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© 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.

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Excel are registered trademarks of Microsoft. Adobe, and Acrobat are registered trademarks of Adobe Systems
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registered trademark of E.I. du Pont de Nemours and Company in the United States and other countries.

All other trademarks are the property of Thermo Fisher Scientific and its subsidiaries.

Thermo Fisher Scientific Inc. provides this document to its customers with a product purchase to use in the
product operation. This document is copyright protected and any reproduction of the whole or any part of this
document is strictly prohibited, except with the written authorization of Thermo Fisher Scientific Inc.

The contents of this document are subject to change without notice. All technical information in this
document is for reference purposes only. System configurations and specifications in this document supersede
all previous information received by the purchaser.

Thermo Fisher Scientific Inc. makes no representations that this document is complete, accurate or error-
free and assumes no responsibility and will not be liable for any errors, omissions, damage or loss that might
result from any use of this document, even if the information in the document is followed properly.

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Release history: Revision A, May 2010; Revision B, March 2012; Revision C, December 2012

Software version: Thermo Foundation 2.0 SP1, Thermo Xcalibur 2.2 SP1

For Research Use Only. Not for use in diagnostic procedures.

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Summary of Contents for ISQ

Page 1: ...ISQ User Guide 1R120555 0003 Revision D January 2013 ...

Page 2: ...this document is strictly prohibited except with the written authorization of Thermo Fisher Scientific Inc The contents of this document are subject to change without notice All technical information in this document is for reference purposes only System configurations and specifications in this document supersede all previous information received by the purchaser Thermo Fisher Scientific Inc make...

Page 3: ...ecautions xx Biological Hazard Warning Note xx Venting Toxic Gases xxi Contacting Us xxi Chapter 1 Confirming Your GC MS System is Working 1 Checking Power to the System 1 Verifying the Carrier Gas Flow Rate 2 Checking Your Carrier Gas Tank Pressure 3 Checking the Vacuum and Temperature 4 Chapter 2 Changing the Column 5 Replacing the Factory Installed Column 7 Connecting the Column to the Transfer...

Page 4: ...ur Method 85 Changing the Chromatographic Separation 85 Finding the Best Way to Make an Injection 86 Improving the Way You Prepare Samples 86 Changing the Scan Rate 86 Narrowing the Mass Range 86 Adjusting the Transfer Line Temperature 87 Modifying an Automatic Tune 88 Chapter 8 Troubleshooting 103 No Ions Present in Scans 104 Checking the ISQ System Firmware 104 How to Know When Your System Needs...

Page 5: ...rds as described in the next section or sections by product name Changes that you make to your system may void compliance with one or more of these EMC and safety standards Changes to your system include replacing a part or adding components options or peripherals not specifically authorized and qualified by Thermo Fisher Scientific To ensure continued compliance with EMC and safety standards repl...

Page 6: ...d by the instrument Notice on the Susceptibility to Electromagnetic Transmissions Your instrument is designed to work in a controlled electromagnetic environment Do not use radio frequency transmitters such as mobile phones in close proximity to the instrument For manufacturing location see the label on the instrument THIS DEVICE COMPLIES WITH PART 15 OF THE FCC RULES OPERATION IS SUBJECT TO THE F...

Page 7: ... Directives and the recyclers in your country WEEE Konformität Dieses Produkt muss die EU Waste Electrical Electronic Equipment WEEE Richtlinie 2002 96 EC erfüllen Das Produkt ist durch folgendes Symbol gekennzeichnet Thermo Fisher Scientific hat Vereinbarungen mit Verwertungs Entsorgungsfirmen in allen EU Mitgliedsstaaten getroffen damit dieses Produkt durch diese Firmen wiederverwertet oder ents...

Page 8: ... compagnies de recyclage dans chaque état membre de l union européenne et ce produit devrait être collecté ou recyclé par celles ci Davantage d informations sur la conformité de Thermo Fisher Scientific à ces directives les recycleurs dans votre pays et les informations sur les produits Thermo Fisher Scientific qui peuvent aider la détection des substances sujettes à la directive RoHS sont disponi...

Page 9: ... of which can be removed from the instrument while still under vacuum What once took hours or even an entire day is now accomplished in minutes About Your System Gas chromatography mass spectrometry GC MS represents a combination of two powerful analytical techniques GC which acts as a separation technique and MS which acts as a detection technique Complex mixtures of individual compounds can be i...

Page 10: ...User Guide PN 1R120555 0003 ISQ Spare Parts Guide PN 1R120555 0004 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 If available for a specific window or dialog box click Help or press the F1 key for information about setting parameters For more informat...

Page 11: ...a descriptor A WARNING is intended to prevent improper actions that could cause personal 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 NTFS format Software Microsoft Windows 7 SP1 Operating System 32 bit and 64 bit Microsoft Windows XP SP3 Microsoft Office 2007 or 2010 32 bit only Thermo Foundation 2 0 SP1...

Page 12: ...uld or might occur FLAMMABLE GAS HAZARD Alerts you to gases that are compressed liquefied or dissolved under pressure and can ignite on contact with an ignition source This symbol indicates this risk could or might cause physical injury GLOVES REQUIRED Indicates that you must wear gloves when performing a task or physical injury could or might occur HAND AND CHEMICAL HAZARD Indicates that chemical...

Page 13: ...dioactive material could or might occur READ MANUAL Alerts you to carefully read your instrument s documentation to ensure your safety and the instrument s operational ability Failing to carefully read the documentation could or might put you at risk for a physical injury TOXIC SUBSTANCES HAZARD Indicates that exposure to a toxic substance could occur and that exposure could or might cause persona...

Page 14: ...h a compressed gas If working with liquid cryogenic hydrogen insulated gloves and protective shoes should be worn in addition to eye protection You should post No Smoking and No Open Flames signs to identify hydrogen sources and cylinders Maintain inspect and leak test all hydrogen sources regularly All hydrogen shutoff valves should be clearly marked and permanent hydrogen piping should be labele...

Page 15: ... that must be in place These are attached to your instrument at the factory Make sure all the covers and panels of the ISQ instrument are firmly attached before powering on the ISQ instrument If you vented the system make sure the vent valve is tightly closed before powering on the system Make sure all fittings ferrules and o rings are sealed prior to powering on the system Figure 1 Hydrogen Safet...

Page 16: ...age and corrosion and also to prevent Hydrogen from entering a building if there is any leakage Fittings All fittings must be of the proper type approved or designed for use with hydrogen gas Use as few fittings as possible to minimize the potential for leaks After installation ensure that leak testing is carried out prior to system use and on a regular basis There must be no PTFE tape or other th...

Page 17: ...gree of hazard the hydrogen generator must only be operated in a non explosive environment because hydrogen buildup can be ignitable This means that your ventilation system for the room or lab hood must maintain an air exchange rate that is at least two orders of magnitude greater than the maximum hydrogen production rate of the hydrogen generator Be sure to follow the manufacturers directions abo...

Page 18: ... oxygen with a 5 ft 1 5 m tall fire barrier with a half hour fire rating or place the cylinders at least 20 ft 6 m apart When moving hydrogen cylinders Remove the regulator and replace the cylinder valve cap before moving Move cylinders on cylinder carts or with other appropriate transport devices Never roll or drop a cylinder and never lift a cylinder by its protective cap Bulk hydrogen systems i...

Page 19: ... Of Practice CP33 The Bulk Storage of Gaseous Hydrogen at Users Premises CGA G 5 Hydrogen CGA G 5 4 Standard for Hydrogen Piping Systems at Consumer Locations CGA G 5 5 Hydrogen Vent Systems CGA G 5 6 Hydrogen Pipeline Systems CGA G 5 8 High Pressure Hydrogen Piping Systems at Consumer Locations FM Global Property Loss Prevention Data Sheets 7 50 Compressed Gases in Cylinders FM Global Property Lo...

Page 20: ...e Burning Characteristics of Building Materials OSHA 29CFR1910 103 1910 103 Hydrogen Hazardous Substances Precautions Biological Hazard Warning Note In laboratories where samples with potential biological hazards are handled the user must label any equipment or parts which might become contaminated with biohazardous material The appropriate warning labels are included with the shipment of the inst...

Page 21: ...e sure to vent the exhaust gases to a fume hood Consult local environmental and safety regulations for instructions in exhausting fumes from your system Contacting Us There are several ways to contact Thermo Fisher Scientific for the information you need To find out more about our products Go to www thermo com ms for information about our products To get local contact information for sales or serv...

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Page 23: ...wer switch on the back If the instrument still doesn t power on check the electrical connections and wall outlet IMPORTANT You need to change the GC column before setting up a method See Chapter 2 Changing the Column for instruction on changing the column Contents Checking Power to the System Verifying the Carrier Gas Flow Rate Checking Your Carrier Gas Tank Pressure Checking the Vacuum and Temper...

Page 24: ...right of the instrument and pull up on the large plastic ribbed power switch on the back If the instrument still doesn t power on check the electrical connections and wall outlet Verifying the Carrier Gas Flow Rate Once you confirm that the system is powered on you need to verify that carrier gas rate is what you expect To check the carrier gas flow rate 1 Access the carrier gas menu On the TRACE ...

Page 25: ...n the carrier gas tank to accommodate the number of samples you plan to run If the pressure is too low you may run out of gas in the middle of a run which could compromise the results of your data 1 Locate your carrier gas tank It might be in a different room depending on how your lab is set up 2 Look at the pressure gauge on the tank 3 Ensure the pressure is more than 500 psi at the primary or fi...

Page 26: ...d the instrument from achieving vacuum If this is the case you need to find and fix the leak then turn the power off and on Most likely the column nut needs to be tightened the column was not installed correctly or the vent valve was not completely closed To check the temperature look at the Heaters light When the Heaters light is a solid green the ISQ instrument is at temperature If it is blinkin...

Page 27: ...y used in process gas analysis but they are not typically used on mass spectrometers There are also metal clad fused silica columns which have the advantages of fused silica but the metal makes them resistant to breakage These columns are less common and more expensive Stationary Phase The stationary phase is the most important consideration when selecting a column The interaction between the stat...

Page 28: ... allow more opportunities for the analytes to interact with the stationary phase The optimal film thickness depends on the internal diameter of the column and desired phase ratio Thick films with small internal diameters will give very strong interactions with the analytes which can result in longer analysis time and peak tailing Large ID columns with thin films will have very little interaction w...

Page 29: ...as unscrew the hydrogen safety screw on the front door Note The procedure below assumes that optional accessories designed to assist in changing column without venting the mass spectrometer are not present For changing the column when one of these accessories is present consult the user guide for that accessory Note If you are running samples stop the acquisition before powering off the system WAR...

Page 30: ...seal the end of the transfer line to prevent contaminants from entering the MS during column conditioning Figure 3 Powering Off the ISQ Instrument Power Switch Vacuum Interlock Shield Vent Valve Knob Hydrogen Safety Screws Hydrogen Safety Screw On Front Door Panel CAUTION INSTRUMENT DAMAGE Do not proceed until the instrument is vented or pieces of the column or ferrule might blow into the instrume...

Page 31: ...Adjust the column position so that the septum contacts the bottom of the retaining nut Use your fingers to tighten the retaining nut until it starts to grip the column h Tighten the column nut finger tight until it starts to grip the column plus a quarter turn i Remove the notched septum from the column 14 Set up the GC parameters a Set the oven and injector temperature to 50 C 122 F b Set the car...

Page 32: ... with carrier gas to the leak check setpoint The system monitors the pressure for one minute If the pressure does not drop more than the maximum allowed sensitivity value then the leak check will pass If the leak check does not pass use the leak detector to find and fix any leaks c Repeat the leak check until no leaks are indicated 16 Calibrate the carrier gas flow column evaluation a Carefully pu...

Page 33: ...f Start the column evaluation i On the column page click Column Evaluation ii Connect a flowmeter to the column flowmeter connector as indicated above iii Press Start The inlet is pressurized to deliver a 5 mL calculated column flow iv Once the pressure has stabilized measure the flow out of the column flowmeter connector Enter the actual flow when prompted The corrected column ID will be displaye...

Page 34: ...he 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 a If there are no conditioning instructions perform the column conditioning by setting a final temperature 10 C 20 C below the column s recommended maximum temperature b Run the slow temperature program that is recommended ...

Page 35: ...ough the transfer line nut and ferrule entering through the tapered end of the ferrule Wipe the column again with a tissue soaked in methanol Figure 5 Transfer Line Nut and SilTite Ferrule Orientation 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 col...

Page 36: ... just stops moving in the ferrule 11 Turn the transfer line nut 1 flat backward so the column is able to move in the ferrule with slight resistance 12 Line up the outlet of the column with the arrows on the end of the column measuring tool Figure 7 Lining Up the Column in the Column Measuring Tool 13 Place a septum with a notch cut into it behind the transfer line nut The septum marks the place on...

Page 37: ...on the column 17 Insert the column into the transfer line Figure 10 Inserting the Column into the Transfer Line 18 Tighten the transfer line nut until it is just secure enough so that you cannot move it 19 Loosen the nut by turning it exactly 1 flat backward 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 n...

Page 38: ...0 C 104 F and allow it to cool before continuing d Retighten the transfer line nut 26 Restore working conditions a Raise the oven temperature to the initial temperature that you will use b Turn on vacuum compensation on the GC c Twist the vent valve clockwise to close the valve Be sure not to pinch the o ring Note If you are using a SilTite ferrule follow the instructions that come with SilTite fe...

Page 39: ...ve the current transfer line nut and ferrule 3 Unwind about one turn of the column from the column outlet end 4 Wipe approximately 300 mm 12 in of the column with a tissue soaked in methanol 5 Choose an appropriate ferrule for the outer diameter of your column 6 Insert the column through the spring loaded transfer line nut and ferrule entering through the tapered end of the ferrule 7 Wipe the colu...

Page 40: ...and break the column Use a magnifying glass to check for an even flat cut Repeat if necessary 10 Use a 5 16 in wrench to hold the column measuring tool steady Figure 13 Column Measuring Tool 11 While holding the column measuring tool steady tighten the spring loaded transfer line nut with a 1 4 wrench until the column just stops moving in the ferrule 12 Turn the spring loaded transfer line nut 1 f...

Page 41: ... nut The septum marks the place on the column where it should exit the nut Figure 15 Positioning the Septum 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 Column Outlet Spring Loaded Transfer Line Nut Septum Column Measuring Tool Column Column Spring L...

Page 42: ...sfer line Figure 17 Inserting the Column into the Transfer Line 19 Tighten the spring loaded transfer line nut until it is just secure enough so that you cannot move it 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 Note The ferrule should still be able to move on th...

Page 43: ...emperature you will operate the GC b Wait 10 minutes c Lower the oven temperature to 40 C 104 F and allow it to cool before continuing 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 c 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 carr...

Page 44: ...w 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 WARNING FIRE HAZARD If you are using hydrogen do NOT reach over the top of the instrument to power it on Instead reach around the right side or go to the back of the instrument and flip up the power swit...

Page 45: ...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 IMPORTANT Be sure to give the ISQ instrument enough time to stabilize Otherwise you may see mas...

Page 46: ...Q 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 To tune the ISQ mass spectrometer using ISQ Autotune 1 Select the tune type you want to use from the list of available tune types See Figure 20 ...

Page 47: ...sfaction then there is no need to perform the more time consuming default or full tunes EI Default Tune This tune creates a default tune file It requires a clean instrument starts with factory tune and sets repeller to 0V and quadrupole voltage to a low value This tune is used to generate a base for all the other tunes As a result you should only use this tune when the ion source is clean The EI d...

Page 48: ...s and tunes the system with a 1 0 mL min flow This tune does not set the detector gain CI Tune This tune is used to analyze samples with positive CI The standard PCI tune performs a mass calibration then tunes the lenses and sets the resolution This type of tune assumes you are using methane as the CI reagent gas and tunes the system with a 1 5 mL min flow This tune does not set the detector gain ...

Page 49: ...ng 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 Otherwise it will interrupt your tune ...

Page 50: ...ntific 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: ...3 Tuning the ISQ Tuning the ISQ Mass Spectrometer Thermo Scientific ISQ User Guide 29 Figure 23 Viewing a Tune Report ...

Page 52: ...leak at the column vent valve or near the component you just serviced In the Tune Results window you can open tune results print report or change the way you view the report To save the report click the icon and save it as a Microsoft Excel file or an Adobe Acrobat PDF file 7 Click Open Tune Results in the top of the window and browse to another tune report on your computer Then click Open Figure ...

Page 53: ... 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 If the sensitivity and resolution are adequate for running the initial samples you are ready to develop or run a method ...

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Page 55: ...to collect your data To create a method for the ISQ mass spectrometer GC and autosampler 1 Click Method Editor on the ISQ Dashboard to open the Method Editor See Figure 27 Contents Creating a Method for the Autosampler Creating a Method for the ISQ Mass Spectrometer Creating a Method for the GC Note For information about creating a method for specific instruments and software refer to the appropri...

Page 56: ...the Autosampler 1 Create a method for the autosampler Instructions for setting common parameters are below Refer to you autosampler documentation for specific guidelines Note All of the configured instruments are shown in the left pane of the Xcalibur Instrument Setup window If the instruments are not shown you need to configure them according to Reconfiguring Your Instrument ...

Page 57: ...n in different runs To prevent this from occurring increase the number of plunger strokes to reduce the chance of an air pocket in your syringe Typical values are between 3 and 10 Viscous Sample Use this field to select Yes if your sample is viscous or No if your sample is non viscous With a viscous sample the syringe is filled more slowly than if it was non viscous Since the amount of time saved ...

Page 58: ...after injection to make sure you do not have sample carryover from one injection to the next You can have the syringe purged with the same solvent that was used in location A B C or D or with solvents A and B or C and D Typically there are 1 to 5 cycles of post injection purges c Configure the Injection group Injection Depth Use the pull down menu to select Standard or Minimum to indicate how the ...

Page 59: ... a acquisition method from the Method Type pull down menu select Acquisition General An Acquisition method is used to collect data Figure 29 Creating a General Acquisition Method for the ISQ Mass Spectrometer 2 Set the MS Transfer Line Temperature This field represents the temperature of the transfer line which is the tube that contains the column as it leaves the GC oven and enters the ISQ mass s...

Page 60: ...ored This setting may help reduce noise but it may also alter the reported isotope ratios because the smaller isotope signals will be preferentially reduced 5 Select EI from the Ionization Mode pull down menu 6 In the Run Completion group select the action you want to occur at the end of a run Note For best results tune the instrument at the same temperature you will run the analyses in your metho...

Page 61: ...sition when all the compounds of interest have eluted but the GC is still at an elevated temperature to keep the column clean We recommend you select this option it because saves burn time on the filament 7 In the Scans pane click a scan row to enter scan information Figure 30 Entering the Scan Information a The Time min column is used to set the time that the ISQ system begins to acquire data aft...

Page 62: ...umn determines the amount of time for each individual scan 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 d The Tune File Name column selects a tune file to be used for this scan It should be the automatic tune file you creat...

Page 63: ...to the GC run the scanning has completely changed Now the scans will repeat every 0 412 seconds until the GC run is complete c The Chrom Filter On column enables the chromatographic filter This filter smooths spectral data as it is acquired which may increase the signal to noise ratio by a factor of 2 or more The chromatographic filter is most useful when at least four full scans are acquired acro...

Page 64: ... 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 h Use the CI Gas Flow column to set the flow rate of your reagent gas Remember to set the CI gas flow in the Groups column as well as at the top of the method ed...

Page 65: ... any GC temperature program In the Initial row enter the initial temperature which must be 4 C above room temperature and less than the maximum operating temperature of your GC column If you set the initial temperature to a value below this limit the GC will not reach the initial temperature If you set the temperature above the limit the GC column will get damaged You can set the initial hold time...

Page 66: ...ll damage your column The prep run timeout is the maximum amount of time that the GC will wait before it gives up on an injection As an example with the default value of 10 minutes if the GC is ready to receive an injection but does not receive it after ten minutes the GC will stop waiting This usually occurs in case of an error The equilibration time is a delay between when the GC is at temperatu...

Page 67: ...RACE 1310 a Useful for diluting high concentrations of sample the split flow is the amount of gas that is swept through the injector to the exhaust port Higher values will give more dilution The split flow will reduce the amount of contamination that builds up in your system The split flow ratio is the ratio of the split flow to the carrier gas flow It is effectively the dilution ratio of the samp...

Page 68: ...um compensation must be on to ensure accurate flow rates c The flow can also be operated in programmed flow or programmed pressure modes In these modes you may have up to three flow rates or pressures to use during an analytical run This is not commonly used but may be necessary if you have a particularly challenging separation d In an effort to reduce the amount of carrier gas used check Carrier ...

Page 69: ...PTV Front or PTV Back tab to configure it The PTV is a low thermal mass injector that allows the instrument to rapidly heat or cool the inlet You can use the PTV tab to program the temperature of the injector 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 f...

Page 70: ...the GC See the GC documentation for instructions b 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 Note The user interface reflects the current configuration of your GC If you add remove or change inlets or detectors re...

Page 71: ...the TRACE 1300 or TRACE 1310 d Select the Inlet or Detector tab as appropriate e 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 ...

Page 72: ...re which must be 4 C above room temperature and less than the maximum operating temperature of your GC column If you set the initial temperature to a value below this limit the GC will not reach the initial temperature If you set the temperature above the limit the GC column will get damaged You can set the initial hold time to a value between 0 and 999 99 minutes The typical initial temperature i...

Page 73: ... the maximum amount of time that the GC will wait before it gives up on an injection As an example with the default value of 10 minutes if the GC is ready to receive an injection but does not receive it after ten minutes the GC will stop waiting This usually occurs in case of an error The equilibration time is a delay between when the GC is at temperature and when the GC reports as being ready Thi...

Page 74: ... will have to optimize the injector temperature for your analysis The SSL temperature can be set between 50 and 400 C a typical value would be 225 C Figure 39 Setting the TRACE GC Ultra SSL Injector Parameters a Useful for diluting high concentrations of sample the split flow is the amount of gas that is swept through the injector to the exhaust port Higher values will give more dilution The split...

Page 75: ...and the oven temperature work together to determine how well the analytes are separated and how long the analysis will take You can select constant pressure or constant flow If you use constant pressure as the column is heated in the oven the flow rate will fall because the hotter column is more resistant to carrier gas flow If you use constant flow the carrier gas pressure will increase as the co...

Page 76: ...Gas Saver mode When used the split flow will be reduced to the gas saver flow after the gas saver time It is not recommended to use a flow of less than 20 mL min because contaminants can build up in the injector column and ISQ instrument which can affect the system performance 6 Click the Run Table tab to configure how to control external valves and devices Consult the appropriate documentation fo...

Page 77: ...r the GC temperature profile is the primary method for separating your analytes from each other the solvent and the matrix Your temperature profile will have to be optimized for your analysis needs b You can also select the maximum allowed oven temperature which should be set to the maximum temperature allowed by your column This will prevent you from accidentally using a temperature that will dam...

Page 78: ... reduce the amount of contamination that builds up in your system The split flow ratio is the ratio of the split flow to the carrier gas flow It is effectively the dilution ratio of the sample This is typically turned on and set to a flow of 50 mL min However this increases the carrier gas usage so for your analysis lower split flows may be more acceptable c Finally if your analysis requires a hig...

Page 79: ... 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 Figure 44 Setting the Carrier Gas Parameters for the FOCUS GC In an effort to reduce the amount of carrier gas used you can activate...

Page 80: ...Figure 45 Setting the Transfer Line Parameters on the FOCUS GC 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 ...

Page 81: ...ethod for the GC Thermo Scientific ISQ User Guide 59 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 ...

Page 82: ...4 Creating a Method Creating a Method for the GC 60 ISQ User Guide Thermo Scientific ...

Page 83: ...ou aren t interested in Refer to your lab s standard operating procedure SOP for your particular sample preparation method Different solvents are used to dissolve different compounds Be sure to choose a solvent that will dissolve the compounds you want to analyze The solvent should be compatible with the stationary phase of your GC column when making sample dilutions Once your sample is prepared y...

Page 84: ...are the instruments for data acquisition as well as monitor the injection and collection of data from the GC MS A sequence can be used to acquire data from a sample or prepare the system for maintenance 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 Xcalib...

Page 85: ...uantitation method Figure 49 Entering the Sample Type Once you select a sample type default information automatically appears in some of the other columns You can also right click on the field to clear copy or paste into the field as well as add and delete rows Note To open an existing sequence you can select File Open from the main menu or click the icon and browse to a sequence Note If you do no...

Page 86: ...le If you double click the field you can browse to a raw data file on your computer You can also right click on the field to clear copy or paste into the field browse to the raw data file or add and delete rows Figure 50 Naming a File Note Your file name cannot contain spaces Tip You can double click in the File Name field and browse to a raw file on your computer ...

Page 87: ...amples so you don t have to enter anything in this field You can right click on the field to clear copy or paste a number as well as add and delete rows 6 Double click the first row in the Path column and select the folder in which to store your data files 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 5...

Page 88: ... a folder on your computer or add and delete rows Figure 52 Opening an Instrument Method Folder 8 Click past the Processing Method column which typically contains the path to your processing method You are in the process of developing your method and the processing method is created after your method is finalized 9 Click the first row in the Position column and enter the sample s vial number if yo...

Page 89: ...5 Running a Sample Running a Sequence Thermo Scientific ISQ User Guide 67 Figure 53 Entering the Sample Vial Position ...

Page 90: ...nly used when you have a processing method Since you are in the process of developing your method you do not have the processing method defined yet 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 g...

Page 91: ...quence Thermo Scientific ISQ User Guide 69 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 ...

Page 92: ...Sample Running a Sequence 70 ISQ User Guide Thermo Scientific 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 ...

Page 93: ...his Sample from the main menu You can also just click the icon on the main tool bar Figure 58 Selecting a Row of Samples to Run 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 ...

Page 94: ...grams 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 Note If you are making a manual injection deselect the autosampler in the Start Instrument and In Use columns Once you...

Page 95: ...he User field you can change your user name The user name defaults to the name that was used to log into the computer h In the Run Rows field enter the rows to be run in the sequence Each value must be separated by a hyphen i Check the Priority Sequence checkbox if this sequence has priority over any other sequence If someone else s sequence is running in the background this setting puts your sequ...

Page 96: ...de Thermo Scientific 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 ...

Page 97: ... files or qualitative processing result files The data in this section refers to an instrument qualification run that was performed in the factory This same run using 1pg octafluoronaphthalene was also performed by a Field Service Engineer at your laboratory Other compounds will have different retention times and ions To view your data in Qual Browser 1 Double click the Xcalibur software icon on y...

Page 98: ...e Qual Browser window select File Open from the main menu or click the icon 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 ...

Page 99: ...togram window and select Ranges from the pull down menu 7 Specify multiple sub panes in the chromatogram window For OFN which has a dominant ion at m z 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 ...

Page 100: ...he OFN is around a retention time of 3 45 minutes Figure 65 Determining the Retention Times To look more closely at your data left click on the peak to zoom in on it You can also hold your mouse down over the peak and draw a line over it to zoom in Another way to zoom in is to return to the Ranges tab and manually enter the time range to display ...

Page 101: ...Guide 79 Figure 66 Manually Entering the Ranges 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 ...

Page 102: ...gram pane and select Display Options Figure 68 Selecting the Display Options 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 ...

Page 103: ...Your Data Thermo Scientific ISQ User Guide 81 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 ...

Page 104: ...6 Exploring Your Data 82 ISQ User Guide Thermo Scientific Figure 71 Setting the Spectrum Range Figure 72 Finding the OFN Peak ...

Page 105: ... pane select subtract spectra and then subtract one range or two 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 Note If the chromatogram window is pinned this action will zoom i...

Page 106: ...th Background Subtraction 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 ...

Page 107: ... temperature final temperature for that ramp and the hold time at that final temperature These temperatures can be adjusted for each ramp It is important to keep in mind that oven changes are strongly dependent on the nature of the compounds you are analyzing At some point the GC oven has to be above the boiling point of the compounds you are looking for If the GC oven is not at the boiling point ...

Page 108: ... the phase of a solid phase extraction cartridge which gives you similar results as changing a solvent You can affect the way you prepare samples by changing the type of cartridge you are using Changing the Scan Rate The precision of your data depends on how well you define your chromatographic peak Typically you get good precision when sampling ten times across the chromatographic peak Increasing...

Page 109: ...uld damage the column or cause a thermal breakdown in the compounds you are analyzing Typically the transfer line temperature should be 10 C over the highest boiling point of the compounds of interest but no more than the maximum safe operating temperature of the column Increase the source temperature as well to improve response for high boiling compounds and prevent column bleed and matrix compou...

Page 110: ...n 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 Figure 76 Accessing the Tune Type Editor from the ISQ Dashboard 2 In the Tune Types dialog box select a tune type to edit and click the Copy button ...

Page 111: ...Q User Guide 89 Figure 77 Using the Tune Types Dialog Box 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 ...

Page 112: ...instrument with a clean ion source 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 Select a specific tune file if you have a reliable tune file you want to use as a test for the new tune file Perform Mass Calibration Select this but...

Page 113: ...ort is selected Methane is commonly used for CI Other gases will change the efficiency and energy of the ionization process CI Gas Flow enabled when you select a CI Gas Type Use this field to enter the flow rate of your CI gas Emission Current Use this field to define the emission current you use to run subsequent tunes but not the emission current that is used for data acquisition Tune File Selec...

Page 114: ...V electron beams Electron Lens Positive Voltage Use this field to allow the electrons to enter the ion volume Default Select this option to use the default electron lens positive voltage which is 15 V Tune File Select this option to use the value used in the tune file you selected in the General tab Custom Select this option if you do not want to use the default value for the tune For the electron...

Page 115: ...g the source This field is not used at this time Set Ion Source Temperature Select this checkbox to enable the temperature field Then enter a value between 0 and 350 C default is 200 C The optimal temperature is determined by the molecular structure and weight of the compounds you are analyzing Heavier compounds require a higher temperature You should set the temperature as high as possible to kee...

Page 116: ...urface which leads to better robustness Typical values are 0 to 5 V although a dirty system may have the repeller climb as high as 12 5 V We do not recommend setting the repeller any higher Lens 1 Select this option to control Lens 1 which is the first of three lenses that the ions see as they leave the ionization region These three lenses act as a focusing element to maximize the ion beam intensi...

Page 117: ...he better the resolution However higher voltages will pull more ions into the quads which leads to better signal This field is typically set between 0 and 5 V Resolution Select this option to adjust 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 th...

Page 118: ... occurs or if no tune points are found meeting the tune criteria Continue Select this option to allow the tune to continue on to the next device when an error occurs 6 Click the Resolution tab to configure the resolution of your tune You can tune the resolution during a lens tune or you can tune the resolution by itself Tune Resolution Select this option to tune the resolution by itself This resol...

Page 119: ... of the peak height Lens Tune Relation Use this pull down menu to set the occurrence of the resolution tune parameters before or after a lens tune Before and After Select this option to use the same resolution parameters before and after a lens tune Before Select this option to use the resolution parameters before a lens tune After Select this option to use the resolution parameters after a lens t...

Page 120: ...ne 98 ISQ User Guide Thermo Scientific 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 ...

Page 121: ...oltage required for a given gain will increase Depending on your sample load and if your system is leak tight oxygen is bad for the detector you should not have to perform this tune very often Tune Detector Select this checkbox to tune the detector Adjust Detector Sensitivity Select this checkbox to tune the detector to generate a consistent area count of a calibration gas ion for the tune report ...

Page 122: ...de Thermo Scientific 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: ... masses to be displayed on your tune report You can select a maximum of five masses one from each menu 11 Once you are finished configuring all the tabs click the Save button to save the tune type Your new tune type is now in the Tune Types window 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 Cl...

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Page 125: ...leshooting 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 If you have an air leak locate and address them Pay particular attention to the transfer line ferrule vent valve knob front panel and vacuum interlock on the ISQ instrument as well as the inlet on the GC If your intensitie...

Page 126: ...s Checking the ISQ System Firmware Confirm that you are running the correct version of the ISQ instrument firmware To find the version of firmware installed on your ISQ system 1 On the ISQ Dashboard click Air Water Tune This opens ISQ Manual Tune IMPORTANT When inserting a cold ion source cartridge such as after cleaning or when switching between EI and CI modes the ion source and lens stack will ...

Page 127: ...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 See ...

Page 128: ...py Info to copy the information to the clipboard on your PC 6 Save this information It may be useful to your Thermo Fisher Scientific Field Service Engineer if you need a service call 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 ...

Page 129: ...hydrocarbon contamination 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 Check the last o ring or ferrule you installed Table 1 Common Contaminants Ions m z To Monitor Compo...

Page 130: ...by regulator Make sure the vacuum compensation is on Carrier gas flow is drifting Check for leaks in injector or flow path Check the carrier gas tank Impurities have accumulated in column Run solvent blank to remove impieties If impurities persistent after multiple solvent blanks Inject solvent from a different source Change syringe liner and septum Clean injector Check impurity levels in your gas...

Page 131: ...ystems for leaks Use correct gas purity with low oxygen content Column is contaminated or damaged Condition or replace the column Oven temperature is higher than column s maximum allowable temperature Reduce oven temperature to the maximum allowable temperature of the column Leak at column fittings Find leak Tighten fittings if loose Replace ferrule if overtightened Transfer line temperature is no...

Page 132: ...e flow to 40 50 ml min Performance of the column has degraded Test the column at the optimum flow rate Injector is dirty Clean or replace the liner Ion source is dirty Clean the ion source and tune the instrument Column is not far enough into the transferline The GC column does not extend into the MS source Use the column measuring tool to confirm column length If the end of the column is inside t...

Page 133: ...olumn connections are poor or obstructed Reconnect the column inlet Stationary phase is not appropriate for your target compounds Replace the column and choose a more appropriate phase for your analysis Final hold oven temperature is too low Increase the column oven temperature Do not exceed the recommended maximum temperature for the stationary phase Transferline temperature is too low If tailing...

Page 134: ... the split vent filter Install an in line filter between the pneumatics and the inlet Missing Peaks Baseline or background present Column is broken Replace the column Column flow is incorrect Make sure the septa are sealing Make sure vacuum compensation is turned on Backflush settings are incorrect Set backflush to off until after injection Column position in S SL injector is incorrect too high Ch...

Page 135: ...light is on during acquisition Make sure the filament is not burned out Injection technique is not appropriate Use a different injection technique Injection parameters are not appropriate Verify the injection temperature and flow rates Sample injection technique is not reproducible Evaluate the sample preparation sequences Compare the results with a series of standard injections Syringe or septum ...

Page 136: ...ngs if damaged Remove debris or broken pieces in the manifold Run a lens check diagnostic Check the connection by removing or inserting the ion source Retention Times Low reproducibility DCC is drifting or unstable Monitor the column pressure or flow Check and replace the controller if necessary Injection technique is inadequate Pick injection technique suitable for the injector and liner you are ...

Page 137: ...reconfigure your ISQ instrument 1 From the Start menu on your computer desktop browse to Thermo Foundation 2 0 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 Figure 89 Finding Avail...

Page 138: ...8 Troubleshooting Reconfiguring Your Instrument 116 ISQ User Guide Thermo Scientific Figure 90 Adding a a Device to be Configured 4 Click Configure ...

Page 139: ... 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 Note You only need to set up the pressure units if you have an ion gauge or convectron gauge installed on your system The readbacks from these components will display in the units set in this window ...

Page 140: ... special software from customer support necessary to reprogram the IP address on your instrument Figure 93 Setting the Network IP Address and the TCP Port 8 Click the Maintenance Intervals tab to set the number of days until you plan to perform maintenance on certain components of your GC MS system As a default the foreline pump and turbo pump oil are automatically enabled You can monitor the prog...

Page 141: ...e 119 number of days in which you want to be reminded to check the oil 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 ...

Page 142: ... cartridge every 730 days and the bearing every 1 460 days Figure 95 Setting the Turbo Pump Oil Maintenance Reminder 11 Select the Filament 1 checkbox to enable the maintenance reminder In a leak free system the filament should last between 30 360 days depending on usage Figure 96 Setting the Filament 1 Maintenance Reminder 12 Select the Filament 2 checkbox to enable the maintenance reminder Then ...

Page 143: ...system the filament should last between 30 360 days depending on usage 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 ...

Page 144: ... of time between source cleanings Figure 98 Setting the Ion Source Cleaning Maintenance Reminder 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 ...

Page 145: ...8 Troubleshooting Reconfiguring Your Instrument Thermo Scientific ISQ User Guide 123 Figure 100 Returning to the Configuration Window ...

Page 146: ...lose 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 In the Status Pane of the Xcalibur Roadmap window you can check the status of all your instruments See Figure 102 ...

Page 147: ...8 Troubleshooting Reconfiguring Your Instrument Thermo Scientific ISQ User Guide 125 Figure 102 Checking All Instrument Statuses in Xcalibur Status Pane ...

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Page 149: ...run 99 documentation survey xxi E EI tune type about 26 electromagnetic compatibility vi EMC compliance v F FCC compliance vi filament voltage setting 92 filament turning off and on 42 fingerprint indications 107 flow rate verifying 2 full scan mode about 40 G gas flow rate 2 tank pressure 3 GC carrier gas 2 creating a method 43 powering on 2 ghost peaks troubleshooting 112 I instrument method sel...

Page 150: ...on times troubleshooting 114 routine maintenance causes 107 S safety standards v samples preparing 61 running 61 scan rate optimizing 86 scans running 39 sensitivity troubleshooting 114 sequences about 62 customizing 71 opening 63 prioritizing 73 running 62 saving 69 SIM mode about 40 solvents choosing 61 purpose of 61 survey link xxi T tailing peaks troubleshooting 111 temperature of the ion sour...

Page 151: ...entific ISQ User Guide 129 Index U EI default tune 25 EI full tune 26 tuning 23 using Autotune 24 with ISQ Autotune 24 U user name about 73 V vacuum checking 4 voltage of filament setting 92 W WEEE compliance vii ...

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