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Thermo Scientific ISQ User Manual

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ISQ
User Guide
1R120555-0003 Revision D January 2013

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  • Page 1 User Guide 1R120555-0003 Revision D January 2013...
  • Page 2 © 2013 Thermo Fisher Scientific Inc. All rights reserved. ISQ, TSQ 8000, TSQ Quantum, TRACE 1300, TRACE 1310, TRACE GC, TRACE GC Ultra, TraceFinder, and FOCUS GC are trademarks, and Xcalibur is a registered trademark of Thermo Fisher Scientific in the United States.

  • Page 3: Table Of Contents

    Accessing ISQ Autotune ......... . 24 Tuning the ISQ Mass Spectrometer ....... . . 24 Chapter 4 Creating a Method.
  • Page 4 No Ions Present in Scans ......... 104 Checking the ISQ System Firmware ....... . 104 How to Know When Your System Needs Maintenance .
  • Page 5 • Direct Probe Controller (DPC) standards: EMC EN 61326-1:2006. Safety IEC 61010-1:2001, IEC 61010-2-081:2001 • ISQ and TSQ 8000 standards: EMC EN 61326-1:2006. Safety IEC 61010-1:2001, IEC 61010-2-081:2001 Low Voltage Safety Compliance This device complies with Low Voltage Directive 2006/95/EC and harmonized standard EN 61010-1:2001.
  • 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 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

    The heated ion volume, lens stack, and ion optics path in the ISQ system ensure that the system stays cleaner longer, but when the system no longer meets your analytical needs, restoring performance is quick and easy.

  • Page 10: Related Documentation

    • ISQ and TSQ 8000 Direct Probe System User Guide PN 1R120505-0006  To view product manuals Go to Start > All Programs > Foundation 2.0 > Manuals > ISQ.  To open Help • From the ISQ window, choose Help > ISQ Help.

  • Page 11: System Requirements

    Preface System Requirements System Requirements Your ISQ data system must meet these minimum requirements. System Requirements Hardware • 2.4 GHz processor with 4 GB RAM • DVD/CD-ROM drive • Resolution display 1280 × 1024 (XGA) • 250 GB hard drive or larger •...
  • Page 12 LIFTING HAZARD: Indicates that a physical injury could or might occur if two or more people do not lift an object. MATERIAL AND EYE HAZARD: Indicates that eye damage could or might occur. ISQ User Guide Thermo Scientific...

  • Page 13: Hydrogen Safety Precautions

    You should ask yourself: “What hydrogen hazards associated with this project are most likely to occur?” “What hydrogen hazards associated with this project have the potential to result in the worst consequences?” Thermo Scientific ISQ User Guide xiii...
  • Page 14 • There should also be contingency plans in place should an incident occur. • The site emergency response team, as well as the local fire department, should know the location of all hydrogen storage tanks. ISQ User Guide Thermo Scientific...

  • Page 15: Using Hydrogen With Isq

    Hydrogen Safety Precautions Using Hydrogen with ISQ To use hydrogen with the ISQ instrument, you must always shut off the GC carrier gas before venting or turning off the ISQ instrument. There are three hydrogen safety screws on the ISQ instrument that must be in place.

  • Page 16: Hydrogen Connection Guidelines

    Ball valves are often chosen because of their superior leak tightness through the valve seat. Pneumatic operators are usually chosen for remotely operated valves so that potential ignition sources (electricity) are remote from the valve. ISQ User Guide Thermo Scientific...

  • Page 17: Purchasing Hydrogen

    Never crack a hydrogen cylinder valve to remove dust or dirt from fittings prior to attaching a regulator, as there is a risk of self-ignition. Thermo Scientific ISQ User Guide xvii...

  • Page 18: Properly Storing Hydrogen

    • As liquid hydrogen systems also have a cryogenic hazard, additional safety considerations for the use of cryogenic liquids may be necessary. xviii ISQ 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 ISQ 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. ISQ User Guide Thermo Scientific...

  • Page 21: Venting Toxic Gases

    To get local contact information for sales or service Go to www.thermoscientific.com/wps/portal/ts/contactus.  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 ISQ User Guide...

  • Page 23: Confirming Your Gc/Ms System Is Working

    To confirm that the ISQ system is powered on, make sure the Power light on the front panel is solid green. If it is not lit, the ISQ system is not powered on. To power it on, reach around the right side of the instrument and pull up the power switch on the back.

  • Page 24: Verifying The Carrier Gas Flow Rate

    Confirming Your GC/MS System is Working Verifying the Carrier Gas Flow Rate Figure 1. Checking the Power on the ISQ System Power To confirm that a TRACE GC Ultra is powered on, make sure the front LCD panel displays information and that it is not blank. To power-on the TRACE GC Ultra, reach over the top center of the instrument and pull up on the large plastic ribbed power switch on the back.

  • Page 25: Checking Your Carrier Gas Tank Pressure

    3. Ensure the pressure is more than 500 psi at the primary (or first) regulator stage. If it is not, you may want to replace the tank if you have to run a lot of samples. 4. Set the second stage regulator pressure between 80 and 100 psi (560 kPa to 700 kPa). Thermo Scientific ISQ User Guide...

  • Page 26: Checking The Vacuum And Temperature

    Use the lights on the front of the ISQ instrument to check the vacuum and temperature of the instrument. To check the vacuum, look at the Vacuum light. When the light is a solid green, the ISQ mass spectrometer is under sufficient vacuum. If it is slowly blinking orange, you have not achieved vacuum yet.

  • Page 27: Chapter 2 Changing The Column

    Changing the Column The ISQ mass spectrometer ships with a factory-tested 15 m x 0.25mm i.d. 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 need to install a column that accommodates the type and quantity of samples you will be running.
  • Page 28 Very short columns (2.5, 5, and 10 m) are also available. Note Contact your local sales representative to order a Thermo Fisher Scientific column. You can also refer to our catalog or visit our website at www.thermoscientific.com/columns. ISQ User Guide Thermo Scientific...

  • Page 29: Replacing The Factory Installed Column

    If you are using hydrogen as a carrier gas, you must cool down and shut off the GC to prevent the buildup of hydrogen in the vacuum manifold. 2. Click Shut Down on the ISQ Dashboard or on the ISQ status page within the instrument software.
  • Page 30 Changing the Column Replacing the Factory Installed Column Figure 3. Powering Off the ISQ Instrument Hydrogen Safety Screws Power Switch Vent Valve Knob Hydrogen Safety Screw Vacuum Interlock Shield (On Front Door Panel) 6. Open the front door of the instrument.
  • Page 31 Bubbles indicate there is flow through the column. If there is no flow, check that the carrier gas is on, the GC inlet is pressurized, and the column is not plugged. If there is still no flow, consult the GC documentation or contact Technical Support. Thermo Scientific ISQ User Guide...
  • Page 32 Repeat the leak check until no leaks are indicated. 16. Calibrate the carrier gas flow (column evaluation): a. Carefully push the capillary column end into the flowmeter section of the column flowmeter connector. See Figure ISQ User Guide Thermo Scientific...
  • Page 33 Select Apply and the K-factor will be adjusted to give the corrected column flow. According to the physical characteristics of the column, the system calculates and displays the relevant column K-factor. At the end of the routine, a message will indicate that the evaluation was successful. Thermo Scientific ISQ User Guide...
  • Page 34 Close the GC door. 18. Condition the column before inserting it into the ISQ system. Column conditioning consists of passing a carrier gas through the column heated to a programmed temperature as described in the column manufacturer’s instructions.

  • Page 35: Connecting The Column To The Transfer Line

    Transfer Line Nut SilTite Ferrule 7. Insert the column into the column measuring tool (see Figure 6), which is in the ISQ Toolkit, so that it is even with the lines at the end of the column. Figure 7 indicates proper positioning of the column in the tool for accurate measuring.
  • Page 36 Figure 8. Positioning the Septum Transfer Line Column Measuring Tool Septum 14. Pull the column back from the transfer line nut. Do not move the septum from its position on the column. ISQ User Guide Thermo Scientific...
  • Page 37 20. Position the column in the transfer line. Use the septum as a guide to measure the correct length you should insert the column. Be careful not to change the location of the septum on the column. Thermo Scientific ISQ User Guide...
  • Page 38 Note If you are using a SilTite ferrule, follow the instructions that come with SilTite ferrules. If you are using a graphite Vespel ferrule, they require conditioning to ensure a leak-tight seal. See the ISQ Spare Parts Guide for information about ordering these ferrules.
  • Page 39 28. Once the ISQ instrument is pumped down and able to scan, click Air & Water / Tune on the ISQ Dashboard view air water spectra and look for evidence of leaks with a large m/z 28 signal.
  • Page 40 Line Nut Ferrule 8. Insert the column into the column measuring tool (see Figure 13), which is in the ISQ Toolkit , so that it is even with the lines at the end of the column. Figure 14 indicates proper positioning of the column in the tool for accurate measuring.
  • Page 41 15. Pull the column back from the spring loaded transfer line nut. Do not move the septum from its position on the column. Figure 16. Pulling the Column Back from the Spring Loaded Transfer Line Nut Spring Loaded Column Transfer Line Nut Septum Thermo Scientific ISQ User Guide...
  • Page 42 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. ISQ User Guide Thermo Scientific...
  • Page 43 Twist the vent valve clockwise to close the valve. Be sure not to pinch the o-ring. d. If you are using hydrogen as a carrier gas, replace the front panel screw. e. Replace all remaining hydrogen safety screws if you are using hydrogen. Thermo Scientific ISQ User Guide...
  • Page 44 29. Once the ISQ 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 45: Tuning The Isq

    If the system has been powered off for a period of time (a cold system), it takes longer (up to 4 hours) for the instrument components to reach stabile vacuum and temperature. If you did not vent the ISQ instrument (system is hot), it takes approximately 30 minutes for the components to reach vacuum and temperature.

  • Page 46: Accessing Isq Autotune

    Accessing ISQ Autotune To access ISQ Autotune  Open the ISQ Dashboard and click Auto Tune to open the ISQ Autotune window. Figure 19. Accessing ISQ Autotune from the ISQ Dashboard The list of available tune types opens. Tuning the ISQ Mass Spectrometer ...
  • Page 47 Tuning the ISQ Tuning the ISQ Mass Spectrometer Figure 20. List of Available Tunes in ISQ Autotune • Daily Tune Check—This tune check is used to check how well your last tune is performing. It is the fastest tune type. The daily tune check performs a leak check, makes sure the mass calibration is okay, and sets the detector sensitivity to generate a m/z 69 ion with an intensity of 20,000,000 counts.
  • Page 48 Tuning the ISQ Tuning the ISQ Mass Spectrometer • EI Full Tune—This tune is used to completely retune the system. It takes the longest amount of time to run, but the advantage of using it is that it re-optimizes nearly all the parameters affecting the signal.
  • Page 49 Tuning the ISQ Tuning the ISQ Mass Spectrometer Figure 21. Displaying a Tune Report 3. Select the Show Spectra checkbox to show the spectra while the system is tuning. 4. Click the Start button to begin tuning. Note Make sure the power options on your computer are not set to go into Standby mode while you’re acquiring data for your tune.
  • Page 50 Figure 22. Showing the Spectra During an Automatic Tune 5. Once the tune completes, your tune report will open in the ISQ Tune Results Viewer. If you did not select the Display Report When Complete checkbox, you can click View Tune Report on the ISQ Dashboard and view the report.
  • Page 51 Tuning the ISQ Tuning the ISQ Mass Spectrometer Figure 23. Viewing a Tune Report. Thermo Scientific ISQ User Guide...
  • Page 52 Tuning the ISQ Tuning the ISQ Mass Spectrometer 6. Compare this tune with a previous tune report. Some changes in peak height are normal, but if the difference is significant, see Troubleshooting. If you have recently serviced the instrument, you most likely have a leak at the column, vent valve or near the component you just serviced.
  • Page 53 Tuning the ISQ Tuning the ISQ Mass Spectrometer Figure 25. Printing a Tune Report 9. Click Report Options to select the charts and reports you want to display and change the name of your instrument. Then click OK. Figure 26. Selecting the Tune Report Options 10.

  • Page 55: Creating A Method

    Creating a Method Once you’ve got the ISQ mass spectrometer tuned, you can create a method for each component of your system. Methods are used to indicate to the GC/MS system how to collect your data. Contents • Creating a Method for the Autosampler •...

  • Page 56: Creating A Method For The Autosampler

    Creating a Method Creating a Method for the Autosampler Figure 27. Accessing the Method Editor from the ISQ Dashboard Creating a Method for the Autosampler 1. Create a method for the autosampler. Instructions for setting common parameters are below. Refer to you autosampler documentation for specific guidelines.
  • Page 57 • Sampling Depth in Vial—Use this pull-down menu to select the depth (Center or Bottom) at which the tip of the syringe needle will be placed in the sample vial when it is being filled. The bottom is the default and most commonly used setting. Thermo Scientific ISQ User Guide...
  • Page 58 The sample vapor is produced closer to the column inlet, which can lead to better sensitivity, but worse reproducibility from one run to the next. ISQ User Guide Thermo Scientific...

  • Page 59: Creating A Method For The Isq Mass Spectrometer

    Creating a Method for the ISQ Mass Spectrometer Click the ISQ icon in the left pane to create a method for the ISQ mass spectrometer. 1. To create a acquisition method from the Method Type pull-down menu, select Acquisition-General.
  • Page 60 5. Select EI from the Ionization Mode pull-down menu. Note Only use CI if you have installed a CI ion volume in the ISQ instrument and you have connected CI reagent gas to your system. If you have CI, select a CI Gas Type from the pull-down menu and set the CI Gas Flow.
  • Page 61 The Time (min) column is used to set the time that the ISQ system begins to acquire data after the GC starts. It is typical to have enough of a time delay to allow the solvent to get through the column before starting an acquisition.
  • Page 62 You should set this value to have 5-20 scans across your GC peak. If you have too few scans, the GC peak area is too imprecise. If you have too many scans, the ISQ instrument’s signal becomes less precise. The default is 0.2 s.
  • Page 63 You can also reorganize the columns by clicking on the heading of a column and dragging it to the left or right. a. The Time column displays the time that the ISQ mass spectrometer begins to acquire this particular group of scans after the GC starts.
  • Page 64 The Use Last Tuned Detector Gain column indicates that you want to use the detector gain set in ISQ Autotune or set and scanned in manual tune. If you do not need to use the gain set in ISQ Autotune, 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.

  • Page 65: Creating A Method For The Gc

    0 and 999.99 minutes. The typical initial temperature is at least 10 °C above the boiling point of your sample solvent and the initial time is usually long enough for the solvent to move through the column. Thermo Scientific ISQ User Guide...
  • Page 66 0 °C to -99 °C. The GC also allows the use of a post run column cleaning. This is not typically used because the material that is purged from the column in this step would go into the ISQ, which can lead to contamination. If you want ISQ User Guide...
  • Page 67 The default purge flow value is 5 mL/min. This reduces the buildup of contaminants in the injector, on the column, and in the ISQ instrument. If you perform a splitless injection, even if the split flow is set, the split flow will be turned off for the splitless time.
  • Page 68 20 mL/min because contaminants can build up in the injector, column, and ISQ instrument, which can affect the system performance. It is also possible for air to diffuse back into the column with low split flows when the column head pressure is low.
  • Page 69 See the GC documentation for details about the PTV or other types of injectors. 5. Click the Run Table tab to configure how to control external valves and devices. Consult the GC documentation for more detailed information. Thermo Scientific ISQ User Guide...
  • Page 70 Add the inlet or detector to the current instrument configuration. Go to Start | All Programs | Thermo Foundation 2.0 | Instrument Configuration. c. In the Configured Devices panel, click the TRACE 1300 or TRACE 1310 icon. Select Configure. ISQ User Guide Thermo Scientific...
  • Page 71 Click Get. The software automatically detects the attached modules. Select the gases as appropriate to your setup. The default Channel names are Channel 1 and Channel 2. You may want to change them to something more descriptive. Your hardware is now configured. Thermo Scientific ISQ User Guide...

  • Page 72: Creating A Method For The Trace Gc Ultra

    0 and 999.99 minutes. The typical initial temperature is at least 10 °C above the boiling point of your sample solvent and the initial time is usually long enough for the solvent to move through the column. ISQ User Guide Thermo Scientific...
  • Page 73 This is not typically used because the material that is purged from the column in this step would go into the ISQ instrument, 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...
  • Page 74 CAUTION - INSTRUMENT DAMAGE. Be sure not to overheat the GC column or it may contaminate the ISQ instrument. 3. If you have a split / splitless inlet (SSL) injector, click the Left SSL or Right SSL tab to configure the injector port settings.
  • Page 75 This reduces the buildup of contaminants in the injector, on the column, and in the ISQ instrument. If you perform a splitless injection, even if the split flow is set, the split flow will be turned off for the splitless time. The septum purge will be turned off for the stop purge time.

  • Page 76: Creating A Method For The Focus Gc

    Because the outlet of the column is in the ISQ instrument, which is under vacuum, the vacuum compensation must be on. a. The flow can also be operated in programmed flow or programmed pressure modes.
  • Page 77 GC is at temperature and when the GC reports as being ready. This delay is typically set to 0.1 minutes. CAUTION - INSTRUMENT DAMAGE. Be sure not to overheat the GC column or it may contaminate the ISQ instrument. Thermo Scientific ISQ User Guide...
  • Page 78 This reduces the buildup of contaminants in the injector, on the column, and in the ISQ instrument. If you perform a splitless injection, even if the split flow is set, the split flow will be turned off for the splitless time. The septum purge will be turned off for the stop purge time.
  • Page 79 Constant flow is more common. Typical flow rates are 1-3 mL/min. The pressure depends on the column length and internal dimensions, so there is not a typical value. Because the outlet of the column is in the ISQ instrument, which is under vacuum, the vacuum compensation must be on.
  • Page 80 5. Click the Run Table tab to configure how to control external valves and other external devices. Consult the appropriate documentation for more detailed information. Figure 46. Locating the Run Table Parameters on the FOCUS GC ISQ User Guide Thermo Scientific...
  • Page 81 Creating a Method for the GC 6. When you are finished creating methods for each component in your GC/MS system, select File | Save As... from the main menu or click the icon. Figure 47. Saving Your ISQ Instrument Method Thermo Scientific ISQ User Guide...
  • Page 82 Creating a Method Creating a Method for the GC ISQ User Guide Thermo Scientific...

  • Page 83: Chapter 5 Running A Sample

    Once your sample is prepared, you can transfer it to a sealed vial so that you can inject it into the GC. It is important to use a sealed vial because you do not want the concentration to be altered, which is what happens when the solvent evaporates. Thermo Scientific ISQ User Guide...

  • Page 84: Running A Sequence

    To run a new sequence of samples 1. Double-click the Xcalibur software icon on your computer desktop. 2. In the Xcalibur Roadmap window, click the Sequence Setup icon. Figure 48. Sequence Setup in Xcalibur Sequence Setup ISQ User Guide Thermo Scientific...
  • Page 85 You can also right-click on the field to clear, copy, or paste into the field, as well as add and delete rows. Note If you do not have some of the columns discussed here, you can add them by selecting Change | Column Arrangement in the main menu. Thermo Scientific ISQ User Guide...
  • Page 86 Note Your file name cannot contain spaces. Figure 50. Naming a File Tip You can double-click in the File Name field and browse to a raw file on your computer. ISQ User Guide Thermo Scientific...
  • Page 87 You can also right-click on the field to clear, copy, or paste into the field, browse to a folder on your computer, or add and delete rows. Figure 51. Selecting a Folder to Store Data Files Thermo Scientific ISQ User Guide...
  • Page 88 9. Click the first row in the Position column and enter the sample’s vial number if you are using an autosampler. You can also right-click on the field to clear, copy, or paste into the field, as well as add and delete rows. ISQ User Guide Thermo Scientific...
  • Page 89 Running a Sample Running a Sequence Figure 53. Entering the Sample Vial Position Thermo Scientific ISQ User Guide...
  • Page 90 12. Now that you’ve set up one row of your sequence, you can stop or you can continue adding tasks. Click in the next row and repeat steps 2-10 for each additional task in your sequence. Remember, you can right-click in most fields to add more rows as you go. ISQ User Guide Thermo Scientific...
  • Page 91 Figure 55. Adding Additional Sequence Setup Tasks 13. Once you’ve created a sequence of all your samples, select File | Save or click the icon to save the sequence. 14. Enter a comment and click OK. Thermo Scientific ISQ User Guide...
  • Page 92 Running a Sample Running a Sequence Figure 56. Entering a Comment About Your Sequence 15. Enter the name of your sequence and click the Save button. Figure 57. Naming and Saving your Sequence ISQ User Guide Thermo Scientific...
  • Page 93 To run the whole sequence, select Actions | Run Sequence from the main menu. You can also just click the icon on the main tool bar. 17. In the Run Sequence window, customize the way you want your sequence to run. Thermo Scientific ISQ User Guide...
  • Page 94 In the Programs group, you can browse to the executables for Pre-Acquisition and Post-Acquisition. These fields are used to automatically run processing methods after the data acquisition is complete. Because you are developing your method, you haven’t defined a processing method for this field. ISQ User Guide Thermo Scientific...
  • Page 95 • On—Select this option to leave the instrument fully ready after an acquisition. • Standby—Select this option to leave the instrument fully ready after an acquisition. • Off—Select this option to turn off the ISQ by turning off the heaters, turbo pump and foreline pump. IMPORTANT If you are using hydrogen as a carrier gas, manually turn off the GC after the sequence completes if you are using this setting.
  • Page 96 19. In the Save As window, select a location on your computer that you want to store your sequence. Then click the Save button. Figure 60. Saving a Sequence to the Computer 20. Once your sequence completes, you are ready to explore your data. ISQ User Guide Thermo Scientific...

  • Page 97: Exploring Your Data

    To view your data in Qual Browser: 1. Double-click the Xcalibur software icon on your computer desktop. 2. In the Xcalibur Roadmap window, click the Qual Browser icon. Figure 61. Xcalibur Roadmap Thermo Scientific ISQ User Guide...
  • Page 98 4. Select the raw file(s) you ran in your sequence and click Open. Figure 62. Selecting the Raw File 5. The chromatogram is shown in the upper pane of the window and the spectra in the bottom pane. ISQ User Guide Thermo Scientific...
  • Page 99 272, select a mass range that contains only this ion. By eliminating all the masses that are not generated by your compound, it is much easier to find and quantify the GC peak area. Thermo Scientific ISQ User Guide...
  • Page 100 Another way to zoom in is to return to the Ranges tab and manually enter the time range to display. ISQ User Guide Thermo Scientific...
  • Page 101 8. Right-click in the Chromatogram pane and select Peak Detection | Toggle Detection in All Plots to enable Qual Browser to find the peaks and define their edges. Figure 67. Finding the Peaks in Qual Browser Thermo Scientific ISQ User Guide...
  • Page 102 10. Click the Labels tab and select Retention Time and Area in the Label With group. Figure 69. Labeling the Display 11. With the MS window pinned, click on the peak to open the mass spectrum at the point you clicked. ISQ User Guide Thermo Scientific...
  • Page 103 Exploring Your Data Figure 70. Opening the Mass Spectrum 12. In this spectrum, there are large peaks at m/z 57 and 99. These are very common ions from hydrocarbons. The OFN peak is near m/z 272. Thermo Scientific ISQ User Guide...
  • Page 104 Exploring Your Data Figure 71. Setting the Spectrum Range Figure 72. Finding the OFN Peak ISQ User Guide Thermo Scientific...
  • Page 105 Usually, a one range subtraction is performed before the peak eluted. The range to be subtracted out should not contain any of your chromatographic peak. The full scan shows the ions from OFN (at m/z 222, 241, and 272) much more clearly than without the background subtraction. Thermo Scientific ISQ User Guide...
  • Page 106 Without background subtraction, the full scan would look like the graphic below. Figure 75. OFN in Full Scan Without Background Subtraction 14. There are many other ways to change the way you data displays in Qual Browser. See the Qual Browser online help for details. ISQ User Guide Thermo Scientific...

  • Page 107: Optimizing Your Method

    If the GC oven is not at the boiling point, the compounds will not volatilize and they will become immobilized. Changing ramp rates is usually used to separate coeluting peaks. Thermo Scientific ISQ User Guide...

  • Page 108: Finding The Best Way To Make An Injection

    A narrower mass range will also allow you to decrease the scan rate and get the same chromatographic peak sampling. Breaking your MS method into groups allows you to create compound-specific MS settings to optimize your data. ISQ User Guide Thermo Scientific...

  • Page 109: Adjusting The Transfer Line Temperature

    Increase the source temperature as well to improve response for high-boiling compounds and prevent column bleed and matrix compounds from dirtying the ion source. Note The transfer line temperature and ion source temperature should be similar to avoid contaminating the ion source. Thermo Scientific ISQ User Guide...

  • Page 110: Modifying An Automatic Tune

    Modifying an Automatic Tune Modifying an Automatic Tune ISQ Autotune is a utility that uses certain parameters in the tune types to optimize system performance when generating a tune file. To modify an automatic tune: 1. Click Tune Types on the ISQ Dashboard to the Xcalibur software icon on your computer desktop.
  • Page 111 3. Configure the options under the General tab. Figure 78. Configuring the General Options • Name—Use this field to enter a name for your tune type. • Description—Use this field to enter details or notes about your tune type. Thermo Scientific ISQ User Guide...
  • Page 112 Select Last Saved to use a tune file saved on the instrument by the most recent successful automatic tune. A tune file may also be loaded and saved to the instrument for the Last Saved tune file using ISQ Manual Tune. –...
  • Page 113 During this time, the Busy light will be lit and you have to wait until the light goes off before using the ISQ software. • CI Gas Flow (enabled when you select a CI Gas Type)—Use this field to enter the flow rate of your CI gas.
  • Page 114 Default—Select this option to use the default electron lens negative voltage, which is -75 V. – Tune File—Select this option to use the value used in the tune file you selected in the General tab. ISQ User Guide Thermo Scientific...
  • Page 115 (if anything) should be done about the resolution of the peak and any errors that occur. Note Click the Advanced Settings check box to access the Lenses tab. Thermo Scientific ISQ User Guide...
  • Page 116 This field is typically set between 0 and -15 V in EI mode. In CI, the optimal voltage may be between 0 and -30 V. ISQ User Guide Thermo Scientific...
  • Page 117 • Measure at %—Use this pull-down menu to select the location on the peak at which you want to measure the maximum width. – 10—Select this option to measure the width at 10% of the peak height. Thermo Scientific ISQ User Guide...
  • Page 118 Note Click the Advanced Settings check box to access the Resolution tab. • Tune Resolution—Select this option to tune the resolution by itself. This resolution will tune the system at 100 and 1000 amu/s scan rates. You may also tune at a higher scan rate. ISQ User Guide Thermo Scientific...
  • Page 119 100 and 1000 amu/s default scan rates. 7. Click the Targets tab to configure how you want to tune your targets. Target tuning is used to adjust the way the ISQ tunes to meet regulatory requirements. Thermo Scientific...
  • Page 120 Figure 82. Configuring the Target Ion Ratios • Tune Target Ion Ratios—Select this checkbox to adjust the ratios based on the results from an injection of tuning compound. 8. Configure the options under the Detector tab. ISQ User Guide Thermo Scientific...
  • Page 121 – Intensity—Use this field to enter the intensity you want to see on the tune report. 9. Click the Diagnostics tab and select a test to confirm the operational ability of the ISQ system. Thermo Scientific ISQ User Guide...
  • Page 122 Optimizing Your Method Modifying an Automatic Tune Figure 84. Accessing the ISQ System Diagnostics 10. Click the Report tab configure how you want to view your data. Figure 85. Configuring the Report Options • Acquire Full-Scan Spectrum—Select this checkbox to display the full spectrum on your tune report.
  • Page 123 12. Click Print to save your tune type information as a pdf or to print a hard copy of the information. Figure 86. Printing the Tune Type Information 13. Click Close to return to the Method Setup window. Now the tune type can be selected during an automatic tune. Thermo Scientific ISQ User Guide...

  • Page 125: Troubleshooting

    A good first step for troubleshooting is to run a tune on the ISQ system. If you have good ion intensities, good peak shapes, and no air leak, you might want to look first at the GC, autosampler, or carrier gas.

  • Page 126: No Ions Present In Scans

    30 min for it to get to temperature, then remove and reinsert it. See the ISQ Hardware Manual for instructions on cleaning and inserting the ion source cartridge.
  • Page 127 Checking the ISQ System Firmware Figure 87. The ISQ Manual Tune Utility 2. Click Firmware in the upper right-hand corner of the home screen in ISQ Manual Tune. 3. A new menu opens. Click Version Info. 4. A dialog box containing opens that lists the firmware versions for the ISQ instrument control drivers, the lens driver board, and the controller interface board.
  • Page 128 Checking the ISQ System Firmware Figure 88. Determining the Firmware Versions Note Depending on the version of ISQ instrument control software you are running, the controller interface board and lens driver board firmware may not be listed. 5. Click Copy Info to copy the information to the clipboard on your PC.

  • Page 129: How To Know When Your System Needs Maintenance

    To avoid fingerprints, you should wear clean, lint-free gloves when performing any type of maintenance on a component in the vacuum manifold of the ISQ. • Air Leaks—If you notice a higher than normal vacuum pressure or poor sensitivity, it is usually an indication of an air leak.

  • Page 130: Investigating Baseline Issues

    Impurities have 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 ISQ User Guide Thermo Scientific...
  • Page 131 Reduce oven temperature to the than column’s maximum maximum allowable temperature of the allowable temperature column. Leak at column fittings Find leak. Tighten fittings if loose. Replace ferrule if overtightened. Transfer line temperature is not set too low. Thermo Scientific ISQ User Guide...

  • Page 132: 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. ISQ User Guide Thermo Scientific...
  • Page 133 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. Thermo Scientific ISQ User Guide...
  • Page 134 Make sure the tune file is correct. collecting data Verify that the Busy light is on during acquisition. Close Xcalibur, open Instrument Configuration, press the Reset button on the ISQ instrument, wait ten seconds, close Instrument Configuration. ISQ User Guide Thermo Scientific...

  • Page 135: 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. Thermo Scientific ISQ User Guide...
  • Page 136 Be sure the GC is inhibited by the MS configured correctly and waits for contact closure by the autosampler. Column temperature is Check the main oven door and cooling unstable flap. Monitor the column temperature. ISQ User Guide Thermo Scientific...

  • Page 137: Reconfiguring Your Instrument

    Instrument Configuration. When the Instrument Configuration utility opens, you can see an icon of the instruments you have connected. 2. Click the ISQ (and other instruments) icon in the Available Devices column and click Add to move it into the Configured Devices column.
  • Page 138 Troubleshooting Reconfiguring Your Instrument Figure 90. Adding a a Device to be Configured 4. Click Configure. ISQ User Guide Thermo Scientific...
  • Page 139 6. Set the remote start. It is used to let the ISQ MS know when the GC has started a run. When you configure the GC, you can tell it what to send out to the ISQ. In this window,...
  • Page 140 You can monitor the progress of these settings in the Status pane of Xcalibur. 9. Select the Foreline pump oil checkbox to enable the maintenance intervals. Then set the ISQ User Guide Thermo Scientific...
  • Page 141 The manufacturer recommends changing the oil every 125 days. If you are using corrosive gases, such as ammonia, you should change the oil every 30 days. Figure 94. Setting the Foreline Pump Oil Maintenance Interval Thermo Scientific ISQ User Guide...
  • Page 142 Figure 96. Setting the Filament 1 Maintenance Reminder 12. Select the Filament 2 checkbox to enable the maintenance reminder. Then set the number of days in which you want to be reminded to check filament 2. In a leak-free ISQ User Guide Thermo Scientific...
  • Page 143 Figure 97. Setting the Filament 2 Maintenance Reminder 13. Select the Ion source checkbox to enable the maintenance reminder. Then set the number of days in which you want to be reminded to check the ion source. The time Thermo Scientific ISQ User Guide...
  • Page 144 14. Select the Multiplier checkbox to enable the maintenance reminder. Then set the number of days in which you want to be reminded to check the electron multiplier. Figure 99. Setting the Electron Multiplier Maintenance Reminder 15. Click OK to return to the main Instrument Configuration window. ISQ User Guide Thermo Scientific...
  • Page 145 Troubleshooting Reconfiguring Your Instrument Figure 100. Returning to the Configuration Window Thermo Scientific ISQ User Guide...
  • Page 146 16. Click the Done button to close the Instrument Configuration utility. 17. You can check the status of your ISQ instrument in the Status tab of the ISQ Dashboard. Figure 101. Checking the ISQ Instrument Status on the ISQ Dashboard 18.
  • Page 147 Troubleshooting Reconfiguring Your Instrument Figure 102. Checking All Instrument Statuses in Xcalibur Status Pane Thermo Scientific ISQ User Guide...
  • Page 149 ISQ Autotune utility, about, ISQ AutoTune, about, EI tune type, about, electromagnetic compatibility leak, indications, EMC compliance leaks, checking for, Thermo Scientific...
  • Page 150 Index: M lights Heater, safety standards Vacuum, samples lights on ISQ preparing, power, running, scan rate, optimizing, scans, running, maintenance, settings, sensitivity, troubleshooting, mass range, narrowing, sequences about, methods customizing, acquisition, opening, creating, prioritizing, optimizing, running, purpose of, saving, SIM mode, about,...
  • Page 151 Index: U EI default tune, EI full tune, tuning using Autotune, with ISQ Autotune, user name, about, vacuum, checking, voltage of filament, setting, WEEE compliance Thermo Scientific ISQ User Guide...

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