To create a new target ion from the list of confirming ions with identical retention times for a compound, select the confirming ion of interest. TSQ 8000 Evo User Guide Thermo Scientific...
  • Page 97 Drag the confirming ion to the compound name at the top of the list. Figure 72. Moving the Confirming Ion to the Compound Name Compound Name c. The confirming ion now appears in the list as a target ion. See Figure Thermo Scientific TSQ 8000 Evo User Guide...
  • Page 98 Figure 73. Locating the New Target Ion New Target Ion d. To add a new confirming ion to a target ion in the list, select the confirming ion of interest. See Figure Figure 74. Adding a New Confirming Ion to a Target Ion Confirming Ion e.
  • Page 99 13. Choose TSQ Series | View Tune Report to view the latest tune report the method will use. Choose Report Options to open the Report Options dialog box (see Figure 77) and add identifying information to the tune report. Thermo Scientific TSQ 8000 Evo User Guide...

  • Page 100: Creating A Gc Method

    0 and 999.99 minutes. The typical initial temperature is at least 10 °C (18 °F) above the boiling point of your sample solvent, and the initial time is usually long enough for the solvent to move through the column. TSQ 8000 Evo User Guide Thermo Scientific...
  • Page 101 GC reports as being ready. The equilibration time is typically set to 0.5 minutes. CAUTION INSTRUMENT DAMAGE. Be sure not to overheat the GC column or it may contaminate the instrument. Thermo Scientific TSQ 8000 Evo User Guide...
  • Page 102 TSQ 8000 Evo, which can lead to contamination. If you want to use this feature, set the GC oven temperature, as well as the amount of time to remain at that temperature after the analytical run is complete.
  • Page 103 Because the outlet of the column is in the TSQ 8000 Evo instrument, which is under vacuum, be sure the vacuum compensation is on to ensure accurate flow rates.
  • Page 104 9. If you have a Programmable Temperature Vaporizer (PTV), click the PTV-Front or PTV-Back tab to configure it. See Figure 80. The PTV is a low thermal mass injector that allows the instrument to rapidly heat or cool the inlet. You can use the PTV page to program the temperature of the injector.
  • Page 105 Add the inlet or detector to the current instrument configuration. Choose Start | All Programs | Thermo Foundation 3.1 | Instrument Configuration. c. In the Configured Devices pane, click the TRACE 1300 or TRACE 1310 icon. Click Configure. Thermo Scientific TSQ 8000 Evo User Guide...
  • Page 106 Figure 82. Adding a GC Inlet or Detector to the Method Editor d. In the TRACE 1300/1310 GC Configuration dialog box, select the Inlets or Detectors tab as appropriate. e. Click Get. The software automatically detects the attached modules. Select the gases as appropriate for your setup.

  • Page 107: Validating And Troubleshooting Methods

    If your method will not validate, a red error icon appears in the Scans pane and an error message that reads Contains Segments with Insufficient Time for All Scans Required appears if you try to save the method. Figure 84 illustrates an unvalidated method. Thermo Scientific TSQ 8000 Evo User Guide...
  • Page 108  To decrease the desired scans per peak • In the Scan Settings area, reduce the number of scans in the Desired Scans Per Peak box. See Figure TSQ 8000 Evo User Guide Thermo Scientific...
  • Page 109 3. While holding down the shift key, click the last problem analyte in the list. 4. Go back to the first analyte you selected, right-click, and choose Fill Down. 5. If the red error icon still appears, and your method allows it, reduce the acquisition windows further. Thermo Scientific TSQ 8000 Evo User Guide...
  • Page 110 Acquisition Windows When your method validates, the warning icon and the red bars disappear from the method editor. See Figure Figure 87. Validated Method You may now save the method as described earlier. TSQ 8000 Evo User Guide Thermo Scientific...

  • Page 111: Chapter 5 Optimizing Your Method

    If the GC oven is not at the boiling point, the compounds will not volatilize and they will become immobilized. You can change ramp rates to separate coeluting peaks. Refer to the GC user documentation for further suggestions on optimizing chromatographic separation. Thermo Scientific TSQ 8000 Evo User Guide...

  • Page 112: Finding The Best Way To Make An Injection

    2. Set the High Priority Multiplier to the desired value. 3. A new Dwell Time Priority option appears in your scan list. The choice are Normal or High. Choosing High multiplies the dwell times by the value set in the previous step. TSQ 8000 Evo User Guide Thermo Scientific...

  • Page 113: Narrowing The Mass Range

    Typically, aim for the transfer line temperature to be 10 °C (18 °F) over the highest boiling point of the compounds of interest, but no higher than the maximum safe operating temperature of the column. Thermo Scientific TSQ 8000 Evo User Guide...

  • Page 114: Optimizing An Srm Method

    Use the following workflow to adjust the low mass when you create an NCI tune. 1. Click Manual Tune button on the TSQ Series Dashboard. Figure 89. Finding Manual Tune on the TSQ Series Dashboard TSQ 8000 Evo User Guide Thermo Scientific...
  • Page 115 3. The Manual Tune Files dialog box opens. Select a PCI Tune file. Figure 91. Loading a PCI Tune File 4. Select the Low Mass tab on the right. Note the ion guide voltage value. Thermo Scientific TSQ 8000 Evo User Guide...
  • Page 116 You may also optimize the ion guide voltage value to any other negative value. 8. Save the changes to the tune file or rename it and save it as a new file. TSQ 8000 Evo User Guide Thermo Scientific...
  • Page 117 Note You may also adjust the emission current for the ionization mode and samples. The higher emission currents often work better in NCI, and the lower emission currents often work better in PCI but the optimal emission currents are typically between 25-100 μA. Thermo Scientific TSQ 8000 Evo User Guide...

  • Page 118: Modifying An Automatic Tune

    Figure 95. Tune Types Dialog Box 3. The Tune Type Editor opens. Configure the parameters under the General tab in the Tune Type Editor. Figure 96. Configuring General Tuning Parameters a. Name—Enter a name for your tune type. TSQ 8000 Evo User Guide Thermo Scientific...
  • Page 119 Note If Tune and Diagnostics is selected, you can select only one Mass Calibration option. 4. Select the Ion Source tab to configure the ion source as follows: Thermo Scientific TSQ 8000 Evo User Guide...
  • Page 120 50 μA. Tune with the same value you are planning to use for your analysis. The use of emission currents above 100 μA may lead to the generation of too many ions in the source and a degradation in resolution. TSQ 8000 Evo User Guide Thermo Scientific...
  • Page 121 If you change your electron energy from 70 eV, this value also changes. Ensure this voltage is at least 5 V below the voltage applied to the filament. Thermo Scientific TSQ 8000 Evo User Guide...
  • Page 122 Figure 98. Configuring Tuning Targets Tune Target Ion Ratios—Select this check box to adjust the ratios based on the results from an injection of tuning compound. 6. Click the Detector tab to configure the detectors. See Figure TSQ 8000 Evo User Guide Thermo Scientific...
  • Page 123 • Mass—Select the calibration gas mass you want to use. • Intensity—Enter the intensity you want to see on the tune report. 7. Click the Diagnostics tab and select a test to confirm the operational ability of the system. See Figure 100. Thermo Scientific TSQ 8000 Evo User Guide...
  • Page 124 8. Click the Report tab configure how you want to view your data Figure 101. Selecting Data Report Options a. Acquire Full-Scan Spectrum—Select this check box to display the full spectrum on your tune report. TSQ 8000 Evo User Guide Thermo Scientific...
  • Page 125 The Rename Tune Type dialog box opens. Assign a valid new name to your tune. You will not be able enter a name that is an invalid file name or already in use. See Figure 103. Thermo Scientific TSQ 8000 Evo User Guide...
  • Page 126 Select the Tune Lenses check box to access the data table. Figure 104. Figure 104. Tuning the Q1 Lenses a. Device—Click in this box to select the component you want to tune according to the settings in the other columns. TSQ 8000 Evo User Guide Thermo Scientific...
  • Page 127 Q1 Resolution—Adjusts the ratio of the quadrupole DC and RF voltages to create the resolution required for your analysis. You can set the desired peak width at a given mass and whether you measure the width at 10% or 50% of the Thermo Scientific TSQ 8000 Evo User Guide...
  • Page 128 peak height. Because there is no static DC voltage involved, the start, stop, and step values are not used. b. Mass—Click in this box to select the ion to be used for tuning. c. Start—Enter the starting voltage for the tune. The start voltage must always be less than the stop voltage.
  • Page 129 (if anything) must be done about the resolution of the peak and any errors that occur. Thermo Scientific TSQ 8000 Evo User Guide...
  • Page 130 Step—Enter the increment for the tuning range. For example, if you tune from 0-50 in increments of 10 V, then you would set the Step field to 10. g. Max Width—Enter the maximum allowable width of the ion during the tune. TSQ 8000 Evo User Guide Thermo Scientific...
  • Page 131 1000 amu/s scan rates. You may also tune at a higher scan rate. You can tune the resolution during a lens tune or you can tune the resolution by itself. See Figure 107. Thermo Scientific TSQ 8000 Evo User Guide...
  • Page 132 • After—Uses the resolution parameters after a lens tune. 5. Tune High Scan Rate—Select this check box to tune the resolution at a scan rate in addition to the 100 and 1000 amu/s default scan rates. TSQ 8000 Evo User Guide Thermo Scientific...

  • Page 133: Chapter 6 Computer Settings

    3. For Put the Computer to Sleep, select Never. See Figure 108. You may set the display to turn off at any time. It will not affect the performance of your TSQ 8000 Evo system. Thermo Scientific TSQ 8000 Evo User Guide...
  • Page 134 4. In the Performance Options dialog box, click the Advanced tab, and then click Change to open the Virtual Memory window. 5. Confirm that Automatically Manage Paging File Size for All Drives check box is selected. See Figure 109. Figure 109. Virtual Memory Settings TSQ 8000 Evo User Guide Thermo Scientific...
  • Page 135 ), select Properties. 3. In the Windows Firewall with Advanced Security on Local Computer Properties window, select Domain Profile | State | Customize. Figure 110. Firewall Settings for the TSQ 8000 Evo System Computer Actions Panel 4. In the Protected Connections for the Domain Profile window, make sure that any instrument checkboxes are not checked.

  • Page 136: Excluding The Xcalibur Directory From Virus Scan

    Failure to exclude these folders might cause interruptions in data acquisition. If you must, for security reasons, scan all system files, set the virus scans so that they occur when you are not using the instrument to acquire data. TSQ 8000 Evo User Guide Thermo Scientific...

  • Page 137: Chapter 7 Troubleshooting

    GC. If your intensities are too low, make sure carrier vacuum compensation is turned on. Thermo Scientific TSQ 8000 Evo User Guide...

  • Page 138: Diagnostics Checks

    The following table provides you with possible corrective actions you can take after failing a diagnostics check on your system. Note If you are unsure about what to do if your system fails a diagnostic, please contact your field service engineer. TSQ 8000 Evo User Guide Thermo Scientific...

  • Page 139: How To Know When Your System Needs Maintenance

    • Air Leaks—Higher than normal vacuum pressure or poor sensitivity usually indicates an air leak. Check the last o-ring or ferrule that you installed. Thermo Scientific TSQ 8000 Evo User Guide...
  • Page 140 Cleaning solvent 105, 106 Xylene Cleaning solvent 151, 153 Trichloroethane Cleaning solvent Plasticizer (phthalates) Use of vinyl or plastic gloves Peaks spaced 14 amu apart Hydrocarbons Fingerprints, foreline pump oil, or other hydrocarbons TSQ 8000 Evo User Guide Thermo Scientific...

  • Page 141: Investigating Baseline Issues

    Check impurity levels in the gas source. accumulated in column Use correct gas purity. Abnormal rise in Impurities have Recondition or replace the column. baseline when oven accumulated in column temperature is high Thermo Scientific TSQ 8000 Evo User Guide...
  • Page 142 Leak at column fittings Find leak. Tighten fittings if loose. Replace ferrule if overtightened. Transfer line temperature is not set too low. TSQ 8000 Evo User Guide Thermo Scientific...

  • Page 143: Investigating Peak Issues

    GC effluent will contact the inside wall. Fronting General Column is overloaded Decrease the injected amount and/or analyte concentrations. Increase the split ratio. Use a column with a thicker film. Thermo Scientific TSQ 8000 Evo User Guide...
  • Page 144 Source temperature is too If tailing occurs on late eluting compounds, it is likely the source or transferline temperature is too low. Poor column Changing the Column characterization information about checking for leaks and column flow. TSQ 8000 Evo User Guide Thermo Scientific...
  • Page 145 Verify that the Busy light is on during acquisition. Make sure the filament is not burned out. Close Xcalibur, open Instrument Configuration, press the Reset button on the mass spectrometer, wait ten seconds, close Instrument Configuration. Thermo Scientific TSQ 8000 Evo User Guide...

  • Page 146: Investigating Results Issues

    Carefully meter the injected amount. suitable Use a clean, good-quality syringe. Ion source is dirty Clean the ion source and retune the instrument. Split flow or ratio control is Monitor the flow. inadequate Replace the in-line filter. TSQ 8000 Evo User Guide Thermo Scientific...
  • Page 147 Vaporization size of sample Reduce the injected amount and/or inject larger than volume of volume. liner Column temperature is Check the main oven door and cooling unstable flap. Monitor the column temperature. Thermo Scientific TSQ 8000 Evo User Guide...

  • Page 149: Index

    WEEE Configuring the TSQ 8000 Evo, maintenance, settings, contaminants, common, mass range, narrowing, contamination, indications, methods acquisition, creating, purpose of, data result issues, investigating,...
  • Page 150 Index: R tailing, EI full tune, profiled data, about, tuning using Autotune, with TSQ 8000 Evo Autotune, regulatory compliance results (troubleshooting) voltage of filament, setting, low reproducibility of peaks area, poor sensitivity, retention times, retention times, troubleshooting, WEEE compliance routine maintenance...

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