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User Guide - Thermo Scientific

1. 2012 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 The following are registered trademarks in the United States and other countries Microsoft Windows and Excel are registered trademarks of Microsoft Adobe and Acrobat are registered trademarks of Adobe Systems Incorporated SilTite is a registered trademark of SGE Analytical Science in the United States Vespel is a 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
2. The Tune File Name column selects a tune file to be used for this scan It should be the automatic tune file you created in Tuning the ISQ You can also use a specific tune file for each of the scans The Scan Name column contains a description of the scan The name may be used as a label to indicate the compound used with the scan The SIM Widths column sets the width range of the SIM window The range of values can be between 0 01 and 10 The default is 1 amu which means the ISQ will collect all the ions from your SIM mass 0 5 amu Narrower SIM widths lead to greater specificity The Ion Polarity column is only used in CI mode which is the only mode for generating positive and negative ions In EI mode this column should be always be set to Positive The Data Type column determines whether you want to collect Profile or Centroided Mass Spectra Centroided mass spectra is most common because it is used by most of the libraries and provides the smallest data files Profiled mass spectra provides detailed mass spectral peaks which results in a large data file that contains details a centroided spectra does not contain Thermo Scientific Thermo Scientific 4 Creating a Method Creating a Method for the ISQ Mass Spectrometer 8 In the Groups pane review the information in each row As you create scans in the Scans pane information in the groups pane is automatically displayed Note If some of the columns mentioned below ar
3. 23 Tighten the spring loaded transfer line nut 1 additional quarter turn 24 Remove the cut septum 25 Close the front door of the GC 26 Condition the graphite Vespel ferrule a Raise the oven temperature to the maximum temperature 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 WARNING BURN HAZARD The oven may be hot Allow it to cool to room temperature before opening it The injector will still be hot so do not touch it 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 Ifyou are using hydrogen as a carrier gas replace the front panel screw e Replace all remaining hydrogen safety screws if you are using hydrogen ISO User Guide 21 2 Changing the Column Connecting the Column to the Transfer Line 28 Power on the ISQ mass spectrometer 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 switch 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
4. C min minutes I Enable Cyo intial u ol m Max Te Pressure Left kPa je Tea CC 350 Ramp 1 100 50 1 00 Pressure Richt kPa Pesan Timeout min 10 00 ANAS 1310 5 i Equiibration c nm ee 05 Ready a You can select a maximum of seven temperature ramps each with their own ramp rates final temperatures and hold times A typical program will have one or two ramps However 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 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 temperature and when the GC reports as being ready This delay is typically set to 0 1 minutes 2 The TRACE GC Ultra also has the option to enable the use of cryogenics to cool the oven If this option is selected then the minimum allow
5. Sample Name Working On Position Raw File Inst Method S TriPlus Autosampler Ready to Download amp TRACE GC Ultra Ready to Download ISQ Ready to Download Status Analyzer Power Maintenance Status Idle F Actual Set Point Ms Lena line 250 C 250 C v lon source temp 200 C 200 C Vacuum OK Foreline pressure 50 mTorr lon gauge pressure 1 3105 Torr Turbo pump speed 100 a Cl reagent gas flow 0 0 mL min 0 0 mL _ a m eh NUM 2 10 2012 For Help press FL 11 Click past the Level column which is only 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 go 72 ISO User Guide Thermo Scientific Thermo Scientific 5 Running a Sample Running a Sequence Figure 61 Adding Additional Sequence Setup Tasks File Edit Change Actions View GoTo Help a SHS 8 MASEM BroOE PEN E Run Manager Ready To Download Sequence Sample Name Working On Position Raw File Inst Method B TnPlus Autosampler Ready to Download B TRACE GC Ultra Ready to
6. 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 This document is not part of any sales contract between Thermo Fisher Scientific Inc and a purchaser This document shall in no way govern or modify any Terms and Conditions of Sale which Terms and Conditions of Sale shall govern all conflicting information between the two documents 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 WE Contents it eT eee er en ix About Your yes keked ar i E E eb eed ead tethered ers ix Related Documentation rer ara ea x System Requirements 0 cee cence eens xi Satety and Special Notices 2 4 ch dedi BER rien era xi Spez Notices nenne arena xi Safety Symbols and Signal Words 2222 eneeeeenee nenn xi Hydrogen Safety Precautions voyeur ren xiii Using Hydrogen with DO Ausser near ae xV Hydrogen Connection Guidelines un uuuesussua0 00000000000 eats xvi Purchasing Fiydrogett 2200 haus as oheddgd eked cabeved ded xvii Properly Storing Hydr gen un ea Be xviii Hydrogen Safety Codes Standards and References 2 222200 xix Hazardous Substances Precautions 2 0 c cece cee
7. no file no file no file data15_10010417 0750 RT 3 33 RT 3 37 AA 272601 AA 666276 o Hu Relative Abundance a 3 8 g KKK miz 27150 27250 Ms icis datat5_10010417 0750 Time min data15_100104170750 322 RT 3 45 AV 1 NL 2 45E6 T 0 0 c El Full ms 50 00 300 00 57 20 100 8 8 Relative Abundance S 128 05 140 08 159 05 169 00 191 09 207 11 221 92 241 12 272 01 281 07 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 85 6 Exploring Your Data Figure 77 Setting the Spectrum Range Spectrum Ranges Ranges Automatic Processing Range Mass range 225 00 275 00 Average 7 Fixscale 1000000 0 Raw File Subtract 1 c xcalibur data ofn datal_100 D Ek ae D D D s Plot properties Detector MS z Time 3 45 Background Subtraction N Time range i 2 Filter Type Scan C Process I Time range 2 Ref Raw file c xcalibur data ofn datal5_100104170750 1ew v I Simulation Figure 78 Finding the OFN Peak MM Thermo Xcalibur Qual Browser data15_100104170750 data15_1001041 70750 raw File Edit Yiew Display Grid Actions Tools Window Help x sels a el 4b wi ele ofe E lea seen SIT mE ole le IM a8 m gel SE C caliburdata OF Nidata15_100104170750 1 4 2010 6 07 50 PM
8. t have that many samples 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 57 Selecting a Folder to Store Data Files 72 Therr 02012 sld w File Edit Change Actions View GoTo Help z _ FE p Pac kare sus Ro TASH APOE gt an Sample Type FileName Sample ID Path Inst Meth Position Inj Vol Status Acquisition Queue 1 Unknown 02102012 01 1 C Xcalibur Dat C Xcalibur methods BC_Test 1 1 0 Run Manager 2 0 0 Ready To Download Sequence Sample Name Working On Position Raw File Inst Method 6 TnPlus Autosampler Ready to Download 6 TRACE GC Ultra Ready to Download Select Directory amp ISQ Ready to Download Directory selected c xcalibur data SSS ES Status Analyzer Power Maintenance amp Xcalibur Dat Status Idle E er sarah gm Actual Set Point MS transfer line E temp 250 C 250 C lonsourcetemp 200 C 200 C Vacuum OK Foreline pressure 51 mTorr I pressure 1 3105 Torr Turbo pump speed 100 z CI reagent gas flow 0 0 mUmin 0 0 mU _ m r
9. 3 50 NL 145E7 TIC MS ICIS datat5_10010817 RT 3 43 iii RT 3 33 RT 3 37 AUSE R AA 272601 AA 506276 5 8 iur Relative Abundance a 3 o jie RT 3 45 NL AA 22318 RSE mize 27150 27250 MS ICIS ddatal6_10010417 0750 8 Time min data15_100104170750 319 325 RT 3 443 46 AV 7 SB 44 3 30 3 42 NL 2 4964 T 10 0 El Full ms 50 00 30 00 55 08 40057 2 2 Relative Abundance 202 98 1144 14 191 03 130 88 1a3 15 1990 177 05 T Figure 81 OFN in Full Scan Without Background Subtraction M Thermo Xcalibur Qual Browser data15_100104170750 data15_100104170750 raw DEAR i File Edit View Display Grid Actions Tools Window Help sels a selv lt gt zlte lsfe E aa Klee Sn le ee delil lus data15_100104170 no file no file no file no file no file no file no file C oaliburdata OFN data15_100104170750 1 4 2010 5 07 50 PM Final Test Method RT 3 25 3 50 NL 145E7 TIC MS ICIS data15 _10010417 RT 3 43 Oreo RT 3 33 RT 3 37 Arno AA 272601 AA 506276 5 8 u Relative Abundance a 3 o H RT 3 45 N AA 22318 poset mize 27150 27250 MS ICIS data15 _10010417 0750 Time min ata15_100104170750 319 325 RT 3443 46 AV 7 NL 2 3766 T 0 0 c El Full ms 60 00 30 00 0722 2 2 3 Relative Abundance Y 8 272 02 281 06
10. Instrument Control Shut Down c Analyzer Power Maintenance Status Idle Actual v MS transfer line temp 250 C v lon source temp 200 C OK 51 mTor v Vacuum Foreline pressure lon gauge pressure Turbo pump speed 100 0 0 mL min 0 0 mL min 1 3x10 Tor Cl reagent gas flow 18 In the Status Pane of the Xcalibur Roadmap window you can check the status of all your instruments See Figure 108 Thermo Scientific 128 ISO User Guide 8 Troubleshooting Reconfiguring Your Instrument 50 mTorr blr 1 310 Torr Turbo pump speed 100 CI reagent gas flow 0 0 mLmin 0 0m _ Status Pane Thermo Scientific ISQ User Guide 129 ee _ I Index A acquisition methods purpose of 37 AutoTune modifying 92 Autotune using 24 baseline troubleshooting drifting 112 baseline issues investigating 112 C centroided data about 40 chromatograms viewing 79 chromatographic separation changing 89 CI gas types selecting 95 CI mode using 38 column leak checking 10 temperature 12 compliance FCC vi regulatory v WEEE vii contaminants common 111 contamination indications 111 data result issues investigating 117 data verifying 79 diagnostics selecting tests to run 103 documentation survey xxi E EI tune type about 26 electromagnetic com
11. These simultaneous full scan and SIM scans will begin 2 5 minutes into the GC run You will get a complete set of scans every 0 816 seconds At 4 minutes into the GC run the scanning is completely changed Now the full scan range is 35 150 amu which is scanned every 0 1 seconds and the two SIM masses are 450 and 614 amu which are scanned for 0 1 and 0 2 seconds respectively All these scans will repeat every 0 412 seconds until the GC run is complete All of these scans use the last tune file that was saved to the instrument The Mass List or Range column tells the ISQ system what masses it needs to scan In full scan mode enter the start and end mass separated by a dash In SIM mode enter individual masses or multiple values in this field as long as they are separated by a comma You must put each full scan range on a separate line Note Each line in a scan must only contain a Full Scan range or individual SIM masses They cannot be mixed in a single line C In SIM mode the Dwell or Scan Times column defines the amount of time in seconds that the ISQ will look at your SIM ion mass If you are in Full Scan mode the Dwell or Scan Times column 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
12. 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 column temperature increases to keep the flow constant Constant flow is more common Typical flow rates are 1 3 mL min The pressure depends on the column length 58 ISO User Guide Thermo Scientific 4 Creating a Method Creating a Method for the GC 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 a 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 b In an effort to reduce the amount of carrier gas used you can activate the 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 for more detailed information Figure 47 Locating the Run Table Settings on the TRA
13. gt B del Es Final Test Method RT 3 25 3 50 m m DA data15_100104170 145E7 no file TIC MS ICIS no file data15_10010417 no file no file no file no file RT 346 no file AA 22318 8 Pett EEE RT 3 43 AA 2892760 E DESI Relative Abundance a 3 KKK Ms ICIS datatS_10010417 pr Time min data15_100104170750 323 RT 3 45 AV 1 NL 2 28E4 T 0 0 c El Full ms 50 00 300 00 1005 5 2 S Relative Abundance 265 19 267 00 255 79 258 58 263 04 86 ISO User Guide Thermo Scientific Thermo Scientific 6 Exploring Your Data 13 Left click on the GC peak and drag a line across it to average several points across the GC peak Note If the chromatogram window is pinned this action will zoom in on the peak but if the mass spectrum window is pinned this action will average the spectrum Figure 79 Averaging the Spectrum MM Thermo Xcalibur Qual Browser data15_1001041 70750 data15_1001041 70750 raw BEE 2 Eile Edit Yiew Display Grid Actions Tools Window Help isis 6 wlelo gt Ixlelelert fe lie Selle Pal x C Xcaliburtdata OF Nidata15_100104170750 1442010 5 07 50 PM 27 Bl FY ade ER Ea lacs Final Test Method RT 3 26 3 50 NL 14567 1007 TIC MS ICIS 3 data15 _10010417 750 data15_100104170 no file no file no file no file no file no file WL no
14. raw x a el mimi 2 ciel x m ele C Xcaliburidata OFNidata15_ 100104170760 1 4 2010 5 07 50 PM Final Test Method gt DA QS TIC data15_10010 JE Mass Range data1 X Mass Range no fi JK Mass Range no fi 3 Mass Range no fi JK Mass Range no fi X Mass Range no fi X Mass Range no fi RT 3 37 o 3 25 3 30 T 0 0 El Full ms 50 00 300 00 5724 100 8 8 Relative Abundance 85 18 99 29 125 07 Time min data15_100104170760 1 RT 2 52 AV 1 NL 2 19E6 4a 142 32 158 33 170 99 191 22 207 00 145E7 TIC MS ICIS datat5_10010417 0750 NL NL 2 8864 miz 271 50 272 50 Ms ICIS datat6_10010417 0750 3 40 350 231 74 251 89 267 05 281 56 ISO User Guide 83 6 Exploring Your Data 9 Right click in the Chromatogram pane and select Display Options Figure 74 Selecting the Display Options Display Options Style Color Labels Axis Normalization Pesan RT 3 25 3 50 NL RT 3 33 145E7 007 AA 272601 TIC MS ICIS datat5_100104170 T Name I Scan number Relative Abundance I Base peak A f 5 RT 3 45 NL I Signaltonoise I Height AA 22318 28864 Label Styles miez 27150 27250 Offset Size 3 5 Ms ICIS I Rotated I Boxed data15_100104170 750 33 3 4 Label threshold foo Time min 10 Click the Labels tab and select Retention Time and Area in the Label With group Figure 75
15. 10 mm are becoming increasingly popular Additionally 0 32 and 0 53 mm ID columns are commonly used Film Thickness With larger film thicknesses there is more capacity for the analyte This capacity can aid in the separation of high concentration samples and in the separation of very volatile samples because thicker stationary phases 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 with the analytes which will result in very fast analysis times with little separation Typical film thicknesses are 0 25 um for a column with an ID of 0 25 mm Other common film thicknesses are 0 1 0 5 and 1 0 pm e Length The length of the column affects how much time the analyte has to interact with the stationary phase Longer columns typically have better resolutions and higher capacities but longer analysis times Longer columns are also more expensive Typical column lengths are 15 or 30 meters for GC MS but 100 m columns may be needed for very complex mixtures like gasoline Very short columns 2 5 5 and 10 m are also available Note Contact your local sales representative to order a Thermo Fisher
16. 14 There are many other ways to change the way you data displays in Qual Browser See the Qual Browser online help for details Thermo Scientific o Optimizing Your Method If you did not quite get the results you were expecting from your method use the suggestions in this chapter to modify it to obtain better results Contents e Changing the Chromatographic Separation e Finding the Best Way to Make an Injection e Improving the Way You Prepare Samples e Changing the Scan Rate e Narrowing the Mass Range e Adjusting the Transfer Line Temperature e Modifying an Automatic Tune Changing the Chromatographic Separation Peak shapes are defined by the chromatographic conditions If your peak is too wide too narrow or not symmetrical enough then changing the chromatographic conditions are the best way to improve your method You should begin by changing the GC carrier gas flow or oven temperatures the initial temperature initial hold time ramp 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 the compounds will not volatilize and they will become immobilized Changing ramp rates
17. Download ISQ Ready to Download Status Analyzer Power Maintenance Status Idle v MS tonser lin 260 C lt lonsourcetemp 200 C 4 Vacuum OK Foreline pressure 50 mTorr lon gauge pressure 13x10 Torr Turbo pump speed 10 CI reagent gas flow 0 0 mUmin Actual Set Point 250 C I m For Help press FL to save the sequence __Sample Type FileName Sample ID Path Inst Meth Position Inj Vol Level 1 Unknown 02102012 01 1 C Xcalibur Dat C Xcalibur methods BC_Test 1 1 0 0 0 NUM 2 10 2012 13 Once you ve created a sequence of all your samples select File Save or click the I icon 14 Enter a comment and click OK ISO User Guide 73 5 Running a Sample Running a Sequence Figure 62 Entering a Comment About Your Sequence File Edit Change Actions View GoTo Help DHS 58 TASEN Bee gt Em Sample Type FileName SampleID Path Inst Meth Pos 1 Unknown 0210201 2 01 1 C Xcalibur Dat C Xcalibur methods BC_Test 1 Friday February 10 2012 1 15 20 PM Modified Friday February 10 2012 1 15 20 PM Last saved by Alvin Number of saves 1 Status Analyzer Power Maintenance Status Idle T Actual Set Point MS transfer line crass 250 C 250 C v lon source temp 200 C 200 C Vacuum OK Foreline pressure 50 mTorr lo
18. Enable Days Foreline pump oil Turbo pump oil bearing Filament 1 Filament 2 lon source OBA Multiplier 1 000 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 105 Setting the Electron Multiplier Maintenance Reminder ISQ Configuration X General Maintenance Interwals Days m 3 a T T Foreline pump oil Turbo pump oil bearing Filament 1 Filament 2 lon source HHA Multiplier Reset All 15 Click OK to return to the main Instrument Configuration window 126 ISO User Guide Thermo Scientific 8 Troubleshooting Reconfiguring Your Instrument Figure 106 Returning to the Configuration Window ei Thermo Fot pation loai m Device Types Al Y Available Devices E Al AS 1310 TRACE 1300 GC IsQ Series IsQ TRACE GC Ultra j 4 y TRACE 2 GC Ultra TriPlus Autosampler Add gt gt lt lt Remove Configure de te Thermo Scientific ISO User Guide 127 8 Troubleshooting Reconfiguring Your Instrument 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 107 Checking the ISO Instrument Status on the ISO Dashboard ro Ar amp Water Tune
19. Foundation 2 0 gt Manuals gt ISQ To open Help e From the ISQ window choose Help gt ISQ Help e Ifavailable for a specific window or dialog box click Help or press the F1 key for information about setting parameters For more information visit www thermoscientific com x ISO User Guide Thermo Scientific Preface System Requirements System Requirements Your ISQ data system must meet these minimum requirements System Requirements Hardware e 2 4 GHz processor with 4 GB RAM e DVD CD ROM drive e Resolution display 1280 x 1024 XGA e 250 GB hard drive or larger e NTFS format Software e Microsoft Windows 7 SP1 Operating System 32 bit and 64 bit e Microsoft Windows XP SP3 e Microsoft Office 2007 or 2010 32 bit only e Thermo Foundation 2 0 SP1 Thermo Scientific software e Xcalibur 2 2 SP1 or later Safety and Special Notices Make sure you follow the precautionary statements presented in this guide The safety and other special notices appear in boxes Special Notices Special notices include the following IMPORTANT Highlights information necessary to prevent damage to software loss of data or invalid test results or might contain information that is critical for optimal performance of the system Note Highlights information of general interest Tip Highlights helpful information that can make a task easier Safety Symbols and Signal Words All safety symbols are foll
20. I ror Help prest NUM 2 10 2012 ISO User Guide 69 5 Running a Sample Running a Sequence 70 ISO User Guide 7 Double click the first row in the Instrument Method column navigate to the folder containing your instrument method Select the instrument method and click the Open button 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 Ther File Edit Change Actions View a GoTo Help Figure 58 Opening an Instrument Method Folder nm a Fra i I zm JS 58 gt MADBHB BE PEN Sample Type Position Inj Vol Status Acquisition Queue known z XcaliburD at C Xcalibur me 1 1 0 Run Manager amp 2 Select Instrument Method eee o0 Ready To Download Sequence Lookin methods P E Sample Name 2 Working On R Name Date modified Type 4 Position ay EE rrao_Exer2_Feb09_4 meth 2 9 2012 5 00 PM Xcalibu hie 4 Recent Places Ef prao Exer2_Feb09_3 meth 2 9 20124 amp 58PM Xcalib TnPlus Autosampler BE rrao_Exer2_Feb09_2 meth 2 9 20124 56 PM Xcalibi Ready to Download Bf rrao_Exer2_Feb09_1 meth 2 9 20124 45PM Xcalibi TRACE GC Utra Desktop BF BC_Test meth 2 9 201210 49 AM Xcalib Ready to Download En EF RoboSWTEST16 meth 2 3 201210 31 AM Xcalib 8 150 u BF RobolsQ meth 1 23 20122 25PM Xcalib x r Libra
21. ISO User Guide 71 5 Running a Sample Running a Sequence 78 ISQ User Guide 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 66 Saving a Sequence to the Computer File Edit Change Actions View GoTo Help zm m Status Acquistion Queue 5 Run Manager Ready To Download Sequence Sample Name Working On Position Raw File Inst Method E TnPlus Autosampler Ready to Download TRACE GC Uhra Ready to Download 15Q Readyto Download Status Analyzer Power Maintenance Status Idle Turbo pump speed 10 Cl reagent gas flow 0 0 mUmin Actual Set Point MS transfer line Zen 250 C 250 C lon source temp 200 C 200 C Vacuum ok Foreline pressure 50 mTorr lon gauge pressure 1 3105 Torr 0 0 mu _ r 20 Once your sequence completes you are ready to explore your data Recent Places Desktop Name WWYO2102012 51d WW rra0_Exer2_Feb09 sid Wat sid WW before sid WWick sid WW testme sid WU rra0 exercise2 1 sld WW sarah_wga sid WW Customer_A sld WW rrao 1 sid Whtestsid 11042011 weekend sid 67 gt Ey Date modified 2 10 2012 1 15 PM 2 9 2012 5 05 PM 2 9 2012 1 18 PM 2 9 2012 11 16 AM 1 27 2012 9 43 AM 1 24 2012 3 15 PM 1 19 2012 4 32 PM 1 5 2012 5 02 PM 12 14 2011 2 09 PM 12
22. Labeling the Display MM Thermo Xcalibur Qual Browser data15_1001041 70750 data15_1001041 70750 raw Eile Edt View Display Grid Actions Tools Window Help B jleg inal Test Method RT 3 25 3 50 TIC data15_10010 L Mass Range data1 K Mass Range no fi Mass Range no fi 8 RT 3 43 RT 3 33 RT 3 37 AA 2892760 NL g 145E7 TIC MS ICIS datat5_10010417 0750 Mass Range no fi AA 272604 AR 566276 Relative Abundance a 3 Mass Range no fi Mass Range no fi RT 3 45 Mass Range no fi AA 22318 Time min data15_100104170750 1 RT 2 52 AV 1 NL 2 19E6 T 0 0 El Full ms 60 00 300 00 5724 Relative Abundance 85 18 99 29 _ NL 2 6864 miz 27150 27250 Ms ICIS datat6_10010417 0750 125 07 44232 158 33 170 99 191 22 207 00 231 74 251 89 267 05 281 56 11 With the MS window pinned click on the peak to open the mass spectrum at the point you clicked 84 ISO User Guide Thermo Scientific 6 Exploring Your Data Figure 76 Opening the Mass Spectrum Pa Thermo Xcalibur Qual Browser data15_1001041 70750 data15_1001041 70750 raw PER ile Edit View Display Grid Actions Tools Window Help SEE a Belo gt Rees fe E Sie sales C AXcaliburidata OF Nidata15_100104170750 4184 2010 5 07 50 PM 2 ERARA Final Test Method RT 3 25 3 50 Ih data15 100104170 NSE E no file TIC MS ICIS no file no file no file
23. MS system select File Save As from the main menu or click the fd icon Figure 53 Saving Your ISO Instrument Method E Us mean Sp Ta DT a a ooo File TRACE Help New Ctrl N Open Ctri 0 Save Ctrl s Save As Summary Information Change Study Name Audit Trail Print Ctrl P Print Preview Print Setup Options 1 OFN_FS mettl Smeh Pressure Flow Mode Constant Pressure v 0 3 00 4 00 5 00 6 00 7 00 8 00 9 00 10 00 2 rrao_OFNB meth kPa 3 rrao_OFNB Jan19 2 meth O 4 BC_Test meth 100 Exit 7 Vacuum Compensation T Gas Saver Gas Saver Flow ml min 20 Gas Saver Time min 2 00 unnn Sa AA AA TT TE Si i I a I I I Te LI I I TTT Save the active document with a new name 64 ISO User Guide Thermo Scientific ee Running a Sample This chapter describes how to prepare a sample and then run a sequence Contents e Preparing Your Sample e Running a Sequence Preparing Your Sample The primary goal of sample preparation is to reduce the amount of unwanted contaminant in a sample or to increase the reliability of sample detection As a result you should prepare your samples to increase the relative abundance of compounds you want to analyze and decrease the relative abundance of the compounds you aren t interested in Refer to your lab s standard operating procedure SOP for your particular sample preparation method Different solvents are
24. Method Ector Air amp Water Tune Analyzer Power Maintenance Status Idle Actual v MS transfer line temp 250 C v lon source temp 200 C v Vacuum OK Foreline pressure 51 mTor lon gauge pressure 1 3x10 Tor Turbo pump speed 100 Cl reagent gas flow 0 0 mL min 0 0 mL min 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 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 34 ISO User Guide Thermo Scientific 4 Creating a Method Creating a Method for the Autosampler Figure 28 Configuring the Autosampler iR Unbtled Thermo Xcakbuar Instrument Setup KA _ i 2 x file TriPlus Autosampler Help olsa S xie Atesan ies EC Ua gt General Washes Sy Advanced PE Ingecton pat sq inpor ingota A SSL Type Sre l Ingecton mode Ww Mode Bane Sampling lection Sagie vol Il 10 mnigh eures o TRACE GC Une ggz dred Pisya indes 3 Preevechondwettmets ao fa miFiieg mode Ao o Postinpelindweilimeis 00 L_ F AS 1310 Sangh a Sampling deth n viat Samele vitco
25. Note If you select a tune file with a prefix only name rather than a tune file with a date time stamp the most recent tune file of with that prefix name will be loaded at the start of each tune Select Factory to use a default factory made file on the instrument that can be used to begin tuning an 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 SQ 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 e Perform Mass Calibration Select this button to enable the system to recalibrate all of the masses during a tune e Check Mass Calibration Select this button to enable the system to confirm that your mass calibration is correct rather than performing a mass calibration 4 Configure the options under the Ion Source tab 94 ISO User Guide Thermo Scientific 7 Optimizing Your Method Modifying an Automatic Tune Figure 85 Configuring the lon Source Options Name My New Tune Description Complete El tuning Tunes and sets detector gain to 3x10 5 Starts with last saved tune Categories Factory Type Tune and diagnostics Diagnostics only E Show advanced settings General lon Source Targets Detector Diagnostics Report lonization mode amp
26. Scientific column You can also refer to our catalog or visit our website at www thermoscientific com columns 6 ISO User Guide Thermo Scientific 2 Changing the Column Replacing the Factory Installed Column Replacing the Factory Installed Column Thermo Scientific 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 To replace the factory installed column Note If you are running samples stop the acquisition before powering off the system 1 Cool down the GC oven and injector See the GC documentation for information After they are cooled down power off the GC WARNING BURN HAZARD The injector oven and transfer line may be hot Allow them to cool to room temperature before touching them 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 3 Click Yes to continue the shutdown process The high voltages heaters and turbomolecular pump power off Once the turbomolecular pump reaches 50 speed or five minutes elapses the foreline pump powers off and you may vent the system Note The amber vacuum light
27. The software will only load files in valid formats If your file is not valid you will receive an error message and will not be able to import the file into the Method Editor Tip Export a timed scan list to see an example of a valid format Choose ISQ Append Timed Scan from File to add scans from previous methods to the end of your open scan list As above you may import csv or xml files The software will only load files in valid formats If your file is not valid you will receive an error message and will not be able to import the file into the Method Editor Choose ISQ Export Timed Scans to export your method as a csv file If you prefer editing your methods in spreadsheet applications you may want to use this option Choose ISQ Create Compound Data Store Export File to prepare your file for the compound data store in the TraceFinder application a Double click one ion of each analyte to set it as the quantitation ion ISO User Guide 47 4 Creating a Method Creating a Method for the GC b Click Create Export File to save your file in the TraceFinder compound data store See the TraceFinder documentation for additional information 15 Choose ISQ Create Segment List From Timed Scan List to import a general acquisition method 16 Choose ISQ View Tune Report to view the latest tune report the method will use Choose Report Options to open the Report Options dialog box see Figure 37 and add identifying infor
28. 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 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 editor The single value at the top of the method is sent when initializing the MS with the method Use the CI Gas Type column to set the type of gas attached to one or both CI gas ports A or B Be sure that the gas you have assigned to a port is actually attached to that port as each CI gas has a specific calibration of flow vs gas viscosity The Cal Gas column turns on the calibration gas during a run This setting can be useful when confirming that the system is generating ions and correctly storing the data to disk Typically the setting is off but you may let a low level of calibration gas into the source by selecting EI If you have a dual flow calibration gas module you may select CI for a high level of gas 9 For Acquisition Timed methods only In the Scans pane do the following Thermo Scientific Thermo Scientific File BQ Help Dasa a x1 4 Creating a Method Creating a Method for the ISO Mass Spectrometer Figu
29. X Method type Acquistion General _r Use general acquisition methods to acquire any data type MS transfer line temp 250 x lonization mode EI v Run completion ERER a0 C Cosy mep G GCruntime C Probe run time I Acquisition threshold 7000 Cigafow 100 miinin Areytoaligros Sopafie 100 min Tay ee Helen RES SAI mem On 250 50 550 0 2 Last Saved Centroid 100 150 200 0 2 0 2 0 2 1 00 1 00 1 Last Saved Centroid 4 00 35 150 01 Last Saved Centroid gt 450 614 01 02 EEE cast saves Centroid 3 View Tune Report Note If some of the columns mentioned below are not shown in the Scans pane you can right click on a heading and display them 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 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 Thermo Scientific ISQ User Guide 39 4 Creating a Method Creating a Method for the ISQ Mass Spectrometer 40 ISO User Guide b As an example in this method the mass range of 50 550 amu will be scanned in 0 2 seconds Beginning from the same start time three different SIM masses at 100 150 and 200 will be looked at for 0 2 seconds each
30. a safe way to transport and store hydrogen However compressed hydrogen gas cylinders like all compressed gas cylinders must be secured in an upright position ideally with a non combustible chain or cable If the cylinder falls over the valve can be knocked off and the pressurized cylinder can take off like a rocket which leads to the release of hydrogen and possibly an explosion severe injury or death 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 ISO User Guide xvii Preface Hydrogen Safety Precautions Properly Storing Hydrogen Storing and handling compressed hydrogen gas and cryogenic liquid hydrogen present potential health and safety hazards Using proper storage and handling techniques is essential to maintaining a safe work environment Use the following guidelines when storing hydrogen xviii ISO User Guide Store spare hydrogen gas cylinders outside and away from doors windows building air intake vents structures and vehicle routes This precaution applies when the hydrogen is or is not in use Indoor storage of spare hydrogen cylinders has special requirements which is beyond the scope of this document Documentation for each vessel should include a description of the vessel a list of available drawings or other documents the most recent inspection results and the responsible person s name Prevent spare cylinders fr
31. according to the settings in the other columns Repeller Select this option to control how the repeller pushes the ions out of the ionization region The voltage applied to this component will have a very strong effect on the energy of the ion beam which will have a strong effect on the resolution and the intensity The lower the voltage the better the resolution However higher voltages will prevent ions from striking the repeller surface 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 intensity that is entering the ion guide This field is typically set between 35 and 50 V Lens 2 Select this option to control Lens 2 which is the second 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 intensity that is entering the ion guide 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 Thermo Scientific 7 Optimizing Your Method Modifying an Automatic Tune Lens 3 Select this option to control Lens 3 which is the last of three lenses that
32. 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 across aGC peak This setting is typically left on d Use the Chrom Filter Peak Width column to set the peak width to match the width ofthe GC peak in seconds If the peak width is set too large signal intensity may be reduced The default value is 1 s ISO User Guide 4 4 Creating a Method Creating a Method for the ISQ Mass Spectrometer 42 ISO User Guide The Filament On column turns the filament on and off in the selected segment Turning off the filament increases the lifetime of the filament and keeps the ion source clean longer However no data will be collected Use this column if you have analytes eluting before the solvent peak You can create a segment to turn off the filament during the solvent peak to preserve the filament Use the Emission Current column to set the emission current used during the acquisition For optimal analytical performance and stability use the emission current at which the system was tuned However if you want to use a different emission current deselect the Use Tune File Emission Current checkbox and enter a value in the Emission Current pA column A high emission current will lead to the production of more ions but the interaction of too many ions in the source can cause a degradation in the resolution and signal The
33. autosampler touches your sample You should always have some sample rinses either before or after injection to make sure you do not have sample carryover from one injection to the next You can configure the settings so that the syringe is 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 is 0 or 1 cycles of pre injection purges Sample Use the Rinses pull down menu to select the number of times the syringe is rinsed with your sample before each injection Rinses help ensure the sample being injected is not diluted by the residual rinse solvents By purging the syringe with your sample before injection the dilution is minimal The standard setting is between 1 and 3 rinses If you have a very limited amount of sample however you may want to set this field to 0 to conserve the sample Post Injection Use the Solvent and Cycles fields to set the number of solvent purges that will occur after the autosampler touches your sample You should always have some sample rinses either before or 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 Configure the Injection group e Injection Depth Use the pull down menu to select Standard or Minimum
34. components will display in the units set in this window 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 Thermo Scientific ISO User Guide 121 8 Troubleshooting Reconfiguring Your Instrument you need to make sure the value matches what you set on the GC The default is Active Low Figure 98 Setting the Remote Start ISQ Configuration General Maintenance Intervals Pressure units Pa v Remote start Active Low 7 Click the Communications button to set the network IP address of the instrument s PC communication board and assign a TCP port The default settings are entered by the factory and should only be changed after consulting you local IT department and obtaining special software from customer support necessary to reprogram the IP address on your instrument Note The instrument must be connected to a dedicated Ethernet port on the PC The instrument cannot be connected through a LAN Figure 99 Setting the Network IP Address and the TCP Port Communications Network address 192 168 1 234 TCP port 30 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 automatical
35. daily tune as frequently as your SOP requires If the system is tuning to your satisfaction 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 OV 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 default tune will start with the tune file stored in the instrument at the factory and then perform a mass calibration and leak check set the repeller to 0 V and tunes the lenses The quadrupole offset voltage will be set to a low value to improve resolution which is also tuned The detector gain will be calibrated to generate 300 000 electrons for every ion that strikes the detector This tune is used in cases where a dirty ion source has been replaced by a clean one or where the computer has been replaced Additionally this tune will generate spectra that are the closest in appearance to the factory tune Note If you are starting with a clean source this is the recommended tune to run Thermo Scientific ISO User Guide 25 3 Tuning the ISO Tuning the ISQ Mass Spectrometer 26 ISO User Guide 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
36. eee eee XX Biological Hazard Warning Note asia XX Venting Tonite Gen cia conta dice cede tenes aioe thes xxi Contacting Us u un eta cat cow eene sg eee as nenn xxi Chapter1 Confirming Your GC MS System is Working 00ee eee eees 1 Checking Power to the System a Be en aha e teee Heres wy 1 Verifying the Carrier Gas Flow Rate 0 an 2 Checking Your Carrier Gas Tank Pressure is nie cccnnce einwlnennowe ness 3 Checking the Vacuum and Temperature u 04220 02 2 an 4 Chapter2 Changing the Column aaaea aaan 5 Replacing the Factory Installed Column nnuaaananuannnunnne eee T Connecting the Column to the Transfer Line rau 220 epee sendy 13 Chapter3 Tuning the ISO cece cece ee eee eee eee eee nanana 23 Accessing ISQ Autoteile 24 Tuning the ISQ Mass Spectrometer aa Soa en ee vas Macks 24 Chapter4 Creating a Method ccc c cece eee ee eee eens 33 Creating a Method for the Autosampler u u er 34 Creating a Method for the ISQ Mass Spectrometer 000000000 ee 37 Thermo Scientific ISO User Guide iii Contents iv ISO User Guide Chapter 5 Chapter 6 Chapter 7 Chapter 8 Creating a Method for the GC ioe aco ee 48 Creating a method for the TRACE 1300 or TRACE 1310 48 Creating a Method for the TRACE GC Ultra 1 ee eee eee eee 55 Creating a Method for the FOCUS GC an 59 Running a Samples iste jini oon caine men
37. 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 lens positive voltage the default is 15 V You should tune with the same value you are planning to use for your analysis This value affects the focusing of the electron beam into the source If you change your electron energy from 70 V this value will also change This voltage must always be at least 45 V above the voltage applied to the filament The voltage applied to the filament is the same number but the opposite sign of the electron energy e Electron Lens Negative Voltage This field is used to allow the electrons to enter the ion volume 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 96 ISO User Guide Thermo Scientific Thermo Scientific 7 Optimizing Your Method Modifying an Automatic Tune Custom Select this option if you do not want to use the default value for the tune For the electron lens negative voltage the default is 75 V You should tune with the same value you are planning to use for your analys
38. file 268E4 RT 3 43 RT 3 33 RT 3 37 AA 2892760 AA 272601 AR 566276 Relative Abundance miz 27150 27250 MS ICIS datat5_10010417 0750 3 40 Time min data15_100104170750 319 325 RT 3 443 468 AV 7 NL 1 56E4 T 0 0 El Full ms 50 00 300 00 Relative Abundance 231 24 ie 265 19 297 09 227 54 234 29 269 81 To perform a background subtraction and improve the spectral library searching right click in the MS 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 ISO User Guide 87 6 Exploring Your Data ISO User Guide Figure 80 OFN in Full Scan With Background Subtraction Thermo Xcalibur Qual Browser data15_100104170750 data15_1001041 70750 raw lle Edit View Display Grid Actions Tools Window Help sels a Melo 1 8lelsist E asia Klee ei ST le ole cll is C Xoaliburdata OFN data15_100104170750 1 4 2010 5 07 50 PM 3 DB ee Final Test Method datal5_100104170 no file no file no file no file no file no file no file APR eR ee Without background subtraction the full scan would look like the graphic below RT 3 25
39. mL min lon gauge pressure Turbo pump speed Cl reagent gas flow The list of available tune types opens Tuning the ISQ Mass Spectrometer To tune the ISO mass spectrometer using ISO Autotune RL yw 1 Select the tune type you want to use from the list of available tune types See Figure 20 Thermo Scientific 24 ISO User Guide 3 Tuning the ISO Tuning the ISO Mass Spectrometer Figure 20 List of Available Tunes in ISQ Autotune Tunetypes El Cl Both Daily Tune builtin Display report 7 Daily Tune Check builtin when complete 7 El Default Tune builtin EI Full Tune builtin 7 Cl Tune builtin 7 Cl Tune built4n 7 Full Diagnostics builtin I Daily Tune with Taraets Now running Action 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 If your SOP allows it you can use this tune to rapidly verify that the previous lens tune is still generating good spectra e Daily Tune This tune is used to quickly tune the system It performs a mass calibration and leak check tunes the lenses and resolution and sets the detector sensitivity to generate a m z 69 ion with an intensity of 20 000 000 counts You can perform a
40. necessary Thermo Scientific Preface Hydrogen Safety Precautions Hydrogen Safety Codes Standards and References Thermo Scientific The following list of safety codes standards and references is in no way an exhaustive list In fact there may be federal state or local codes that apply to your specific location Check with all appropriate agencies with jurisdiction before installing or using a hydrogen system Air Products Safetygram 4 Gaseous Hydrogen ANSI AIAA standard for hydrogen safety guidelines is AIAA G 095 2004 Guide to Safety of Hydrogen and Hydrogen Systems ASME B31 1 Power Piping Code ASME B31 3 Process Piping Code ASME B31 8 Gas Transmission and Distribution Systems BCGA Code Of Practice CP4 Industrial Gas Cylinder Manifolds and Gas Distribution Pipework BCGA Code 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 Loss Prevention Data Sheets 7 91 Hydrogen IGC Doc 121 04 E Hydrogen Transportation Pipelines System Design Features NASA NSS 1740 16 Safety Standard For Hydrogen And Hydrogen Systems Guidelines for Hydrogen System Design Materials Select
41. on the TRACE 1300 or 1310 reach over the top 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 Note The TRACE GC Ultra beeps to indicate that the carrier gas is turned off or set incorrectly To check the carrier gas flow rate 1 Access the carrier gas menu On the TRACE GC Ultra press the Carrier button on the front of the GC On the TRACE 1310 choose Instrument Control and then Front Back Inlet On a TRACE 1300 open the Xcalibur software by clicking on the Xcalibur icon on the computer desktop On the Xcalibur roadmap select the TRACE 1300 from the instrument list in the side panel This opens the Status Panel 2 Display the column flow 2 ISO User Guide Thermo Scientific 1 Confirming Your GC MS System is Working Checking Your Carrier Gas Tank Pressure 3 If the actual and set point amounts in Col Flow are the same then you have good carrier gas flow If the amounts are different see the troubleshooting section of your GC user documentation Checking Your Carrier Gas Tank Pressure Make sure you have enough pressure in the carrier gas tank to accommodate the number of samples you plan to run If the pressure is too low you may run out o
42. 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 Tip If you intend to use ammonia reagent gas attach methane to one CI reagent gas port and ammonia to the other port Tune the instrument using methane then switch to the ammonia port Allow plenty of time for the new reagent gas to purge the CI tubing before starting your analysis Note To add a tune type to the list see Modifying an Automatic Tune 2 Select the Display Report When Complete checkbox so that you can view the tune report after running the tune Thermo Scientific 3 Tuning the ISO Tuning the ISO Mass Spectrometer Figure 21 Displaying a Tune Report I El Default Tune builtin T EI Full Tune builtin IT Cl Tune builtin I Ch Tune builtin Full Diagnostics builtin I Daily Tune with Taraets Now running i F Show spectra m 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 Thermo Scientific ISO User Guide 27 3 Tuning the ISO Tuning the ISQ Mass Spect
43. temperature of the column 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 ISO User Guide 91 7 Optimizing Your Method 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 Figure 82 Accessing the Tune Type Editor from the ISO Dashboard ISQ Dashboare ISQ Dashboar Ka Air amp Water Tune Status Analyzer Power Maintenance Status Idle Actual v MS transfer line temp 250 C 200 C OK 51 mTor v lon source temp v Vacuum Foreline pressure lon gauge pressure Turbo pump speed Cl reagent gas flow 1 2x10 Tor 100 0 0 mL min 0 0 mL min 2 In the Tune Types dialog box select a tune type to edit and click the Copy button Thermo Scientific 92 ISO User Guide Thermo Scientific 7 Optimizing Your Method Modifying an Automatic Tune Figure 83 Using the Tune Types Dialog Box RS ee View Tune Report N a Tu
44. the column outlet in a small vial of methanol 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 ISO User Guide 9 2 Changing the Column Replacing the Factory Installed Column Eol 10 ISQ User Guide Allow the column to purge for at least 10 minutes If you used methanol to detect column flow remove column from methanol during purge time Insert the column into the fitting of the column flowmeter connector that blocks the column flow 15 Perform a column leak check a C On the TRACE 1310 select the Leak Check icon in the Maintenance menu Otherwise perform the leak check through the Chromatography Data System Refer to the TRACE 1300 and TRACE 1310 Series GC User Guide for instructions Note Ifyou are using a TRACE GC Ultra or a FOCUS GC refer to your GC user documentation for instructions on performing a leak check Start the leak check The split and purge valves of the selected channel are automatically closed and the channel is pressurized 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 dete
45. the instrument To confirm that the instrument is vented check how much the glass cover compresses the top cover o ring in the manifold Once the o ring surface touching the glass is about 1 mm it is safe to open the instrument and remove the column 9 Turn off the carrier gas and if used the detector gas See the GC documentation for information about using detector gases WARNING BURN HAZARD The injector oven and transfer line may be hot Allow them to cool to room temperature before touching them 10 Unscrew the transfer line nuts and remove the column 11 Attach a blanking ferrule and nut to seal the end of the transfer line to prevent contaminants from entering the MS during column conditioning ISQ User Guide Thermo Scientific 2 Changing the Column Replacing the Factory Installed Column 12 Remove the column from the column rack and from the GC 13 Connect the new column to the injector inside the GC Note Wear clean lint and powder free gloves when you handle the column and injector ferrule a Unwind the column enough to easily connect its ends to the injector and MS b Wipe about 100 mm 4 in of the column with a tissue soaked in methanol c Insert the column through the injector retaining nut and ferrule larger end up If the M4 retaining nut is used slide it on the column through the side cut Wipe the column again with a tissue soaked in methanol Tip Slide a notched septum on the colu
46. 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 100 ISO User Guide Thermo Scientific 7 Optimizing Your Method Modifying an Automatic Tune My New Tune Description Complete El tuning Tunes and sets detector gain to 3x10 5 Starts with last saved tune Categories Factory Type Tune and diagnostics Diagnostics only Show advanced settings 7 Tune resolution E Tune high scan rate 10000 amu sec e Mass Use this pull down menu to select the ion to be used for tuning e Peak Width Use this field to enter the target peak width e Measure at Use this pull down menu to select the location on the peak at which you want to measure the target peak width 10 Select this option to measure the width at 10 of the peak height 50 Select this option to measure the width at 50 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 tune Tune High Scan Rate Select this checkbox to
47. to ensure a leak tight seal See the JSQ Spare Parts Guide for information about ordering these ferrules 25 Condition the graphite Vespel ferrule a Raise the oven temperature to the maximum temperature you will operate the GC column b Wait 10 minutes c Lower the oven temperature to 40 C 104 F and allow it to cool before continuing WARNING BURN HAZARD The oven may be hot Allow it to cool to room temperature before opening it The injector will still be hot so do not touch it 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 16 ISO User Guide Thermo Scientific 21 28 RL 2 Changing the Column Connecting the Column to the Transfer Line d Ifyou are using hydrogen as a carrier gas replace the front panel screw e Replace all remaining hydrogen safety screws if you are using hydrogen Power on the ISQ mass spectrometer 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 switch Once the ISQ instrument is pumped down and able to scan click Air amp Water Tune on the ISQ Dashboard view air water spectra and look for e
48. tool bar Figure 64 Selecting a Row of Samples to Run File Edit Change Actions View GoTo Help Check Disk Space Run This Sample Shan MASAN BYOB Sample Type FileName Sample ID Path Inst Meth Unknown 02012 1 CAXoalbu sibur met Status Acquistion Run Sequence 02102012 01 1 C Xcalibur Dat C Xcalibur methods BC_Test i ET 0 0 Run Manager Batch Reprocess Ready To Doy Sequence Open File Sample Name Working On Start Analysis Position 2 Raw File Stop Analy Inst Method Pause Analysis B TnPlus ae Ready to Doi Devices On TRACE GC Ultra Devices Standby H Readyto Dow Devices Off amp ISQ Ready to Dow Automatic Devices On Reinstate Warnings Status Analyzer Power Maintenance Status Idle F Actual Set Point MS transfer line v 7 250 C 250 C v lon source temp 200 C 200 C Vacuum OK Foreline pressure 50 mTorr lon preseure 1 3105 Torr Turbo pump speed 10 pe CI reagent gas flow 0 0 mUmin 0 0 mL _ m r Run this sample NM _ 21 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 75 5 Running a Sample Running a Sequence Figure 65 Customizing a Sequen
49. use 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 ISO User Guide 103 7 Optimizing Your Method Modifying an Automatic Tune Figure 90 Accessing the ISO System Diagnostics Edit Tune Type My New Tune ion Complete El tuning Tunes and sets detector gain to 3x10 5 Starts Z with last saved tune Factory Type Tune and diagnostics Diagnostics only Show advanced settings General lon Source Targets Detector Diagnostics Report F Communication Check a 7 Detector Check Filament Check F lon Guide Frequency Check Leak Check LensCheck 7 Power Supply Check 10 Click the Report tab configure how you want to view your data Figure 91 Configuring the Report Options edit Tune Type Name My New Tune Description Complete El tuning Tunes and sets detector gain to 10 5 Stats Cancel ne lt cms Categories Factory Print Type Tune and diagnostics Diagnostics only Show advanced settings General lon Source Targets Detector Diagnostics Report Acquire full scan spectrum Acquisition threshold 3 000 SiMmasses 69 i31 z219 a4 502 A
50. 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 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 ISO User Guide 65 5 Running a Sample Running a Sequence Running a Sequence Once youve prepared your sample you can use Xcalibur to run your sample s Xcalibur uses a sequence series of tasks to prepare 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 Torun 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 54 Sequence Setup in Xcalibur Sequence Setup File Actions View Tools GoTo Help 66 ISQ User Guide Thermo Scientific Thermo Scientific 5 Running a Sample Running a Sequence 3 In the Sequence Setup window click in the first row of the Sample Type column and select a sample type from the drop down m
51. 13 2011 2 36 PM 11 21 2011 3 47 PM 11 4 2011 331 PM 11 3 2011 5 38 PM Wiosna ci File name My_New_Sequencel Xcalib Xcaliby Xcalib Xcaliby Xcaliby Xcalib Xcaliby Xcalib Xcalibu Xcalib Xcalib Xcalibt Xcaliby r Saveastype Xcalibur Sequences sid Header Information Created Modified Last saved by Number of saves 1 Comment Friday February 10 2012 1 15 20 PM Friday February 10 2012 1 15 20 PM Alvin Thermo Scientific ee i Exploring Your Data Once you have acquired your data you need to look at your data to make sure the peaks have a good shape and that the peak area is large enough for your needs The Qual Browser utility of Xcalibur allows you to view chromatograms and spectra from raw 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 1 pg 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 your computer desktop 2 In the Xcalibur Roadmap window click the Qual Browser icon Figure 67 Xcalibur Roadmap File Actions View Tools GoTo Help gt mu For Hel
52. 99 7 Optimizing Your Method Modifying an Automatic Tune 50 Select this option to measure the width at 50 of the peak height Threshold Use this field to enter the change in intensity that has to occur when the tune to select a new voltage For example if you set this field to 1 1 the tune will not select a new voltage for that component unless the intensity is 110 of the old intensity If you set this field to 1 anytime the new voltage has an intensity larger than the old intensity the tune will select the new intensity Note Ifa value less than 1 is chosen for ramped devices the tune will step back in energy until the lower intensity is detected For example if 0 8 is chosen the device value lower in energy than the device value with the maximum response which gives an intensity closest to 80 of the maximum intensity will be chosen On Error Use this pull down menu to select how to handle an error in the tune Fail Select this option to stop the tune when an error 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 Note Click the Advanced Settings check box to access the Resolution tab Tune Resolution Select
53. C EN 61326 1 1997 A1 1998 A2 2001 Safety EN 61010 1 2001 Direct Probe Controller DPC standards EMC EN 61326 1 2006 Safety IEC 61010 1 2001 IEC 61010 2 081 2001 e 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 FCC Compliance Statement THIS DEVICE COMPLIES WITH PART 15 OF THE FCC RULES OPERATION IS SUBJECT TO THE FOLLOWING TWO CONDITIONS 1 THIS DEVICE MAY NOT CAUSE HARMFUL INTERFERENCE AND 2 THIS DEVICE MUST ACCEPT ANY INTERFERENCE RECEIVED INCLUDING INTERFERENCE THAT MAY CAUSE UNDESIRED OPERATION CAUTION Read and understand the various precautionary notes signs and symbols A contained inside this manual pertaining to the safe use and operation of this product before using the device 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 Notice on the Proper Use of Thermo Scientific Instruments In compliance with international regulations Use of this instrument in a manner not specified by Thermo Fisher Scientific could impair any protecti
54. CE GC Ultra 6 Untitled Thermo Xcalibur Instrument Setup a m E O File TRACE Help TRACE GC Ultra Al AS 1310 osa S x 2 Oven Left SSL Left Camier Right PTV Right Canier Run Table Time tem Initial values I Extemal Event 1 On I Extemal Event 2 On 7 Extemal Event 3 On 7 Extemal Event 4 On Creating a Method for the FOCUS GC To create a method for the FOCUS GC Setting I Extemal Event 5 On 7 Extemal Event 6 On 7 Extemal Event 7 On I Extemal Event 8 On 1 Click the Oven tab to set the oven temperatures There is always at least one temperature and time in 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 Thermo Scientific ISO User Guide 59 4 Creating a Method Creating a Method for the GC 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 600 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 Figure 48 Setting the FOCUS GC Oven Parameters Rf Untitled E Eile Focus Thermo
55. 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 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 I icon and save it as a Microsoft Excel file or an Adobe Acrobat PDF file your computer Then click Open Figure 24 Opening a Tune Results File Click Open Tune Results in the top ofthe window and browse to another tune report on Mt E Fe u d Users Public Public Documents ThermolSQ TuneResults Organize v New folder Fr Favorites Name Date modified EE Desktop E Default_EI_2012 01 05 16 46 36 isgtuneres 1 5 2012 4 46 PM Downloads E Default_EI 2011 12 08 11 31 45 isgtuneres 12 8 2011 11 31 AM Recent Places E Default_El_2011 11 18 17 19 10 isqtuneres E AutoTune_El_2011 11 18 16 57 32 isqtun 11 18 2011 5 19 PM 11 18 2011 4 57 PM Libraries AutoTune_El_2011 11 18 16 31 49 isqtun 11 18 2011 4 31 PM E Documents E AutoTune_El_2011 11 14 15 01 25 isqtun 11 14 2011 3 01 PM d Music 5 E AutoTune_El_2011 11 14 14 37 41 isqtun 11 14 2011 2 37 PM Pictures E AutoTune_EI_2011 11 11 15 03 24 isqtun 11 11 2011 3 03 PM B Videos E AutoTun
56. Method for the ISQ Mass Spectrometer To import an TSQ 8000 or TSQ Quantum Series MS method choose ISQ Import MS Method See Figure 36 Note This will only import the MS part of the method You must set the GC and autosampler parameters Figure 36 Importing Methods Untitle o File 1SQ Help D Show Group Settings import A port timed scans Append timed scan from file y Use timed acquisition methods to acquire timed SIM data Export timed scans Create compound data store export file lonizats de EI Run completion Create segment list from timed scan list 3 5 On Clges tune Mr e Pot A GC run time Probe run time z 2 C after 100 mit View Tune Report Clgas fow 100 mumin p min TRACE GC Ultra Instrument settings Scan settings Tune file Emission current Peak width Tune file Last Saved z Use tune file emission current Min baseline peak width 3 03 sec Tune File Autotune_NCI Use specified emission current 50 uA Desired scans per peak 4 Detector gain Full scan TriPlus Use last tuned detector gain I Use full scan with mass range 50550 Daca C Use specified detector gain 0 Full scan time 0 043 sec Positive Start time 2 00 min End time 10 00 min Choose ISQ Import Timed Scans to import csv or xml files of previous methods
57. Range Al Number of copies fi a Selection Current Page G Pages EEE 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 Options i ae J Diagnostics Device settings I Tune type settings Custom report 7 Use custom report definition File name 10 If the sensitivity and resolution are adequate for running the initial samples you are ready to develop or run a method Thermo Scientific ISO User Guide 31 ee B 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 e Creating a Method for the Autosampler e Creating a Method for the ISQ Mass Spectrometer e Creating a Method for the GC To create a method for the ISO mass spectrometer GC and autosampler Note For information about creating a method for specific instruments and software refer to the appropriate documentation 1 Click Method Editor on the ISQ Dashboard to open the Method Editor See Figure 27 Thermo Scientific ISO User Guide 33 4 Creating a Method Creating a Method for the Autosampler Figure 27 Accessing the Method Editor from the ISO Dashboard Auto Tune rA View Tune Report ra Tune Types l i
58. Setup aan ww i File TRACE Help Deu S x Oven Left SSL Left Camier Right PTV Right Camier Run Table R Inlet 7 Temperature C 200 u 17 Split Flow ml min 50 Split Ratio 10 W Spitless Time min 1 00 TRACE GC Ultra Purge a 5 Stop Purge For min Surge AIAS 1310 Surge Pressure kPa 3 Surge Duration min 0 00 Mode Split 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 sample This setting is typically turned on and set to a flow of 50 mL min However more carrier gas will be used so for your analysis lower split flows may be more acceptable Thermo Scientific ISO User Guide 57 4 Creating a Method Creating a Method for the GC Tip We recommend turning on the septum purge which means an additional 5 mL min of carrier gas will go through the injector 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 After these times the split flo
59. Transfer Line When connecting the column to the transfer line you may use either the regular transfer line nut or the spring loaded transfer line nut with the graphite Vespel ferrule To connect the column using the regular transfer line nut 1 Lower the oven temperature and allow it to cool 2 Confirm that the MS is vented and remove the current transfer line nut and ferrule 3 Unwind about one turn of the column from the column outlet end Note Wear clean lint and powder free gloves when you handle the column and transfer line ferrule 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 Note If the maximum oven temperature in your method is 290 C 554 F Thermo Fisher Scientific recommends using a spring loaded transfer line nut with a graphite Vespel ferrule or a SilTite nut and ferrule By cycling the oven at and above this temperature expansion and contraction of the graphite Vespel material can cause leaks in the transfer line 6 Insert the column through 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 Flat on the Transferline Nut A Transfer Line Nut SilTite Ferrule 7 Insert the column into the column measuring tool see Fig
60. Xcalibur Instrument Setup Help oem S x Al AS 1310 Focus GC IsQ Ready CAUTI 60 ISO User Guide 1 Oven 2 SSL Inlet 2 Carrier dh MS Transfer Line 2 Run Table S 254 0 4 0 00 020 040 060 O80 1 00 120 140 160 180 200 220 240 260 280 300 Ramps Oven Rate Temp Hold Time z C min CC minutes Maximum Temperature 350 C Initial 40 1 00 i Prep Run Timeout 10 00 min Rampt 100 50 10 Equilibration Time 0 50 min You can select a maximum of seven temperature ramps each with their own ramp rates final temperatures and hold times A typical program will have one or two ramps However 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 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 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 a 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 tempera
61. ake You can select either constant pressure or constant flow If you use constant pressure as the column is heated in the oven the flow rate will fall because a hotter column is more resistant to carrier gas flow If you use constant flow the carrier gas pressure will increase as the column temperature increases to keep the flow constant 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 Figure 50 Setting the Carrier Gas Parameters for the FOCUS GC ES Untitled Thermo Xcalibur Instrument Setup BAR Eile Focus Help Dale S x i Oven 9 SSLinlet E2 Carrier dh MS Transfer Line 3 Run Table Flow Mode Constant Pressure v Pressure a kPa Vacuum Compensation IV AIAS 1310 Kn Gas Saver o Focus GE Enabled Flow Time IsQ Ready In an effort to reduce the amount of carrier gas used you can activate the 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 system performance 4 Click the MS Transfer Line tab to set the temperature of the transfer line fo
62. al protective equipment according to the safety requirements oba 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 instrument It is the users responsibility to label the relevant parts of the equipment gt When working with biohazardous materials you are responsible for fulfilling the following mandatory requirements e Providing instructions on how to safely handle biohazardous material e Training operators to be aware of potential hazards XX ISO User Guide Thermo Scientific Preface Contacting Us e Providing personal protective equipment e Providing instructions for what to do if operators are exposed to aerosols or vapors during normal operation within the intended use of the equipment or in case of single fault situations such as a broken vial The protective measures must consider potential contact with the skin mouth nose respiratory organs and eyes e Providing instructions for decontamination and safe disposal of relevant parts WARNING The user or operator is responsible for the safe handling of hazardous chemicals or biological compounds including but not limited to bacterial or viral samples and the associated waste according to international and local regulations Vent
63. alibur Qual Browser data15_100104170750 data15_1001041 70750 raw File Edit Yiew Display Grid Actions Tools Window Help 6 Exploring Your Data EIER SERIE BET gt ple 9 f amp E alexa e HI Tome FFECCN C Xcaliburdata OFNidata15_ 100104170750 Final Test Method 1442010 5 07 50 PM Ferne RT 3 25 3 50 EE TIC data15_10010 1 Mass Range data1 X Mass Range no fi XK Mass Flange no fi ce 8 3 35 3 37 338 339 NL 145E7 J TIC MS data5 _1001041 3 X Mass Range no fi X Mass Range nofi X Mass Range no fi Mass Range no fi Relative Abundan a 3 Bo 3 26 328 320 332 333 334 336 337 339 Time min miz 27150 27250 ms datat5_1001041 70750 3 41 3 42 data15_100104170750 1 RT 2 52 AV 1 NL 2 1966 T 0 0 c El Full ms 50 00 300 00 67 24 Relative Abundance Time 3 41 Intensity 7 41e 006 Scan Filter none 125 07 442 32 168 33 170 99 191 22 207 00 231 74 261 89 calle 281 56 ET DP SS a 220 250 280 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 73 Finding the Peaks in Qual Browser PA Thermo Xcalibur Qual Browser File Edit View Display Grid Actions Tools Window Help siela a selo gt IRlt 8 8 E slalla ei data15_100104170750 data15_1001041 70750
64. ce Run File Edit Change Actions View GoTo Help Cals Bo MASAN OPSE pan EURE Sample Type File Name Sample ID Path Inst Meth Position Inj Vol Status Acquisition Queue L 1 Unknown 02102012 01 1 C Xcalibur Dat C Xcalibursmethods BC_Test 1 1i E Run Manager ar Ready To Download Sequence Sample Name Working On Run Sequence Position Raw File Acquisition Options Inst Method User EI TPlus Autosampler Instrument Start Instrument Ready to Download TriPlus Autosampler Yes i TRACE GC Utra TRACE GC Ultra Bun Rows 1 Ready to Download 2 15Q Ready to Download IsQ E Priority Sequence V Start When Ready Change Instruments Processing Actions Instrument Method C Quan ree eee stp ce a Shut Down Browse Status Idle m Reports Programs E Programs Pre Acquisition B STA Actual Set Point Create Quan Summary i Post Acquisition li p D ozo antore 250 C 250 C ne V Pre Acquisition V Post Acquisition v lon source temp 200 C 20 C After Sequence Set System NETS er On Standby Foreline pressure 50 mTorr pressure 1 3 105 Torr Turbo pump speed 100 CI reagent gas flow 0 0 mUmin 0 0 mL _ a m For Help press FL NUM a Select the Start When Ready checkbox to run the sequence when the instruments are ready b Click the Change Instrumen
65. covered under the D gt O i 1 amp CA standard warranty LIFTING HAZARD Indicates that a physical injury could or might occur if two or more people do not lift an object amp MATERIAL AND EYE HAZARD Indicates that eye damage could or might occur xii ISO User Guide Thermo Scientific Preface Hydrogen Safety Precautions Descriptor RADIOACTIVE HAZARD Indicates that exposure to radioactive 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 personal injury or death For the prevention of personal injury this general warning symbol precedes the WARNING safety alert word and meets the ISO 3864 2 standard In the vocabulary of ANSI Z535 signs this symbol indicates a possible personal injury hazard exists if the instrument is improperly used or if unsafe actions occur This symbol and another appropriate safety symbol alerts you to an imminent or potential hazard that could cause personal injury Hydrogen Safety Precautions Thermo Scientific Hydrogen is a colorless odorless highly flammable gas with the molecular formula H3 Hydrogen gas pre
66. cquire Full Scan Spectrum Select this checkbox to display the full spectrum on your tune report 104 ISO User Guide Thermo Scientific Thermo Scientific 7 Optimizing Your Method Modifying an Automatic Tune Acquisition Threshold Use this field to enter a minimum peak height for the data file If your peak has an intensity that is below this threshold it will not be stored SIM Masses Use these pull down menus to select 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 92 Printing the Tune Type Information i gd Save as PDF Print report 18 Tune Type Report My New Tune Complete Ei tuning Tunes and sets detector gain to 3x10 S Stats win last saved une Factory Tune and Diagnostics Dutpat tune Sie pretx AutoTune Stating Tune Fie Lest Sevec Bearing Tune Source wsettre Mass Calbeton Action WA Er ema 61510785 emu GES t1325 amu 122 5 t0 220 5 amu 20 5 t0 415 5 amu soa 415 5 ama and above Detector Sensitivity Bat intel geim Yes GE O5 Tune detector gein Yes Adjust detector sensittvity Yes Mass 69 intensity 10000000 Qi Lens 13 Click Close to return to the Me
67. ctor to find and fix any leaks Tip Leaks can be caused by not tightening the fitting on the column flowmeter connector Check the fitting before looking for the leak elsewhere CAUTION INSTRUMENT DAMAGE Do not allow the column flowmeter connector to exceed 80 C 176 F Otherwise it will melt and damage the instrument 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 4 Thermo Scientific 2 Changing the Column Replacing the Factory Installed Column Figure 4 Column Flowmeter Connector To flowmeter b Connect the flowmeter to the dedicated fitting on the column flowmeter connector c Ifyou have a TRACE 1310 select the Back Column or Front Column button in the Configuration menu Otherwise perform the column evaluation through the Chromatography Data System See the TRACE 1300 and TRACE 1310 User Guide for instructions d Select Column and input the column s physical characteristics e Ifa pre post column is present set the length and nominal internal diameter of the pre post column in the same valid ranges for the column Note For the most reproducible results you should conduct a more detailed column evaluation However the following steps while recommended are not required f Start the column evaluati
68. d with a mass spectrometer Large diameter columns made of steel are widely 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 stationary phase and the analyte determines how well the analytes separate from each other resolution and also affects how quickly the separation occurs analysis time Choose a stationary phase that is compatible with the nature of your analytes and the maximum GC oven temperature you are going to use ISO User Guide 5 2 Changing the Column Internal Diameter The smaller the diameter of the column the better the separation However smaller diameter columns do not have as much capacity for matrix or analytes As a result smaller diameter columns are subject to overloading which leads to retention time shifts and peak shape changes Larger diameter columns can accept larger concentrations of material but will require longer columns or slower GC oven temperature ramps which increases the analysis time to match the separation power of shorter columns Typical column sizes for GC MS have inside diameters ID of 0 25 mm Smaller ID columns such as the 0 15 and 0
69. e aad wee demas 65 Preparing Your Sample ot cca stancib sciadeaved 44 0 arene ae conrindea a cheated ead 65 Running ASeQUER CE ou ee nen re 66 Exploring Your Data 2000 e cece eee nennen nennen nenn 79 Optimizing Your Method 0 cece eee eee eee eee eens 89 Changing the Chromatographic Separation 0 00 cee eee eee eee 89 Finding the Best Way to Make an Injection 0 0 cee eee eee ee 90 Improving the Way You Prepare Samples 1 1 0 0 0 eee 90 Chaiieitig the Scan Rate a he Lane actus aiden een 90 Narrowing the Mass Ranges 1 We ah 90 Adjusting the Transfer Line Temperature ceennocceeeeeeennnnn 91 Modifying an Automatic Tune ia eine wet ogeebs 92 Troubleshooting 0 0 ccc cece cece cece e eee nun nennen 107 No Ions Present in Scans cecene cece eens 108 Checking the ISQ System Firmware tas foun uch 108 How to Know When Your System Needs Maintenance 045 111 Investigating Baseline Issues u 2 een ae ee 112 Investigating Peak Issues As er 114 Investigating Results Issues uns mau 117 Reconfiguring Your Instrument wre entre ee 119 Thermo Scientific Declaration Manufacturer Thermo Fisher Scientific Thermo Fisher Scientific is the manufacturer of the instrument described in this manual and as such is responsible for the instrument safety reliability and performance only if e installation e re calibration e changes and repair
70. e not shown in the Groups pane you can right click on a heading and display them You can also reorganize the columns by clicking on the heading of a column and dragging it to the left or right Methodtype Acquisition General v Use general acquisition methods to acquire any data type Ion source temp 200 C Claastype Methane Pot ee RD I Acquisition threshold 1000 Clgas flow 100 mUmin Apply tall groups MStransferlinetemp 250 21 C lonizationmode E v Run completion C Stop after 10 0 min Dwell or Scan SIM Widths Times sec 02 fre 5 Chrom Filter On 1 000 sec 0 2 0 2 0 2 1 00 1 00 1 Filament On Yes 01 01 02 Electron energy Use last tune value a The Time column displays the time that the ISQ mass spectrometer begins to acquire this particular group of scans after the GC starts b The Total Scan Time column indicates the sum of all the scans in each segment The total scan time also contains the stabilization time that occurs between each scan In this method beginning 2 5 minutes into the GC run you will get a complete set of scans every 0 816 seconds At 4 minutes into 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
71. e the instrument Column is not far enough The GC column does not extend into into the transferline the MS source Use the column measuring tool to confirm column length If the end of the column is inside the transfer line an excessive amount of 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 114 ISQ User Guide Thermo Scientific Table 3 Troubleshooting Peak Issues in Your Data continued Sheet 2 of 3 Behavior Tailing Thermo Scientific Characteristic Sample peaks Cause Column degradation is causing activity 8 Troubleshooting Investigating Peak Issues Remedy Inject a test mixture and evaluate the column Replace column if necessary Liner is dirty Ion source is dirty Clean or replace the liner Clean the ion source Run the method with higher source temperature making certain not to start running samples in matrix until the source has had several hours to reach thermal equilibrium Glass wool or inlet liner is causing activity Replace wool with fresh silanized wool and install a clean inlet liner Inlet temperature is too low Increase the temperature of the inlet Column connections are poor or obstructed Stationary phase is not appropriate for your target compounds Reconnect the column inlet Replace the column and choo
72. e_El_2011 11 11 11 52 26 isqtun 11 11 2011 11 52 E AutoTune_EI_2011 11 11 11 34 28 isqtun 11 11 2011 11 34 jM Computer E Default_EI 2011 11 11 10 59 23 isqgtuneres 11 11 2011 10 59 amp Local Disk C m Removable Disk Gia Network E AutoTune_EI_2011 11 11 10 38 50 isqtun AutoTune_EI_2011 11 11 10 20 42 isqtun m E Defauit_EI_2011 11 11 09 52 20 isgqtuneres a AutoTune_EI_2011 11 09 11 48 23 isqtun 11 11 2011 10 38 11 11 2011 10 20 11 11 2011 9 52 AM 11 9 2011 11 48 AM File name z Search TuneResults Pp v Type Size pA i ISQ Tune Results 47 KB ISQ Tune Results 49 KB SQ Tune Results 49 KB SQ Tune Results 51 KB SQ Tune Results 14 KB I ISQ Tune Results 64 KB ISQ Tune Results 14 KB I SQ Tune Results 64 KB SQ Tune Results 51 KB ISQ Tune Results 53 KB La ISQ Tune Results 48 KB SQ Tune Results 42 KB SQ Tune Results 49 KB ISQ Tune Results 47 KB i ISQ Tune Results 51 KB v Tune result files isgtuneres v 8 Click Print Report to open a print dialog box and print your report 30 ISO User Guide Thermo Scientific 3 Tuning the ISO Tuning the ISO Mass Spectrometer Figure 25 Printing a Tune Report General r Select Printer fib Add Printer Fax Microsoft XPS Document Writer Status Ready J Print to file Preferences Location Gooi Find Printer r Page
73. ed temperature in a temperature ramp will fall from 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 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 56 ISO User Guide Thermo Scientific 4 Creating a Method Creating a Method for the GC remain at that temperature after the analytical run is complete You can also set the amount of pressure used to push the carrier gas through the column 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 The inlet should be turned on and set to a temperature that is at least 10 C higher than the boiling point of your least volatile analyte The material should be injected into the port to vaporize and move into the GC column quickly Higher temperatures can lead to thermal decomposition of some analytes so you 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 45 Setting the TRACE GC Ultra SSL Injector Parameters fp Untitled Thame Kealipur instrument
74. ensitivity if it reduces the number of compounds analyzed in a segment If the windows do not overlap you will not notice an improvement by reducing the acquisition window i In the Mass column enter the mass of the ion you wish to monitor j Use the Ion Polarity column if you are using CI mode to tell the instrument to generate positive or negative ions Only use this column if you are using CI mode In EI mode this column should always be set to Positive k Ifyou want to adjust individual peak widths select Set Peak Width Individually for Analytes found in the Options dialog box accessed by the ISQ main menu See Figure 33 Increasing a peak width will be reflected in the Show Analysis view Adjustments in this column are for display purposes only and will not affect your acquisition Figure 33 Options Dialog Box fle BQ Help Ojsia 8 xl Acquistion Tred x Use med acqasinon methods to scqure heed SM ante asa MS warater line wep 50 HC kenizatien mode E Fun conglason e e g mamae 700 e Oye eter GC nn tme Probe run time N z s DT Acquisition tresheld 1000 4 Cl gas Bow 10 elma Sup ater 150 ala JE TRACEGCUMa Instrument setings pen Vagis Emanen current wog Tune het oe Unetme Sie eminaien cum 33 se Reming ital sean ime 0500 see SNRA rao paan o Une spected emiasian curet 5 ON ae we ph Min dwol me 00012 see TP l Click Show Analysis see Figure 34 to val
75. enu You should select Unknown when you are developing an analytical method The other types of samples require a quantitation method Note To open an existing sequence you can select File Open from the main menu or click the g icon and browse to a sequence Figure 55 Entering the Sample Type 7 ce Setup 0210201251 m AE File Edit Change Actions View GoTo Help m ra pe A SMe Zus Ho MASEN BPOE SEMN Sample Type FileName Sample ID Path Inst Meth Position Inj Vol Status Acquistion Queue 1 Unknown 210201201 1 C Xcalbur Dat C Xcalburimethods BC_Test 1 1 9 3 Run Manager 7 oo Ready To Download Unknown Sequence Blank Sample Name ac Working On Std Bracket Postion Raw Fie Inst Method E TnPlus Autosampler Ready to Download S TRACE GC Uta Ready to Download D 15Q Readyto Download Status Analyzer Power Maintenance Status Idle Actual Set Point vom ine 250 C 250 C Y lonsourcetemp 200 C 200 C Vacuum ok Foreline pressure 50 mTorr i ae 1 3105 Torr Turbo pump speed 100 Cl reagent gas flow 0 0 mLUmin 0 0 mL _ i in eet For Help press Fl i NUM 2 10 2012 2 40 PM 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 If you do not have some of the colu
76. ermo Xcalibur Qual Browser data15_100104170750 data15_ 1001041 70750 raw File Edit View Display Grid Actions Tools Window Help SEs a lelo gt lelelsiefe FB aada ol elle ee mime A 2 0 al _ _ _ C Xcaliburidata OF Nidata15_1001041707650 1442010 5 07 50 PM DB IRT 0 00 18 02 FERIEN NL JE TIC data15_10010 g 100 SET JE Mass Range datal Tic ms Mass Range no fi fae ail X Mass Range no fi Mass Range no fi 667 7 19 811 376 1084 Mass Range no fi _ 10 90 12 41 13 95 14 59 15 88 17 06 Relative Abundan a 3 o Mass Range no fi Mass Range no fi 8 NL 2 8864 miz 27150 27250 datatS_1001041 70750 4247 13 78 15 87 16 69 Time min data15_100104170750 1 RT 2 52 AV 1 NL 2 19E6 T 0 0 El Full ms 50 00 300 00 400 so 60 40 Relative Abundance 85 18 99 29 12507 442 32 168 33 170 99 19122 207 00 231 74 251 89 267 05 281 56 rr mu van man Ln var am a 20 260 280 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 82 ISQ User Guide Thermo Scientific Thermo Scientific Figure 72 Manually Entering the Ranges ff Thermo Xc
77. ethods iii Select the Allow for Asymmetric Acquisitions check box to add extra time to the beginning or end of an acquisition window without affecting other timing in your scan When you select this option Pre width and Post width columns are added to your method Enter the extra times in these columns e Ifyou want to link to an external method select the Link to External File check box You may link to a csv or xml method file Note In order to edit the scans within the ISQ Method Editor clear the Link to External File check box Figure 32 Linking to External Method Files ie BQ Help TRACE GC UM zz Dede iS 2 Se gE a Merwan tady f Either enter the analyte name in the Name column referring to the analyte name or in your external file enter the analyte name in the first column You may also 44 ISO User Guide Thermo Scientific 4 Creating a Method Creating a Method for the ISQ Mass Spectrometer right click this window to search for an analyte within your method This function is useful if you need to edit an analyte in a complex method g Inthe RT column enter retention times for SIM methods The retention time is the time it takes an analyte to pass from the column inlet to the detector h In the Window min column set the acquisition times Smaller acquisition windows increase sensitivity but can cause you to miss your peak if set too small Changing the window size only affects s
78. f 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 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 ISO User Guide 3 1 Confirming Your GC MS System is Working Checking the Vacuum and Temperature 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 If it is blinking orange quickly you have a large leak that prevented 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 Figure 2 Using the Lights on the ISQ Instrument Vacuum Heaters To check the temperature look at the Heaters light When the Heaters light is a solid green the ISQ instrumen
79. fectively the dilution ratio of the sample This setting is typically turned on and set to a flow of 50 mL min However more carrier gas will be used so for your analysis lower split flows may be more acceptable If you set the split ratio the software will calculate the correct split flow The reverse is true also Tip We recommend turning on the septum purge which means additional carrier gas will go through the injector 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 The septum purge will be turned off for the stop purge time After these times the split flow and septum purge will be reactivated Thermo Scientific Thermo Scientific 4 Creating a Method Creating a Method for the GC You can set the carrier mode to Constant Flow Constant Pressure Programmed Flow or Programmed Pressure The gas flow and the oven temperature work together to determine how well the analytes are separated and how long the analysis will take 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 column temperature increases to keep the flow constant Constant flow i
80. fter the data is acquired or deselect it to run the executable in parallel with data acquisition f Configure the After Sequence Set System group e 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 e Off Select this option to turn off the ISQ by turning off the heaters turbo pump and foreline pump IMPORTANT Ifyou are using hydrogen as a carrier gas manually turn off the GC after the sequence completes if you are using this setting g Inthe 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 sequence ahead of theirs j In the Processing Actions group select Quan Qual Reports Programs or Create Quan Summary Since you are developing your method you can skip this setting Note The Reports checkbox is only enabled when you select the Qual checkbox The Reports and Create Quan Summary checkboxes are only enabled when you select the Quan checkbox 18 Click OK to run the sample or sequence and store your data on the computer Thermo Scientific
81. g the Column Back from the Transfer Line Nut Column Column Measuring Tool Transfer Line Nut Septum 15 Loosen the transfer line nut from the column measuring tool 16 Remove the column transfer line nut and ferrule from the column measuring tool making sure not to move the septum from its location on the column 17 Insert the column into the transfer line Figure 10 Inserting the Column into the Transfer Line Ferrule Transfer Line Nut Column Ban A Transfer Line Septum 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 not to change the location of the septum on the column Thermo Scientific ISO User Guide 15 2 Changing the Column Connecting the Column to the Transfer Line Figure 11 Positioning the Column in the Transfer Line Transfer Line Column Septum 21 Tighten the nut 1 flat forward back to where it is secure enough in the transfer line that you cannot move it 22 Tighten the nut 1 additional quarter turn 23 Remove the cut septum 24 Close the front door of the GC 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
82. he quadrupole DC and RF voltages to create the resolution required for your analysis You can set the desired peak width at a given mass and whether you measure the width at 10 or 50 of the peak height Because there is no static DC voltage involved the start stop and step values are not used e Mass Use this pull down menu to select the ion to be used for tuning e Start Use this field to enter the starting voltage for the tune The start voltage must always be less than the stop voltage For example 35 is smaller than 0 e Stop Use this field to enter the final voltage for the tune e Step Use this field to enter the increment for the tuning range For example if you tune from 0 50 in increments of 10 V then you would set the Step field to 10 Note If the start and stop values are the same value the device will be set to that value and ignore the step size You may notice that in some tunes devices are set to a value before tuning them in another line This is done because ramping devices will not allow the tune to run at values higher than those chosen for higher masses for the same device e Max Width Use this field to enter the maximum allowable width of the ion during the tune e 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 ISO User Guide
83. hromatographic Peaks Thermo Scientific Characteristic General Cause Excessive column bleed at high oven temperatures 8 Troubleshooting Investigating Baseline Issues Remedy Reduce the column temperature Bake out the column Install a high temperature column Install oxygen filters in carrier gas line Check pneumatic and inlet systems 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 not set too low ISO User Guide 113 8 Troubleshooting Investigating Peak Issues Investigating Peak Issues Table 3 Troubleshooting Peak Issues in Your Data Sheet 1 of 3 Behavior Characteristic Cause Remedy Broadening General Column higher than Reduce the flow Make sure vacuum optimum of column compensation is turned on Column flow lower than Increase the flow optimum of column Split flow is too low for Increase the flow to 40 50 ml min split injection Performance of the column Test the column at the optimum flow has degraded rate Injector is dirty Clean or replace the liner Ion source is dirty Clean the ion source and tun
84. idate your method A chart appears with all your analytes by name and in order of their retention times Thermo Scientific ISQ User Guide 45 4 Creating a Method Creating a Method for the ISQ Mass Spectrometer Figure 34 Accessing the Show Analysis Feature p Resulting total scan time 0500 sec tidth 3077 sec ur SIM Time 0 500 sec Min dwell time 0 001 sec mass range 50 550 7 2 aie 1 sec a 5 min End time 70 00 H min Allow for asymetric peaks Show analysis zy Show Analysis Button m Use the scroll bar on the right to view all your analytes You may also click Walk Analytes to have the software automatically run through your list of analytes When an analyte is yellow it is the active analyte While the analyte walking process is active the Walk Analytes button will read Stop Walking instead Click Stop Walking to stop the process at any time Tip If your SIM windows are too congested to achieve the total scan time at the minimum dwell time the event will be highlighted in red This warning indicates that you might get fewer scans across the peak than you want To correct this reduce the desired scans across the peak reduce the acquisition windows or reduce the minimum dwell time to correct Figure 35 Walking Analytes 46 ISO User Guide Thermo Scientific Thermo Scientific 10 11 12 13 14 4 Creating a Method Creating a
85. iled information Thermo Scientific Thermo Scientific 4 Creating a Method Creating a Method for the GC Figure 41 Locating the Run Table Settings on the TRACE 1300 or TRACE 1310 GC File TRACE1300 Help olsa S x A Oven S SL Front PTV Back FID Front ECD Back Run Table A Time tem Action Add THALE 1300 i eries 5 2 TriPlus RSH Autosampler IsQ Note The user interface reflects the current configuration of your GC If you add remove or change inlets or detectors redo your instrument method according to the new GC configuration 6 To add an inlet or detector to the method editor user interface a Attach the inlet or detector to 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 Inthe Configured Devices panel click the TRACE 1300 or TRACE 1310 icon Select Configure ISO User Guide 53 4 Creating a Method Creating a Method for the GC Figure 42 Configuring the Inlets or Detectors on the TRACE 1300 or TRACE 1310 igg Inermo rounaat on Instrument Lonriguration peasy Device Types au Configuration B General IO Inlets Detectors Ausilary Configured Devices Detectors and Data Channels Sample rat Detector type Makeup gas Channel name He sae ing F
86. ime GC carrier gas line has leaks Syringe is leaking during injection Run a leak test and correct leaks Replace syringe or piston seals if necessary Split injection temperature is too low Increase the temperature of the injector Voltage is not reaching the lens Replace the lens plate and springs 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 118 ISO User Guide DCC is drifting or unstable Injection technique is inadequate Monitor the column pressure or flow Check and replace the controller if necessary Pick injection technique suitable for the injector and liner you are using Vaporization size of sample inject larger than volume of liner Reduce the injected amount and or volume Handshaking is not configured correctly Be sure the GC is inhibited by the MS and waits for contact closure by the autosampler Column temperature is unstable Check the main oven door and cooling flap Monitor the column temperature Thermo Scientific 8 Troubleshooting Reconfiguring Your Instrument Reconfiguring Your Instrument If your instrument loses communication with the computer you have reinstalled Xcalibur or you have a new computer you may need to reconfigure the ISQ instrument To reconfigure your ISQ instrument 1 Fro
87. imize leakage The hydrogen piping system must be flexible enough to endure routine thermal expansion and contraction The system should also include considerations for the most severe condition of temperature and pressure expected during service Piping and supports must be able to withstand static loading introduced by such things as ice and snow and dynamic loading from high wind and earthquake Caution should be used if burying hydrogen piping Proper controls should be used to protect against damage and corrosion and also to prevent Hydrogen from entering a building if there is any leakage e 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 things like plumbers putty used to enhance a seal as this actually is a detriment to a good seal Ideally the best installation would use stainless steel tubing with appropriate gas tight fittings Welding is usually preferred for joints in hydrogen piping systems since welding provides a better connection and reduces the potential for leaks compared to mechanical fittings Soft solder joints are not permitted for hydrogen systems due to the low melting point of soft solder and its potential for brittle failure at cryogenic temperatures Brazed
88. ing Loaded Transfer Line Nut Spring Loaded Column Transfer Line Nut 3 Ai Septum Thermo Scientific ISQ User Guide 19 2 Changing the Column Connecting the Column to the Transfer Line 16 Loosen the transfer line nut from the column measuring tool 17 Remove the column transfer line nut and ferrule from the column measuring tool making sure not to move the septum from its location on the column Note The ferrule should still be able to move on the column Use the septum to mark the correct location where the column should exit the nut 18 Insert the column into the transfer line Figure 17 Inserting the Column into the Transfer Line Spring Loaded Transfer Line Nut coun a op lll ae Transfer Line Septum 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 20 ISO User Guide Thermo Scientific Thermo Scientific 2 Changing the Column Connecting the Column to the Transfer Line Figure 18 Positioning the Column in the Transfer Line Transfer Line Column ER pe A771 Septum Spring Loaded Transfer Line Nut 22 Tighten the spring loaded transfer line nut 1 flat forward back to where it is secure enough in the transfer line that you cannot move it
89. ing Toxic Gases Contacting Us Thermo Scientific When analyzing toxic compounds be aware that during the normal operation of the GC some of the sample might be vented outside the instrument through the split and purge flow vents therefore be sure to vent the exhaust gases to a fume hood Consult local environmental and safety regulations for instructions in exhausting fumes from your system 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 service Go to www thermoscientific com wps portal ts contactus To suggest changes to documentation or to Help e Fill out a reader survey online at www surveymonkey com s PQM6P62 e Send an e mail message to the Technical Publications Editor at techpubs austin thermofisher com ISO User Guide xxi ee _ IE Confirming Your GC MS System is Working Use the information in this chapter to confirm that your GC MS system has power the carrier gas rate is correct the gas tank has enough pressure the system has reached vacuum and temperature and is leak free 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 e Checking Power to the System e Verifying the Carrier Gas Flow Rate e Chec
90. ion Operations Storage and Transportation NFPA 52 Vehicular Fuel Systems Code 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 ISO User Guide xix Preface Hazardous Substances Precautions e NFPA 497 Recommended Practice for the Classification of Flammable Liquids Gases or Vapors and of Hazardous Classified Locations for Electrical Installations in Chemical Process Areas e NFPA 13 Standard for the Installation of Sprinkler Systems e NFPA 45 Standard on Fire Protection for Laboratories Using Chemicals e NFPA 55 Standard for the Storage Use and Handling of Compressed Gases and Cryogenic Fluids in Portable and Stationary Containers Cylinders and Tanks e NFPA 68 2007 Standard on Explosion Protection by Deflagration Venting e NFPA 69 Standard on Explosion Prevention Systems e NFPA 91 Standard for Exhaust Systems for Air Conveying of Vapors e NFPA 255 Standard Method of Test of Surface Burning Characteristics of Building Materials e OSHA 29CFR1910 103 1910 103 Hydrogen Hazardous Substances Precautions WARNING Before using hazardous substances toxic harmful and so on please read the hazard indications and information reported in the applicable Material Safety Data Sheet MSDS Use person
91. ion polarity Cl gas type Cl gas flow Emission current Electron energy Electron lens positive voltage Electron lens negative voltage Y Set ion source temperature e Ionization Mode and Ion Polarity Use this pull down menu to select a mode Select EI to run a tune in Electron Ionization EI mode Select CI to run a tune in Chemical Ionization CI mode and positive ions Select CI to run a tune in CI mode and negative ions e CI Gas Type only enabled if you select CI or CI Use this pull down menu to select a gas type but make sure your selection is the reagent gas attached to your system and that the correct gas port is selected Methane is commonly used for CI Other gases will change the efficiency and energy of the ionization process Note When changing CI gas types or gas port there is a two minute delay while the reagent gas is purging During this time the Busy light will be lit and you have to wait until the light goes off before using the ISQ software e 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 Select this option to use the value in the tune file you selected in the General tab Default Select this option to use the default e
92. irmware Versions Version Info Instrument Control Software 2 0 0 37 Instrument ID 811003 PC Communication Board Firmware 210 0 77 17 Controller Interface Microcontroller 11 FPGA 33 Lens Driver Microcontroller 1 21 Microcontroller 2 20 CPLD 6 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 6 Save this information It may be useful to your Thermo Fisher Scientific Field Service Engineer if you need a service call 110 ISO User Guide Thermo Scientific 8 Troubleshooting How to Know When Your System Needs Maintenance How to Know When Your System Needs Maintenance Typically you will notice that your instrument needs maintenance when you are analyzing your data on the computer Some of the most common reasons and indications are as follows Contamination If you notice excessive background in your mass spectra it is usually an indication that your instrument is contaminated Use the mass spectrum in the table below to understand the origin of the contamination If you notice cleaning solvent peaks it is usually an indication that your ion source cartridge was installed before it was completely dried Fingerprints If you notice a series of mass peaks in your data that are 14 amu apart it is usually a
93. is This value affects how well the electrons are kept from entering the ion source when they are not supposed to If you change your electron energy from 70 V this value will also change This voltage should always be at least 5V below the voltage applied to the filament The voltage applied to the filament is the same number but the opposite sign of the electron energy If you set this value to be smaller than the electron energy for example if the EE is 70 eV and the negative voltage is set to 50 V then electrons can not be stopped from entering the ionization region If the negative voltage is set to 75 V though the electrons will be blocked from entering 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 keep the ion source clean and maintain the right amount of sensitivity Tip If you will be tuning regularly between running sample sets you can save time waiting for the temperatures to equilibrate by setting the tune temperatures to the same temperature used in your acquisition method 5 Configure the options under the Lenses tab The lens tune is the main portion of the
94. is usually used to separate coeluting peaks Thermo Scientific ISO User Guide 89 7 Optimizing Your Method Finding the Best Way to Make an Injection Finding the Best Way to Make an Injection Adjusting the way you get the sample from the needle into the column can sometimes improve the results of your data Try modifying the autosampler method injecting a different amount of liquid adjusting the injector port temperature or flow or changing the speed of your injection You can also try using a hot or cold needle injection In some cases adjusting your injection port liners may give you better results For detailed instructions see the user guide for your autosampler Improving the Way You Prepare Samples Although sample preparation adds time and expense to the overall analysis a more focused method can give you better results Try extracting your sample in a solvent that increases the solubility of the analytes of interest but does not increase the solubility of the other compounds Try switching solvents if your method will allow it You can also use or change 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 chr
95. joints are permitted but such joints should be protected against the possibility of external fire Tubing connections should be clamped to barbed or press fit type connections Hose clamps or jubilee clamps must not be used e Valves All valves must be suitable for hydrogen service and for the specific operating conditions Valves including regulators must not be used for hydrogen unless they are designed and identified for such a use 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 xvi ISO User Guide Thermo Scientific Preface Hydrogen Safety Precautions Manual shutoff valves should be provided near each point of use within immediate reach If a hydrogen cylinder or hydrogen generation system is located within immediate reach a separate point of use shutoff valve is usually not necessary Line regulators that have their source away from the point of use should have a manual shutoff valve near the point of use An emergency gas shutoff device in an accessible location outside the use area should be provided in addition to the manual point of use valve in each educational and instructional laboratory space that has a piped gas supply system If necessary the piping system should have uninterruptible pressure relief The pressure relief system sh
96. king Your Carrier Gas Tank Pressure e Checking the Vacuum and Temperature Note Many nitrile and latex gloves not certified for clean room use contain silicone mold releasing agents that will contaminate the instrument For this reason clean room gloves are strongly recommended when you work with the ISQ We recommend Cardinal Health CP100 Nitrile Cleanroom Gloves See the JSQ Spare Parts Guide for ordering information Checking Power to the System 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 If the instrument still doesn t power on check the electrical connections and wall outlet Thermo Scientific ISO User Guide 1 1 Confirming Your GC MS System is Working Verifying the Carrier Gas Flow Rate Figure 1 Checking the Power on the ISO 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 To confirm that a TRACE 1300 is powered on make sure that power light on the status panel is solid green To confirm that a TRACE 1310 is powered on see if the touchscreen main menu has appeared To power
97. lit vent filter Install an in line filter between the pneumatics and the inlet Missing Peaks Baseline or background Column is broken Replace the column 116 ISO User Guide present 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 Check the position of the column No baseline or background present Poor or missing electrical connection Check the cable connections ISQ instrument is not collecting data Make sure the tune file is correct 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 Thermo Scientific Investigating Results Issues Table 4 Troubleshooting Results Issues in Your Data Sheet 1 of 2 Behavior Low Reproducibility of Peaks Area Thermo Scientific Characteristic General Cause Detector gain is set too low 8 Troubleshooting Investigating Results Issues Remedy Retune the gain Increase the electron multiplier voltage Increase the target ion count Concentration is not compatible with the dynamic range of the detection system Verify that the sample concentration is suitable for the MS Chromatogram and spectr
98. lumn and contaminate the ISQ instrument if you set the transfer line temperature above the maximum allowed temperature of the column ISQ User Guide 37 4 Creating a Method Creating a Method for the ISO Mass Spectrometer Untitled The File ISQ Help e S x 2 Methodtype E Use acquisition methods to acquire data GCruntime C Probe run time lon source temp 200 G Cl gas type None z T Acquisition threshold 1000 Clgas flow 000 mUmin MStransferlinetemp 250 C lonizationmode EI x ies Stop after 10 0 min aff Autotune E View Tune Report 3 Set the Ion Source Temperature You can enter a value between 0 and 350 C The optimal temperature depends on the analyte Higher temperatures will keep the ion source cleaner but will lead to increased fragmentation which may reduce sensitivity For most compounds a source temperature of 275 C default is adequate Note For best results tune the instrument at the same temperature you will run the analyses in your method 4 Select the Acquisition Threshold checkbox and enter a value for the minimum peak height for the data file if needed If your peak has an intensity that is below this threshold it will not be stored 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 p
99. ly enabled 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 122 ISO User Guide Thermo Scientific Thermo Scientific 8 Troubleshooting Reconfiguring Your Instrument 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 100 Setting the Foreline Pump Oil Maintenance Interval ISQ Configuration X General Maintenance Intervals Enable Days Foreline pump oil 30 Turbo pump oil bearing Filament 1 Filament 2 lon source Multiplier ISO User Guide 123 8 Troubleshooting Reconfiguring Your Instrument 10 Select the Turbo pump oil bearing checkbox to enable the maintenance reminder Then set the number of days in which you want to be reminded to check the oil The manufacturer recommends changing the oil cartridge every 730 days and the bearing every 1 460 days Figure 101 Setting the Turbo Pump Oil Maintenance Reminder ISQ Configuration General Maintenance Intervals Enable Days 30 364 Foreline pump oil Turbo pump oil bearing Filament 1 Filament 2 lon source Multiplier al oO O oO Reset All 11 Select the Filament 1 checkbox to enable the maintenance reminder In a leak free sys
100. m 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 95 Finding Available Devices w Device Types Al Mi Available Devices Configured Devices Al AS 1310 Focus GC IsQ TRACE GC Ultra yi Ji y TRACE 2 GC Ultra TriPlus Autosampler 4 l Add gt gt lt lt Remove Configure Dore ei Help 3 Click the each instrument icon you want to configure and click Add Thermo Scientific ISO User Guide 119 8 Troubleshooting Reconfiguring Your Instrument Fig AlAS 1310 Isa m isa TRACE GC Ultra E MAT HOE U DE TRACE 2 GC Ulta TriPlus Autosampler Add gt gt 4 Click Configure 120 ISO User Guide Thermo Scientific 8 Troubleshooting Reconfiguring Your Instrument 5 In the General tab set the pressure units Figure 97 Setting the Pressure Unites ISQ Configuration n General Maintenance Intervals Pressure units Remote start Communications 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
101. mation to the tune report Figure 37 Configuring the Tune Report Options Report Options wm Instrument name Cancel Calc relative abundance using la gt I Include signature line Optional reports Diagnostics IT Device settings Tune type settings Custom report Use custom report definition File name Creating a Method for the GC Click the GC icon in the left pane to create aGC method Creating a method for the TRACE 1300 or TRACE 1310 To create a method for the TRACE 1300 or TRACE 1310 1 Click the Oven tab to set the oven temperatures There is always at least one temperature and time in 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 to a value between 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 48 ISO User Guide Thermo Scientific Thermo Scientific 2a 4 Creating a Method Creating a Method for the GC Figure 38 Setting the GC Oven Parameters on the TRACE 1300 o
102. mission current which is 50 pA Thermo Scientific ISO User Guide 95 7 Optimizing Your Method Modifying an Automatic Tune Custom Select this option if you want to use a value other than 50 pA when increasing or decreasing the sensitivity of the instrument For the emission current the default is 50 pA You should tune with the same value you are planning to use for your analysis The use of emission currents above 100 pA may lead to the generation of too many ions in the source lower filament lifetime and cause unnecessary source degradation Electron Energy Use this field to indicate the energy of the electrons that come off the filament and to extend the lifetime of your filament Default Select this option to use the default electron energy which is 70 V Tune File Select this option to use the value in the tune file you selected in the General tab Custom Select this option to set the energy of the electrons emitted by the filament For example you could change the voltage if you wanted to change the ionization efficiency and fragmentation of the sample This is typically set to 70 V because the standard EI libraries are based on 70 eV electron beams Note Reducing the electron energy to less than 70 eV is not recommended The calibration compound will not be sufficiently ionized for tuning or calibrating at low electron energies Electron Lens Positive Voltage Use this field to allow the
103. mn before the injector retaining nut to make it easier to measure the proper distance between the nut and end of the column d Use a scoring wafer to score and break the column about 1 cm 0 4 in from the end Check for an even flat cut using a magnifying glass Repeat if necessary e Insert a notched septum on the column to hold the retaining nut at this position Thread the retaining nut into the injector but do not tighten f Ensure that the end of the column is the proper distance into the injector For the TRACE 1300 1310 GC the injector depths are measured from the top of the ferrule and are splitless 5 mm split 10 mm PTV and PTVBKF 30 mm Note If you are using a GC other than the TRACE 1300 1310 GC refer to the GC user documentation for the correct insertion depth g 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 carrier gas flow to 1 0 mL min c Turn off vacuum compensation which is located on the Carrier menu of the GC d Use the column flowmeter connector to verify that there is flow through the column If you do not have a flowmeter dip
104. mns discussed here you can add them by selecting Change Column Arrangement in the main menu ISO User Guide 67 5 Running a Sample Running a Sequence 4 Click the first row in the File Name column and enter a file name for your first data file 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 Note Your file name cannot contain spaces Figure 56 Naming a File O8 em Date modified Type Automation 2 2 2012 4 55 PM File folder Recent Places Desktop Status Analyzer Power Maintenance Status Idle T Actual Set Point MS transfer line v temp 250 C 250 C v lon source temp 200 C 200 C Header Information Vacuum OK Foreline pressure 49 mTorr lon gauge pressure 1 2x105 Torr Turbo pump speed 10 CI reagent gas flow 0 0 mUmin 0 0 mL _ Tip You can double click in the File Name field and browse to a raw file on your computer 68 ISO User Guide Thermo Scientific Thermo Scientific 5 Running a Sample Running a Sequence 5 Click past the Sample ID column which typically contains the number of the sample Since you are in the process of developing your method you don
105. n gauge ae 1 3x10 Torr Turbo pump speed 10 CI reagent gas flow 0 0 mUmin 0 0m _ m r 15 Enter the name of your sequence and click the Save button Figure 63 Naming and Saving your Sequence 1 1 0 2 men m i a _ Savein methods Ot fF m ez Name Date modified Type ay WWYo2102012 sId 2 10 20121 15PM Xcalibu Recent Places WW rrao_Exer2_Feb09 sid 2 9 2012 5 05PM Xcalibu m WW 11 sic 2 9 2012118PM Xcalibu WY before sid 2 9 201211 16 AM Xcalibu Desktop WWYkk sid 12772012943 AM Xcalib u WWhtestme sid 1 24 2012315PM Xcalibu a WW rrao exercise2 L sld 1 19 20124 32PM Xcalib Libraries WY sarah_wqa sld 1 5 2012 5 02PM Xcalibu WW Customer A sld 12 14 2011 2 09 PM Xcalib u Tu WY rrao 1 5id 12 13 2011 2 36 PM Xcalib Computer WYtestsid 11 21 2011 3 47 PM Xcalib T UP L1042011weekend sid 11 4 2011 3 31PM _ Xcalib amp Wero22011 s4 aan 538 PM _Xcalib 4 m r 2 Network Dr File name My_New_Sequencel X 250 C 250 C Save astype _ Koslbur Sequences sid z neo 200 C 200 C Header Information OK 50 mTorr 10 Torr 100 z 0 0 mUmin 0 0 mL gt 74 ISO User Guide Thermo Scientific 5 Running a Sample Running a Sequence 16 Click the row you want to run and select Actions Run This Sample from the main menu You can also just click the d icon on the main
106. n indication of fingerprint or other 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 e 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 lons m z To Monitor Compound Possible Source 13 14 15 16 17 29 41 57 Methane CI gas 18 28 32 44 or 14 16 19 H O N Oz CO or N O Residual air and water air leaks outgassing from Vespel ferrules 69 100 119 131 169 181 214 PFTBA and related ions PFTBA tuning compound 219 264 376 414 426 464 502 576 614 31 Methanol Cleaning solvent 43 58 Acetone Cleaning solvent 78 Benzene Cleaning solvent 91 92 Toluene or xylene Cleaning solvent 105 106 Xylene Cleaning solvent 151 153 Trichloroethane Cleaning solvent 149 Plasticizer phthalates Use of vinyl or plastic gloves Peaks spaced 14 amu apart Hydrocarbons Fingerprints foreline pump oil or other hydrocarbons Thermo Scientific ISO User Guide 111 8 Troubleshooting Investigating Baseline Issues Investigating Baseline Issues Table 2 Troubleshooting Baseline Issues in Your Data Sheet 1 of 2 Cause Stationary phase has accumulated in column Remedy Replace the column or cut off the end of the c
107. ne Types v MS transfer line temp 250 C 250 C v lon source temp 200 C 200 C v Vacuum OK Foreline pressure 51 mTor lon gauge pressure 1 2x10 Tor 3 Configure the options under the General tab Figure 84 Configuring the General Options Description Complete El tuning Tunes and sets detector gain to 3 10 5 Starts Cancel with last saved tune v canca Categories Factory Pant Type Tune and diagnostics Diagnostics only Show advanced settings General lon Source Targets Detector Diagnostics Report Output tune filename prefix Auto Tune Starting tune file Last Saved X Mass calibration Perform mass calibration D Check mass calibration e Name Use this field to enter a name for your tune type e Description Use this field to enter details or notes about your tune type ISO User Guide 93 7 Optimizing Your Method Modifying an Automatic Tune e Type Select Tune and Diagnostics to run a lens tune with diagnostics or select Diagnostics Only if you are creating a diagnostics test e Output Tune Filename Prefix Use this field to enter a prefix to be added to the title of your tune report For example if you are always running BFB reports you could enter BFB here to distinguish it from other reports you are generating Starting Tune File Use this pull down menu to select a tune file that your tune type will be based on
108. nty Sampling depth mode Hat Semele type Non vacan Sane Say m L a Configure the Sampling group e Sample Volume Use this field to enter the sample volume to be injected into the GC Typical values are between 0 5 and 5 pL Plunger Strokes Use this pull down menu to select the number of plunger strokes to use when drawing up the sample Air bubbles in the syringe change the amount of sample injected which can cause signal variation in different runs To prevent this from occurring increase the number of plunger strokes to reduce the chance of an air pocket in your syringe Typical values are between 3 and 10 e 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 is so small it may be easier to just set this option to Yes 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 ISO User Guide 35 4 Creating a Method Creating a Method for the Autosampler 36 ISO User Guide b Configure the Pre Injection group e Pre Injection Use the Solvent and Cycles fields to set the number of solvent purges that will occur before the
109. olumn Chromatographic baseline is high Replace the column or cut off the end of the column Carrier gas pressure is too low Check for leaks in injector or flow path Replace the carrier gas cylinder if it is empty or low Increase the pressure if maximum injector pressure in method is greater than carrier line pressure set 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 Use the correct gas purity and filter Behavior Characteristic Drifting Baseline General Falling Rising Carrier gas leak in the system Column is baking out Impurities have accumulated in column Perform a leak test and tighten the connections to the carrier gas line if leak is found Wait for the column to stabilize Check impurity levels in the gas source Use correct gas purity Abnormal rise in baseline when oven temperature is high 112 ISO User Guide Impurities have accumulated in column Recondition or replace the column Thermo Scientific Table 2 Troubleshooting Baseline Issues in Your Data continued Sheet 2 of 2 Behavior Noisy C
110. olumn flowmeter connector including its fittings from the oven and set them aside c 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 instructions a Ifthere are no conditioning instructions perform the column conditioning by setting a final temperature 10 C 20 C below the column s recommended maximum temperature P 7 CAUTION INSTRUMENT DAMAGE The material released from the column column bleed during conditioning may contaminate the ion source if the a column is inserted into the transfer line during the high temperature stage of conditioning WARNING FIRE HAZARD Do not use hydrogen as the carrier gas for conditioning your column It could vent into the oven and present an explosion hazard b Run the slow temperature program that is recommended by the manufacturer A typical program would hold the column at 40 C 104 F for 15 minutes and then ramp at 10 C min 50 F min up to 10 20 C below the maximum allowed column temperature Hold the column at this temperature for two hours R CAUTION INSTRUMENT DAMAGE Never exceed the column manufacturer s maximum operating temperature 12 ISQ User Guide Thermo Scientific 2 Changing the Column Connecting the Column to the Transfer Line Connecting the Column to the
111. om toppling by wrapping them with chains The chains should also be protected against corrosion and excessive heat Separate spare hydrogen cylinders from oxidizing gases such as 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 include either gaseous or liquid hydrogen in fixed installations in some gas systems a semi permanent trailer tube trailer can be used Storage vessels for compressed hydrogen gas or liquid hydrogen should be designed constructed tested and maintained in accordance with applicable codes and standards Bulk hydrogen systems represent a level of complexity again which is beyond the scope of this document however some general guidelines are provided The bulk hydrogen storage system should not be located beneath electric power lines close to other flammable gases liquids or close to public areas It should be readily accessible to authorized personnel and delivery equipment but protected from physical damage or tampering As liquid hydrogen systems also have a cryogenic hazard additional safety considerations for the use of cryogenic liquids may be
112. omatographic peak Increasing the scan rate increases the number of times youve sampled across the peak However increasing the scan rate too much results in mass spectral noise which decreases your analytical precision To optimize your scan rate select a rate that will give you 8 12 points across a chromatographic peak Narrowing the Mass Range By narrowing your mass range you can look directly at the compounds of interest However if youre looking at a large number of compounds that have a broad range of mass fragments a wide mass range makes sense To narrow the mass range refine your scan parameters to a smaller number 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 90 ISO User Guide Thermo Scientific 7 Optimizing Your Method Adjusting the Transfer Line Temperature Adjusting the Transfer Line Temperature If your transfer line temperature is set too low the less volatile compounds may get stuck in the transfer line and never make it into the ion source On the other hand if your transfer line is too hot you could 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
113. on 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 displayed v 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 ISO User Guide 11 2 Changing the Column Replacing the Factory Installed Column Expect a K factor of approximately 0 7 0 9 fora 15 m 0 25 mm i d column 1 3 2 0 for a 30 m 0 25 mm i d column If the column does not report a K factor within this range or within 0 1 units of the previous stored value check for a leak or broken column using the leak detector The K factor is a measured resistance for the column A K factor that is too low may indicate a leak in the system while a K factor that is too high may indicate a blockage g Fix any issues found and rerun column evaluation until an appropriate K factor is achieved 17 Disconnect the column flowmeter a Disconnect the column from the column flowmeter connector b Remove the c
114. on provided 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 WEEE Compliance This product is required to comply with the European Union s Waste Electrical amp 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 See www thermoscientific com rohsweee for further information on Thermo Fisher Scientific s compliance with these Directives and the recyclers in your country WEEE Konformitat Dieses Produkt muss die EU Waste Electrical amp Electronic Equipment WEEE Richtlinie 2002 96 EC erf llen 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 entsorgt werden kann Mehr Information ber die Einhaltung dieser Anweisungen durch Thermo Fisher Scientific ber die Verwerter und weitere Hinweise die n tzlich sind um die Produkte zu identifizieren die unte
115. on the front of the instrument starts blinking rapidly indicating that the mechanical pump has powered off after a five minute period with the turbomolecular pump off such as when the instrument is shut down or due to a sustained vacuum fault lasting five minutes When the turbomolecular pump spins down below 50 speed due to the shut down process the vacuum light turns off 4 Reach around the right side to the back of the instrument and push down on the power switch to power off the ISQ instrument 5 If you are using hydrogen as a carrier gas unscrew the hydrogen safety screw on the front door WARNING FIRE HAZARD If you are using hydrogen do NOT reach over the top of the instrument to power it off Instead reach around the right side or go to the back of the instrument and flip down the power switch ISO User Guide 7 2 Changing the Column Replacing the Factory Installed Column Figure 3 Powering Off the ISO Instrument Hydrogen Safety Screws Power Switch Vent Valve Knob i Safety Screw On Front Door Panel Vacuum Interlock Shield 6 Open the front door of the instrument 7 Look behind the right side of the vacuum interlock shield and twist the vent valve knob one and a half times in a counter clockwise direction to open the vent 8 Wait five minutes for venting to complete CAUTION INSTRUMENT DAMAGE Do not proceed until the instrument is vented or d pieces of the column or ferrule might blow into
116. ontains the repeller source lenses and RF lens all 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 Contents e About Your System e Related Documentation e System Requirements e Safety and Special Notices e Hydrogen Safety Precautions e Hazardous Substances Precautions e Contacting Us 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 injected into the GC either manually or through the use of an optional autosampler and then separated for presentation to the MS The MS will then generate a mass spectrum of the GC eluent and its components which can be used for qualitative identification as well as accurate and precise quantification of the individual compounds present in the sample Thermo Scientific ISO User Guide ix Preface Related Documentation Related Documentation ISQ includes Help and these manuals as PDF files ISQ Preinstallation Requirements Guide PN 1R120555 0001 TSQ Hardware Manual PN 1R120555 0002 e ISQ User Guide PN 1R120555 0003 ISQ Spare Parts Guide PN 1R120555 0004 SQ and TSQ 8000 Direct Probe System User Guide PN 1R120505 0006 To view product manuals Go to Start gt All Programs gt
117. ould be designed to provide a discharge rate sufficient to avoid further pressure increase and should vent to a safe location outside or to a ventilation system exhaust Purchasing Hydrogen Thermo Scientific Use the following guidelines when purchasing hydrogen e Hydrogen Generator Because it minimizes the amount of hydrogen present and reduces the degree of hazard a hydrogen generator also called an electrolyzer is the safest way to purchase hydrogen in the quantity used in GC MS However to minimize the degree 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 about proper use and maintenance of the regulator To prevent the possibility of releasing hydrogen the hydrogen generator should be set to shut down if There is a loss of flow to the ventilation system A hydrogen detector alarms at 25 of the lower flammable limit of hydrogen in air The oxygen exhausted by the electrolyzer should be vented to the outside as well Hydrogen Cylinder Hydrogen can be delivered in standard laboratory gas bottles or cylinders These cylinders have a limited amount of hydrogen in them and are
118. ove into the GC column quickly Higher temperatures can lead to thermal decomposition of some analytes so you will have to optimize the injector temperature for your analysis The SSL temperature can be set up to 400 C a typical value would be 225 C Figure 39 Locating the Settings for the SSL Injector on the TRACE 1300 or TRACE 1310 lf Untitled Thermo Xcalibur Instrument Setup Dee S xl Oven S SL Front PTV Back FID Front ECD Back Run Table jog SISL mode Split v Carrier mode Constant Pressure X Backflush Inlet Carrier pressure Backflush enable M TRACE 1300 Backfl ime GC Series Temperature Pressure 100 00 kPa ishi start irre 1 50 min Split flow Backflush duration i d Split ratio Erion i ji C 50 mi m 3 Sohllons ann Specific duration 1 50 min TriPlus RSH Autosampler Surge Surge pressure 5 00 kPa Surge duration 0 00 min Carrier options b Septum purge Vacuum compensation a IS rm a Purge flow 5 0 mUmin Carrier gas saver r Constant septum purge V Gas saver flow 20 0 mUmin Stop purge time 0 00 min Gas saver time 2 00 min 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 ef
119. owed by WARNING or CAUTION which indicates the degree of risk for personal injury instrument damage or both Cautions and warnings are following by a descriptor A WARNING is intended to prevent improper actions that could cause personal Thermo Scientific ISO User Guide xi Preface Safety and Special Notices injury A CAUTION is intended to prevent improper actions that might cause personal injury or instrument damage You can find the following safety symbols on your instrument or in this guide Descriptor BIOHAZARD Indicates that a biohazard will could or might occur BURN HAZARD Alerts you to the presence of a hot surface that could or might cause burn injuries ELECTRICAL SHOCK HAZARD Indicates that an electrical shock could or might occut FIRE HAZARD Indicates a risk of fire or flammability could or might occur gt PPP 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 damage or physical injury could or might occur INSTRUMENT DAMAGE Indicates that damage to the instrument or component might occur This damage might not be
120. p press FL NUM 2 10 2012 2 25 PM Thermo Scientific ISQ User Guide 79 6 Exploring Your Data 3 In the Qual Browser window select File Open from the main menu or click the amp icon 4 Select the raw file s you ran in your sequence and click Open Figure 68 Selecting the Raw File f Thermo Xcalibur Qual Browser File View Tools Help alele S el bIXIt 18 E leise E am elel gt PP de thus Look in amp 20100205 e amp Be Blank uns My Recent My Documents My Computer File name Blank gt Files oftype RawFilesfan Header Information Replace Window Friday February 05 2010 10 Friday February 05 2010 10 ears vse C Cell C Piot Add Window Plot Default Layout X 5 The chromatogram is shown in the upper pane of the window and the spectra in the bottom pane 80 ISQ User Guide Thermo Scientific Thermo Scientific 6 Exploring Your Data Figure 69 Viewing the Chromatogram PH Thermo Xcalibur Qual Browser data15_1001041 70750 data15_1001041 70750 raw File Edit View Display Grid Actions Tools Window Help SE 6 alel lt gt lelelelese E rela miele S RT 0 00 18 02 E Eenennaam wasr 2 BB Final Test Method u data15_100104170 no file no file no file no file no file no file no file PRD Relati
121. patibility vi EMC compliance v Thermo Scientific F FCC compliance vi filament voltage setting 96 filament turning off and on 42 fingerprint indications 111 flow rate verifying 2 full scan mode about 40 G gas flow rate 2 tank pressure 3 GC carrier gas 2 creating a method 48 powering on 2 ghost peaks troubleshooting 116 instrument method selecting 70 ion source temperature setting 38 97 ISQ changing the column 5 confirming it is working 1 creating a method 33 exploring data 79 optimizing methods 89 powering on reconfiguring 119 running a sample 65 troubleshooting 107 tuning 23 ISQ Autotune utility about 24 ISQ AutoTune about 92 L leak indications 111 leaks checking for 10 ISO User Guide 131 Index M lights Heater 4 Vacuum 4 lights on ISQ power 1 maintenance settings 122 mass range narrowing 90 methods acquisition 37 creating 33 optimizing 89 purpose of 33 NCI mode using 38 0 opening a sequence 67 P PCI mode using 38 peak height minimum 38 peak issues investigating 114 peaks troubleshooting broadening 114 fronting 114 ghost 116 none 116 tailing 115 power checking 1 preparing samples 65 pressure carrier gas tank checking 3 profiled data about 40 raw file selecting 80 reconfiguring the ISQ 119 regulatory compliance v results troubleshooting low reproducibility of peaks area 117 poor
122. r TRACE 1310 File TRACE1300 Help olja amp x12 TRACE 1300 GC Series inlet E PTV mode Split v Temperature Vv Split flow Vv Split ratio Splitless time 3c wo mUmin 000 min TriPlus RSH Autosampler ef Surge Surge pressure Surge duration Septum purge Purge flow Constant septum purge Stop purge time 5 00 kPa 0 00 min 5 0 mUmin Vv 0 00 min LLAMA A AAs AMAA AA AAA Ae Fi Oven S SL Front PTV Back FID Front ECD Carrier mode Constant Pressure v r Carrier pressure Pressure E m Carrier options Vacuum compensation Carrier gas saver Gas saver flow Gas saver time 100 00 kPa D r 20 0 mUmin 2 00 min m Injection phases Press kPa Cisec Injection 7000 Transfer 21000 145 20 E Evaporation phase I Transfer temp i A Cleaning phase r Post cycle i temperature Ramped pressure ss Show Chart 4 If you have a Programmable Temperature Vaporizer PTV click the PT V 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 for more deta
123. r TRACE 1310 Untitled Xcalibur Instrument Setup File TRACE1300 Help osm S x 2 Oven S SL Front PTV Back FID Front ECD Back Run Table TRACE 1300 GC Series TriPlus RSH ae R 5 Autosampler Ramps op gt Data acquisition time Rate Temperature Hold Time Oven run time 3 00 min Specific time 10 00 min C min CC min i 5 40 0 1 00 Options 10 0 50 0 1 00 Max temperature 350 0 C En Prep run timeout 10 00 min Eauilibration time 0 50 min Ready delay 0 50 min Ready a You can select a maximum of 32 temperature ramps each with their own ramp rates final temperatures and hold times A typical program will have one or two ramps 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 method not the maximum allowed by your column The maximum temperature allowed by the GC is 450 C This will prevent you from accidentally using a temperature that will 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 recei
124. r a different instrument This tab is not used on the ISQ mass spectrometer 62 ISO User Guide Thermo Scientific Thermo Scientific 4 Creating a Method Creating a Method for the GC Figure 51 Setting the Transfer Line Parameters on the FOCUS GC EJ Untitled Thermo Xcalibur Instrument Setup File Focus Help olem S x ne 5 7 N Oven 9 SSLiniet 2 Carrier gt MS Transfer Line 3 Run Table r Transfer Line S Temperature 30 C Al AS 1310 Focus GC TITTEN oaro TOU TOOT TOTO GNSS LESSEE a eo a eS i ae aa oa a EHEN Ready ae 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 52 Locating the Run Table Parameters on the FOCUS GC 9 Untitled Thermo Xcalibur Instrument Setup DER File Focus Help olsu 61 x12 i N Dven 2 SSLinlet E2 Carier h MS Transfer Line Run Table a Setting Add E A Al AS 1310 Edit A Remove Focus GC A I Extemal Event 1 On 1 Extemal Event 2 On Initial values Daad ISQ User Guide 64 a A v x 5 zl AAAA AAAA AAA AASA AAAA ASS AA AAAA SA AAAA ASA AAAA SS OS ANAA _ RSS OSS TSS 63 4 Creating a Method Creating a Method for the GC 6 When you are finished creating methods for each component in your GC
125. r diese ROHS Anweisung fallen finden sie unter www thermoscientific com rohsweee Thermo SCIENTIFIC Conformit DEEE Ce produit doit tre conforme a la directive europ enne 2002 96 EC des D chets d Equipements Electriques et Electroniques DEEE Il est marqu par le symbole suivant Thermo Fisher Scientific s est associ avec une ou plusieurs compagnies de recyclage dans chaque tat membre de Punion europ enne et ce produit devrait tre collect ou recycl par celles ci Davantage d informations sur la conformit de Thermo Fisher Scientific 4 ces directives les recycleurs dans votre pays et les informations sur les produits Thermo Fisher Scientific qui peuvent aider la detection des substances sujettes la directive RoHS sont disponibles sur www thermoscientific com rohsweee ee i Preface This guide contains detailed information about how to use the Thermo Scientific ISQ single quadrupole GC MS system The ISQ system is designed to stay cleaner longer to maximize your instrument s uptime and improve your lab s productivity The need to break vacuum cool off your system and spend hours cleaning reassembling and restoring the system is gone 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 The ExtractaBrite source incorporates a cartridge that c
126. re 31 Acquisition Timed Scan Settings acoure med SIM dats Vien Tune Report Use the Tune File to select a tune file or files to be used for this scan If you are using EI only the Tune File pull down menu is available If you are using negative CI select a tune file from the Tune File pull down menu Choose AutoTune_NCI to use the most recent negative CI automatic tune file you created in Chapter 3 Tuning the ISQ If you are using positive CI select a tune file from the Tune File pull down menu Choose AutoTune_PCI to use the most recent positive CI automatic tune file you created in Chapter 3 Tuning the ISQ The software defaults to the most recent AutoTune_NCI or AutoTune_PCI tune file you created In the Detector Gain arca set the detector gain Select the Use Last Tuned Detector Gain option to indicate that you want to use the detector gain set in ISQ Autotune 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 or saturate the electrometer with too much signal when concentrated samples are detected To manually set the detector gain select the Use Specified Detector Gain radio button and enter the desired value in the Detector gain box Use the Emission Current box to set the emission current used during the acquisition For optimal analytical performance and stability use
127. re optimizes nearly all the parameters affecting the signal This type of tune will perform a mass calibration tune the lenses and resolution and perform a leak check The detector gain will be calibrated to generate 300 000 electrons for every ion that strikes the detector You should run an EI full tune when the daily tune or the daily tune check is not adequate when the electron multiplier is getting old tuning to high electron multiplier voltages or the first tune after you replace the electron multiplier Unless your SOP requires it this is not the best tune to use on a daily basis because of the length of time it takes to run it e CI Tune This tune is used to analyze samples with negative CI The standard NCI 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 0 mL min flow This tune does not set the detector gain Note Chemical ionization tunes are very different from the electron ionization tunes You should not use a CI tune unless your instrument has a CI ion volume and CI reagent gas installed Note If the instrument was last used in EI mode and tuned with a high repeller voltage before switching to a clean CI ion Source a tune file with a low repeller voltage should be loaded in manual tune and saved to the instrument before tuning in CI mode e CI Tune This tune is used to analyze
128. ree hydrogen safety screws on the ISQ instrument that must be in place These are attached to your instrument at the factory Figure 1 Hydrogen Safety Screws on the ISO Instrument Left lop Cover Screw Front Panel Screw 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 Thermo Scientific ISQ User Guide xv Preface Hydrogen Safety Precautions Hydrogen Connection Guidelines Use the following guidelines to safely connect hydrogen to your system Piping Hydrogen must be delivered to equipment using appropriate piping and be done in such a way as to pose essentially no hazard to end users Piping systems for the delivery of hydrogen should be designed and installed by a person qualified by specific training and experience with hydrogen piping systems Stainless steel is usually recommended because it is a safe cost effective material Piping of black iron or copper must not be used as the pipe can become brittle with age Elastomeric plastic tubing of various plastics and polymers should not be used unless the tubing is approved for use with hydrogen If elastomeric plastic tubing is used for hydrogen gas delivery the tubing should be tested for hydrogen permeability to min
129. ries BE rrao_OFNB Jan19 2 meth 1 19 2012 4 20PM Xcalib Ef rrao_OFNB Jan19 1 meth 1 19 20124 19 PM Xcalibi Status A Power Mai W BF Sherry meth 1 10 2012 2 35PM Xcalib Computer BF sarah_wga_tiny meth 1 5 2012501PM Xcalib 4 Status Idle T Th in 5 File name SE Se Fies of type Instrument method meth v ei I fine 250 C 250 C Open as read only v lon source temp 200 C 200 C Header Information v Vacuum OK Foreline pressure 49 mTorr lon gauge pressure 1 310 Torr Turbo pump speed 100 CI reagent gas flow 0 0 mUmin 0 0 mU m r For Help press FL NUM 2 1 SSS 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 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 Thermo Scientific Thermo Scientific Figure 59 Entering the Sample Vial Position File Edit Change Actions View GoTo Help 5 Running a Sample Running a Sequence io Sample Type FileName Sample ID Path Inst Meth Inj Vol Level Unknown 0210201201 1 C Xcalibur Dat C Xcalibur me
130. rometer Figure 22 Showing the Spectra During an Automatic Tune I El Default Tune builtin 7 El Full Tune built in IT Cl Tune builtin I Cl Tune builtin Full Diagnostics builtin I Daily Tune with Taraets Now running Daily Tune Check Tune Report Spectra IV Show spectra Action Getting spectrum at mass 69 00 E E SEES WERE ESSENER REICHE FR Peak intensity 1 96E 07 5 Once the tune completes your tune report will open in the JSQ 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 28 ISO User Guide Thermo Scientific Thermo Scientific 3 Tuning the ISO Tuning the ISQ Mass Spectrometer Figure 23 Viewing a Tune Report B Open Tune Results A Save Report to PDF lt j Print Report BY Report TEA of 1 gt Pi WholePage 1SQ Tune Results Tune Complated Thu Jan 5 16 26 36 2012 Tune Fila Datault_ 1_2012 01 05 16 26 96 Jequune 250 0 C 2 200 0 C mTorr 13 10 5 Tor Full Scan Spactum Not Acquired Mass Theory Abundance ReisfveAbundanse isolpelMass 65 99 63 00 18 331 514 100 00 219 03 21899 14 997 158 8181 OST 785 109 425 Air Water Check H20 1869 20 48 N2 28 9 s551 02 43269 1357 CO2 4489 210 N2 H20 28 18 272 Primad on Friday February 10 2012 ISO User Guide 29 3 Tuning the ISO Tuning the ISQ
131. ront NPD Nitrogen NPD fio TRACE 1300 GC TriPlus RSH Back FID v Nitrogen x FID 10 x Series Autosampler Options i IsQ TRACE 1300 GC Series sA l Add gt gt lt lt Remove l Configure l Done l Help 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 54 ISO User Guide Thermo Scientific 4 Creating a Method Creating a Method for the GC 7 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 fd icon Figure 43 Saving a TRACE 1300 or TRACE 1310 Method TE Untitled Thermo Xcalibur Instrument Setup File ISQ Help New Open Save Sache tthods to acquire data Summary Information 3 v Run on Change Study Name pe fE z completion Audit Trail oe GCruntime C Probe run time Print Ctrl P TEE in C Stop after 100 min Print Preview Print Setup 1 Set_update meth Exit Al AS 1310 Autotune 3 View Tune Report Creating a Method for the TRACE GC Ultra To create a method for the TRACE GC Ultra Note This process only covers the left SSL but the process i
132. s have been carried out by authorized personnel and if e the local installation complies with local law regulations e the instrument is used according to the instructions provided and if its operation is only entrusted to qualified trained personnel Thermo Fisher Scientific is not liable for any damages derived from the non compliance with the aforementioned recommendations Regulatory Compliance Thermo Fisher Scientific performs complete testing and evaluation of its products to ensure full compliance with applicable domestic and international regulations When the system is delivered to you it meets all pertinent electromagnetic compatibility EMC and safety standards 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 replacement parts and additional components options and peripherals must be ordered from Thermo Fisher Scientific or one of its authorized representatives EMC Directive 89 336 EEC EMC compliance has been evaluated by Professional Testing e Polaris Q ITQ and Ion Trap Series standards EMC EN 61326 1 2006 Safety IEC 61010 1 2001 IEC 61010 2 081 2001 e DSQ II standards EM
133. s before an ignitable concentration can accumulate You should also consider purging the hydrogen to further reduce hazards and ensure anyone who will be working with hydrogen has basic hydrogen safety training As with laboratory safety in general be sure to wear safety glasses laboratory coats gloves etc Typically there are no specific requirements for gaseous hydrogen other than eye protection when working with 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 labeled as such at the supply or discharge point and at regular intervals along its length Where hydrogen gas piping passes through a wall the piping should be labeled on both sides of the wall 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 Thermo Scientific Preface Hydrogen Safety Precautions Using Hydrogen with ISO 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 th
134. s 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 to ensure accurate flow rates 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 In an effort to reduce the amount of carrier gas used check Carrier Gas Saver 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 It is also possible for air to diffuse back into the column with low split flows when the column head pressure is low Finally if your analysis requires a higher flow to quickly sweep the analytes into the column which may be needed with high temperature injectors and thermally labile compounds you can use the surge pressure to increase the column flow for the surge duration time ISO User Guide 51 4 Creating a Method Creating a Method for the GC 52 ISO User Guide Figure 40 Locating the Carrier Gas Settings for the TRACE 1300 o
135. s the same for the right SSL For information on how to use the other injector types consult the TRACE GC Ultra documentation 1 Click the Oven tab to set the oven temperatures There is always at least one temperature and time in 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 to a value between 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 ISO User Guide 55 4 Creating a Method Creating a Method for the GC Figure 44 Setting the TRACE GC Ultra Oven Parameters E Untitied Thermo Xcalibur Instrument Setup iain m y File TRACE Help osa S x Oven Left SSL Left Camier Right PTV Right Canier Run Table sQ Tine Ta OL ra Ta L oem ma aa Ts u SE ea Te j Lo ea 00 020 040 060 080 100 120 140 160 180 200 220 240 260 oo T 1 2 80 3 00 TRACE GCUIka p Ramps 1 Post Run Conditions Oven Rate Temp Hold Time Temperature C 0
136. se 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 occurs on late eluting compounds it is likely the source or transferline temperature is too low Source temperature is too low If tailing occurs on late eluting compounds it is likely the source or transferline temperature is too low Poor column characterization See Changing the Column for information about checking for leaks and column flow ISO User Guide 115 8 Troubleshooting Investigating Peak Issues Table 3 Troubleshooting Peak Issues in Your Data continued Sheet 3 of 3 Behavior Characteristic Cause Remedy Ghost Peaks General Incomplete elution of Increase the final oven program previous sample temperature or total run time Increase the column flow rate Carrier gas is contaminated Replace the gas cylinder or filter Laboratory glassware has Ensure the glassware is clean and caused contamination contaminant free Injected sample has Decrease the injection port temperature decomposed Use the on column injection technique Injection solution has Adequately clean up your sample prior matrix present to injection Inlet or pneumatics are Remove the column and bake out the contaminated inlet Use a high quality septum Replace the sp
137. sensitivity 118 retention times 118 retention times troubleshooting 118 routine maintenance causes 111 132 ISO User Guide S safety standards v samples preparing 65 running 65 scan rate optimizing 90 scans running 39 sensitivity troubleshooting 118 sequences about 66 customizing 75 opening 67 prioritizing 77 running 66 saving 73 SIM mode about 40 solvents choosing 65 purpose of 65 survey link xxi T tailing peaks troubleshooting 115 temperature of the ion source 38 temperature of the transfer line 91 temperature of transfer line 37 temperature checking 4 transfer line temperature setting 37 transfer line about 37 troubleshooting about 107 baseline issues 112 carrier gas tank pressure 3 GC display is blank 2 peak issues 114 results issues 117 transfer line temperature 37 tune report 30 tune types adding 26 tune reports example report 30 printing 30 settings 30 tune types CI tune 26 CI tune 26 daily tune check 25 Daily Tune 25 daily tune 24 Thermo Scientific EI default tune 25 EI full tune 26 tuning 23 using Autotune 24 with ISQ Autotune 24 U user name about 77 V vacuum checking 4 voltage of filament setting 96 W WEEE compliance vii Thermo Scientific Index U ISQ User Guide 133
138. sents a hazard as it is combustible over a wide range of concentrations at ambient temperature and pressure this ranges from about 4 to 74 2 by volume Hydrogen has a flash point of 423 F 253 C and an auto ignition temperature of 1 040 F 560 C It has a very low ignition energy and the highest burning velocity of any gas If hydrogen is allowed to expand rapidly from high pressure it can self ignite Hydrogen burns with a flame that can be invisible in bright light WARNING FIRE HAZARD The use of hydrogen as a carrier gas is dangerous Hydrogen is potentially explosive and must be used with extreme care Any use of hydrogen gas must be reviewed by appropriate health and safety staff and all installations of hydrogen systems must be performed to applicable codes and standards Thermo Fisher Scientific assumes no liability for the improper use of hydrogen as a carrier gas Before you begin using hydrogen you should conduct a risk assessment based on the quantity of hydrogen to be used and the conditions of your laboratory 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 ISO User Guide xiii Preface Hydrogen Safety Precautions xiv ISO User Guide Try to reduce or eliminate the higher risks by using the proper ventilation to remove hydrogen ga
139. small increments until no leaks appear when scanning 22 ISO User Guide Thermo Scientific ee ie Tuning the ISO Tuning will improve the performance of your ISQ mass spectrometer For optimum stability you should start tuning after the lights on the front of the instrument are a solid green These lights indicate that the instrument has reached vacuum and that it is at the last set temperature 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 IMPORTANT Be sure to give the ISQ instrument enough time to stabilize Otherwise you may see mass drift mass spectral changes or changes in the fragmentation of your data Contents e Accessing ISQ Autotune e Tuning the ISQ Mass Spectrometer Thermo Scientific ISO User Guide 23 3 Tuning the ISO Accessing ISO Autotune Accessing ISO Autotune To access SQ Autotune Open the ISQ Dashboard and click Auto Tune to open the ISQ Autotune window Figure 19 Accessing ISO Autotune from the ISO Dashboard Status Analyzer Power Maintenance Status Idle v MS transfer line temp v lon source temp v Vacuum Foreline pressure 51 mTor 1 2x10 Tor 100 0 0 mL min 0 0
140. t Higher values will give more dilution The split flow will also 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 Tip We recommend turning on the septum purge which means an additional 5 mL min of carrier gas will go through the injector 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 After these times the split flow and septum purge will be reactivated C Finally if your analysis requires a higher flow to quickly sweep the analytes into the column which may be needed with high temperature injectors and thermally labile compounds you can use the surge pressure to increase the column flow for the surge duration time ISQ User Guide 61 4 Creating a Method Creating a Method for the GC 3 Click the Carrier tab which is used to set the carrier gas flows The gas flow and the oven temperature work together to determine how well the analytes are separated and how long the analysis will t
141. t is at temperature If it is blinking orange the ion source or transfer line are not at temperature If the light is not lit the heaters are not turned on Note Until the Vacuum light is a solid green high vacuum is achieved the heaters will not power on and the Heaters light will not be lit 4 ISO User Guide Thermo Scientific Changing the Column Thermo Scientific 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 You should choose a column that gives you the best possible resolution analysis speed and quantitation Note Many nitrile and latex gloves not certified for clean room use contain silicone mold releasing agents that will contaminate the instrument For this reason clean room gloves are strongly recommended when handling the column We recommend Cardinal Health CP100 Nitrile Cleanroom Gloves See the SQ Spare Parts Guide for ordering information When determining the type of column for your particular needs here are a few things to consider e Column Material Columns made out of fused silica are economical and widely used Columns made out of this material have a wide range of stationary phases and are available in many sizes that can be use
142. t 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 9 Use a scoring wafer to score 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 gt 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 flat backward so the column is able to move in the ferrule with slight resistance 13 Line up the outlet of the column with the arrows on the end of the column measuring tool 18 ISO User Guide Thermo Scientific 2 Changing the Column Connecting the Column to the Transfer Line Figure 14 Lining Up the Column in the Column Measuring Tool Column Outlet 14 Place a septum with a notch cut into it behind the transfer line nut The septum marks the place on the column where it should exit the nut Figure 15 Positioning the Septum Spring Loaded Column Transfer Line Nut Column Measuring Tol N e Fonai K p Jua ui be AS e l _ gt AOW 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 Spr
143. tem the filament should last between 30 360 days depending on usage Figure 102 Setting the Filament 1 Maintenance Reminder ISQ Configuration General Maintenance Intervals pCR 7 Enable Days Foreline pump oil 30 Turbo pump oil bearing 365 Filament 1 190 Filament 2 Oo lon source F Multiplier l 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 124 ISQ User Guide Thermo Scientific 8 Troubleshooting Reconfiguring Your Instrument system the filament should last between 30 360 days depending on usage Figure 103 Setting the Filament 2 Maintenance Reminder ISQ Configuration General Maintenance Intervals Enable Days 30 365 Foreline pump oil Turbo pump oil bearing Filament 1 Filament 2 lon source OOBWAA A Multiplier Reset All 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 ISO User Guide 125 8 Troubleshooting Reconfiguring Your Instrument between cleaning depends very strongly on your analysis You will have to determine the correct length of time between source cleanings Figure 104 Setting the lon Source Cleaning Maintenance Reminder 180 Configuration rg General Maintenance Intervals
144. the emission current at which the system was tuned However if you want to use a different emission current select the Use Specified Emission Current radio button and enter a value in the Emission Current pA box A high emission current will lead to the production of more ions but the interaction of too many ions in the source can cause a degradation in the resolution and signal The margin of error is 0 5 pA As appropriate use the options in the Scan Settings area to further adjust your method i Under Peak Width you can change the minimum baseline peak width and desired scans per peak These values are used to calculate the SIM Time The ISO User Guide 43 4 Creating a Method Creating a Method for the ISQ Mass Spectrometer minimum baseline peak width should be set roughly to the shortest chromatographic peak time in your analysis ii Under Full Scan you indicate if a Full Scan is to be run along with SIM The Mass Range Scan Time Start and End Time can be set after the Use Full Scan button is selected The Full scan time will reduce the SIM time without increasing the total scan time If you only want to use full scan for part of your method you can enter full scan start and end times Tip While the system software will calculate the minimum dwell times from your method you may change it If you have a method with many transitions setting the minimum dwell time to more than 0 001 s may improve sensitivity in complex m
145. the ions see as they leave the ionization region These three lenses act as a focusing element to maximize the ion beam intensity that is entering the ion guide This field is typically set near the same voltage as lens 1 Ion Guide DC Select this option to control the ion guide s DC offset voltage It can potentially help focus the ions into the quadrupole while ensuring that neutral noise is eliminated The voltage on this component is mass dependant and should be set at several different masses This field is typically set between 1 and 15 V depending on the mass of the ion Ion Guide RF Select this option to control the ion guide s RF voltage It can potentially help focus the ions into the quadrupole while ensuring that neutral noise is eliminated The voltage on this component is mass dependant and should be set at several different masses This field is typically set between 0 and 5 V depending on the mass of the ion Q1 Select this option to control the voltage that pulls the ions into the quadrupole The voltage applied to this component will have a very strong effect on the energy of the ion beam which will have a strong effect on the resolution and the intensity The lower the voltage the 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 t
146. thod Setup window Now the tune type can be selected during an automatic tune ISO User Guide 105 Troubleshooting Thermo Scientific This section contains information to help you diagnose problems within your data A lot of times your experience as a scientist will enable you to look at your data and detect that something is wrong either with the instrument or your sample This chapter describes the most common indications of a problem with a baseline peak or result Contents e No Ions Present in Scans e Checking the ISQ System Firmware e How to Know When Your System Needs Maintenance e Investigating Baseline Issues e Investigating Peak Issues e Investigating Results Issues e Reconfiguring Your Instrument As you review your data you may notice issues with the baseline peaks or results Use the information in this section to troubleshoot and resolve the issue If there is an issue with the hardware see the Troubleshooting section of the SQ Hardware Manual WARNING ELECTRICAL SHOCK HAZARD When troubleshooting any issue that requires removing a cover on the ISQ you should power off and vent the instrument to avoid any harm to yourself 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 If you have an air leak locate and address them Pay particular attention
147. thods BC_Test td 1 0 00 Ready To Download Sequence Sample Name Working On Position Raw File Inst Method S TiPlus Autosampler Ready to Download S TRACE GC Ultra Ready to Download 8 15Q Ready to Download Status Analyzer Power Maintenance z Status Idle F Actual Set Point MS transfer line temp 250 C 250 C v lon source temp 200 C 200 C v Vacuum OK Foreline pressure 50 mTorr lon gauge pressure 1 3105 Torr Turbo pump speed 100 a CI reagent gas flow 0 0 mLmin 0 0 mL _ T gt For Help press FL NUM 2 10 2012 2 43 PM ISO User Guide n 5 Running a Sample Running a Sequence 10 Click the first row of the Injection Volume column and enter the amount of sample you are injecting 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 Note This field is not used by the AI AS 3000 or AI AS 1300 which use an injection volume from the instrument method The TriPlus and TriPlus RSH autosamplers must be configured to read this value Figure 60 Setting the Injection Volume File Edit Change Actions View GoTo Help aM DaekS eho DADBH Pree EN Sample Type FileName Sample ID Path Inst Meth Position Inj Vol Level 1 Unknown 02102012 01 1 C Xcalibur Dat C Xcalibur methods BC_Test 1 1 i 0 0 Status Acquisition Queue Run Manager Ready To Download Sequence
148. to indicate how the sample is introduced into the GC If you select Standard the autosampler will insert the needle all the way into the injection port If you select Minimum the autosampler will barely enter the injection port Pre inj Dwell Time s Use this field to enter the time in seconds that the needle will be in the injection port before the plunger injects the sample Post inj Dwell Time s Use this field to enter the time in seconds that the needle will be in the injection port after the plunger injects the sample The two main forms of injection are a hot needle technique and a cold needle technique In a hot needle injection the needle is preheated before the sample is introduced which causes the sample to vaporize before it leaves the needle The vapor is then mixed with carrier gas and swept into the column Ina cold needle injection the needle is kept as cold as possible so that the sample can be introduced as a liquid stream that vaporizes in the injector 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 Thermo Scientific 4 Creating a Method Creating a Method for the ISQ Mass Spectrometer To use the hot needle technique select the standard injection depth and use a pre injection dwell time of at least 2 seconds To use the cold needle technique select a minimum injection depth and do not use a pre injection d
149. 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 intensities are too low make sure carrier vacuum compensation is turned on ISO User Guide 107 8 Troubleshooting No lons Present in Scans 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 expand as the source cartridge heats often pushing the ion volume and lenses away from the rear of the instrument where they are firmly held by the RF Lens spring contacts To avoid intermittent electrical contacts to the lenses you should insert the ion source cartridge wait 30 min for it to get to temperature then remove and reinsert it See the SQ Hardware Manual for instructions on cleaning and inserting the ion source cartridge No lons Present in Scans Try the following solutions if you cannot see ions in any scans 1 Remove and reinstall the ion source cartridge 2 Switch filaments 3 Confirm the starting tune file is appropriate for ionization mode or source cleanliness level 4 Confirm the correct ion volume is inserted EI or CI 5 Run diagnostic checks diagnostics only tune type 6 Clean the ion source Try the following if you do not see ions in Cl mode 1 Confirm that the CI ion volume is installed 2 Confirm that the reagent gas is connected and turned on 3 S
150. ts button and use the In Use and Start Instrument columns to define the instruments that are in use and the instrument that will define the start of the sequence Then click the OK button Note If you are making a manual injection deselect the autosampler in the Start Instrument and In Use columns Once you make the injection press the Start button on the GC Note Even if the autosampler or GC are not in use they can prevent the sequence from starting if they are not ready If the autosampler or GC is not powered on or not in the ready state remove its device driver from instrument configuration before starting a sequence that does not use the device c In the Instrument Method group you can browse to the sequence to be used when the instrument starts up or shuts down d Inthe 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 76 ISO User Guide Thermo Scientific 5 Running a Sample Running a Sequence e Configure the Run Synchronously group e Pre Acquisition Select this option to enable the executable to run before the data is acquired or deselect it to run the executable in parallel with data acquisition e Post Acquisition Select this option to enable the executable to run a
151. ttings General lon Source Targets Detector Diagnostics Report Initial detector gain 3 x105 V Tune detector V Adjust detector sensitivity Mass 69 Z Intensity 10 000 000 Initial Detector Gain Select this option to set the true gain of the electron multiplier The gain is the number of electrons generated for every ion that strikes the detector This is typically set between 1 x10 and 3x10 electrons per ion Gains larger than this will generate more electrons per ion but both the analyte ion and the noise ion signals will be larger You can also tune to lower gain values which decreases the signal strength Lower values also increase the chance that an ion will not be detected As the electron multiplier ages the voltage 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 e 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 Because the intensity of the cal gas varies depending on the atmospheric pressure and temperature of the lab this option will result in larger variation in the analytical runs as compared with using a fixed detector gain Mass Use this pull down menu to select the calibration gas mass you want to
152. tune algorithm In this section you can choose which components to tune which mass to optimize for the tune what the range of allowed values are how to move through the range how much the signal must change for a new value to be selected and what 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 ISO User Guide 97 7 Optimizing Your Method Modifying an Automatic Tune 98 ISO User Guide Figure 86 Configuring the Lenses Options My New Tune Complete El tuning Tunes and sets detector gain to 3x10 5 Starts Cancel with last saved tune v Cm Type Tune and diagnostics Diagnostics only V Show advanced settings General lon Source Targets Detector Diagnostics Report Lenses Resolution Y Tune lenses Device Mass Sat Stop Step Max Measure Threshold On Erom Width at 10 3 lon Guide vot 502 15 1 025 Continue lon Guide vot 219 10 02 lon Guide vot 69 10 02 lon Guide vot 40 10 02 lonGuideRF 502 1 3 00 lonGuideRF 219 04 19 0 2 lonGuideRF 69 02 los lom lonGuideRF 02 o7 lom MI abana en 1n In in Continue Continue Continue Continue Continue Continue Continue Continue _ netiew se r bin nn In IN N 888383833588 T 1 1 1 T8 B e Device Use this pull down menu to select the component you want to tune
153. tune the resolution at a scan rate in addition to the 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 ISO User Guide 101 7 Optimizing Your Method Modifying an Automatic Tune 102 ISO User Guide Figure 88 Configuring the Target lon Ratios Type General Target mass 50 amu 69 amu 131 amu 219 amu 414 amu 502 amu My New Tune Complete El tuning Tunes and sets detector gain to 3c10 5 Starts with last saved tune Factory Tune and diagnostics Diagnostics only lon Source Targets Detector Diagnostics 7 Tune target ion ratios Ratio 1 1 100 90 70 2 13 25to 51 5 amu 61 5to 78 5 amu 78 5to 132 5 amu 132 5to 220 5 amu 220 5to 415 5 amu 415 5 amu and above 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 Thermo Scientific 7 Optimizing Your Method Modifying an Automatic Tune Figure 89 Configuring the Detector Options m Name My New Tune Description Complete Eltuning T d sets detect in to 31075 Start ion oa per unes and seis ector gain to ans Categories Factory Type Tune and diagnostics Diagnostics only 7 Show advanced se
154. ture and when the GC reports as being ready This delay is typically set to 0 1 minutes ON INSTRUMENT DAMAGE Be sure not to overheat the GC column or it may contaminate the ISQ instrument Thermo Scientific Thermo Scientific 4 Creating a Method Creating a Method for the GC 2 Ifyou have a split splitless inlet SSL injector click the SSL tab to configure the injector port settings Figure 49 Setting the SSL Parameters on the FOCUS GC a Untitled Thermo Xcalibur Instrument Setup Split Flow B Split Ratio Splitless Time min File Focus Help osm S x 2 Al A51310 1 Oven F SSL inlet Jez Carrier dh MS Transfer Line 93 Run Table Inlet Temperature TC v 50 ml min Purge r k Sp Stop Purge Time min Surge Surge Pressure kPa Surge Duration min Mode Split x The inlet should be turned on and set to a temperature that is at least 10 C higher than the boiling point of your least volatile analyte The material injected into the port will vaporize and move into the GC column quickly Higher temperatures can lead to thermal decomposition of some analytes so you will have to optimize the injector temperature for your analysis Set the SSL temperature between 50 and 375 C a typical value would be 225 C Useful for diluting high concentrations of sample the split flow is the amount of gas that is swept through the injector to the exhaust por
155. ull 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 There will be a two minute delay when you change ports for the CI Gas Type Typical values for Methane CI for NCI are 1 0 1 5 mL min For Methane CI for PCI the gas flows are typically 1 5 2 0 mL min 6 In the Run Completion group select the action you want to occur at the end of a run 38 ISQ User Guide Thermo Scientific 4 Creating a Method Creating a Method for the ISQ Mass Spectrometer a GC Run Time Select this option if you want the ISQ system run to end when the GC run is complete This is the most common setting b Probe Run Time Select this option if you have a probe controller installed and you want the ISQ system run to end when the probe run is complete c Select Stop After Select this option to set the number of minutes you want the ISQ system to run The end of the run can be between 0 and 1 000 minutes This option allows you to stop the acquisition 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 eu
156. um are blank Make sure the tune file is correct Verify that the Busy 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 is leaking Check and replace the syringe and or septum at regular intervals Injection port is leaking Check the column connections Run a leak check Injection technique is not suitable Carefully meter the injected amount Use a clean good quality syringe Ion source is dirty Clean the ion source and retune the instrument Split flow or ratio control is inadequate Monitor the flow Replace the in line filter ISO User Guide 117 8 Troubleshooting Investigating Results Issues Table 4 Troubleshooting Results Issues in Your Data continued Sheet 2 of 2 Characteristic With increased retention time Behavior Poor Sensitivity Cause Carrier gas flow rate is too low Remedy Increase the carrier gas flow rate Locate and remove possible obstructions in the carrier gas line Check the septum for leaks Check the injector column ferrules for leaks With normal retention t
157. ure 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 Thermo Scientific ISO User Guide 13 2 Changing the Column Connecting the Column to the Transfer Line 8 Use a scoring wafer to score and break the column Use a magnifying glass to check for an even flat cut Repeat if necessary 9 Use a 5 16 in wrench to hold the column measuring tool steady Figure 6 Column Measuring Tool RE gt 10 While holding the column measuring tool steady tighten the transfer line nut with a 1 4 in wrench until the column 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 Column Outlet 13 Place a septum with a notch cut into it behind the transfer line nut The septum marks the place on the column where it should exit the nut Figure 8 Positioning the Septum Transfer Line Column Measuring beni lia Nur Tool f mn 14 Pull the column back from the transfer line nut Do not move the septum from its position on the column 14 ISQ User Guide Thermo Scientific 2 Changing the Column Connecting the Column to the Transfer Line Figure 9 Pullin
158. ve Abundance NL 3 91E7 mie MS data15_10 010417075 0 10 74 1185 12 41 1395 15 88 16 43 Coe a 8 10 12 14 16 Time min data15_100104170750 1 RT 2 52 AV 1 NL 2 1966 T 0 0 El Full ms 50 00 300 00 100 80 Relative Abundance 5724 35 18 99 29 Mono Of 442 32 158 33 170 99 191 22 207 00 231 74 251 89 267 05 281 56 6 Right click on the pinned chromatogram 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 ISO User Guide 81 6 Exploring Your Data Figure 70 Selecting the Mass Range Chromatogram Ranges Ranges Automatic processing Range Time range minutes iz T Fixed scale Type Range Scan fiter Delay min Scale Raw file TIC 0 00 C Xcalibur s MassRange 272 00 0 00 c xcaliburkc o z F a x Plot properties Raw file c xcalibur data ofn data15_100104170750 raw X 2 Detector MS v Scan fiter Peak algorithm ICS Plot type Mass Range X r x Delay min 0 00 Fi t Range s 272 00 With only the m z 272 ion shown it is apparent that the OFN is around a retention time of 3 45 minutes Figure 71 Determining the Retention Times E Th
159. ve 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 This delay is typically set to 0 5 minutes CAUTION INSTRUMENT DAMAGE Be sure not to overheat the GC column or it may contaminate the ISQ 2 The TRACE 1300 and 1310 also have the option to enable the use of cryogenics to cool the oven If this option is selected then the minimum allowed temperature in a temperature ramp will fall from 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 ISO User Guide 49 4 Creating a Method Creating a Method for the GC 50 ISO User Guide File TRACE1300 Help to use this feature set the GC oven temperature as well as the amount of time to remain at that temperature after the analytical run is complete You can also set the amount of pressure used to push the carrier gas through the column Ifyou have a split splitless inlet SSL injector click the SL Front or S SL Back tab to configure the injector port settings The inlet should be turned on and set to a temperature that is at least 10 C higher than the boiling point of your least volatile analyte The material should be injected into the port to vaporize and m
160. vidence 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 To connect the column using the spring loaded transfer line nut Note If you use a graphite Vespel ferrule with your column Thermo Fisher Scientific recommends using the spring loaded transfer line nut with it See the JSQ Spare Parts Guide for ordering information L 2 Thermo Scientific Lower the oven temperature and allow it to cool Confirm that the MS is vented and remove the current transfer line nut and ferrule Unwind about one turn of the column from the column outlet end Note Wear clean lint and powder free gloves when you handle the column and transfer line ferrule Wipe approximately 300 mm 12 in of the column with a tissue soaked in methanol Choose an appropriate ferrule for the outer diameter of your column Insert the column through the spring loaded transfer line nut and ferrule entering through the tapered end of the ferrule Wipe the column again with a tissue soaked in methanol ISO User Guide 17 2 Changing the Column Connecting the Column to the Transfer Line Figure 12 Transfer Line Nut and Graphite Vespel Ferrule Orientation Flat on the Transferline Nut Spring Loaded Transfer Ferrule Line Nut 8 Insert the column into the column measuring tool see Figure 13 which is in the ISQ Toolkit so that i
161. w and septum purge will be reactivated b Finally if your analysis requires a higher flow to quickly sweep the analytes into the column which may be needed with high temperature injectors and thermally labile compounds you can use the surge pressure to increase the column flow for the surge duration time Figure 46 Setting the Carrier Gas Parameters on the TRACE GC Ultra EE Untitled Thermo Xcalibur Instrument Setup TT pe File TRACE Help Dei S x Oven Left SSL Left Camier Right PTV Right Camier Run Table 1 00 150 WR EL 40 5 00 6 00 7 00 TRACE GC Ultra Ramps Options Pressure Flow Mode Constant Pressure v IY Vacuum Compensation a8 ae 54 2 3 34 zd 8 1 Sj 3 lt a 83 18 T Gas Saver Al AS 1310 Ready 4 If you have a Programmable Temperature Vaporizer PTV click the Left PTV or Right PTV 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 Left Carrier or Right Carrier tab The gas flow 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
162. well time The post injection dwell time can be used to bake out the needle and ensure that all semi volatile compounds are cleaned out of the system before the next injection is made Creating a Method for the ISQ Mass Spectrometer Thermo Scientific 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 or Acquisition Timed An Acquisition method is used to collect data Note The maintenance method is used to bake out or cool down the ISQ instrument during a sequence This can be useful if you know you want to perform these tasks and you want to do them in an automated way as part of your data acquisition Figure 29 Creating a General Acquisition Method for the ISO Mass Spectrometer Method type a ee ee c me TiPhbenni lon source temp 200 C Cigsstype ethane Pona z ooa ame I Acquisition threshold 1000 Cl gas flow 100 mumin Apply to all groups C Stop after 10 0 min TRACE GC Ultr Time Mass List or Dwell or Scan Tae Total Scan BEE SE em em View Tune Report 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 spectrometer The maximum allowable temperature is 400 C However you will damage the co
163. witch filaments 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 amp Water Tune This opens ISQ Manual Tune 108 ISO User Guide Thermo Scientific 8 Troubleshooting Checking the ISQ System Firmware Figure 93 The ISO Manual Tune Utility T ISQ Manual Tune load Tune File qj Save Tune File 4 Get from Instrument J Save to Instrument amp Reset Multiplier Mass amp Resolution Tune Frequency Tune Target Tune Factors E v lonization mode B x Cl gastype 9 gt Start s I amu sec lon polarity Positive Cl gasflow mL min Scan Det gain 3E 05 evion Cal gaslevel Of Changing Ci gas type may take two minutes Q1 Voltage Rex gt 748 802 o Ss o a o o o l 4 L 2 a E 3 E 3 a 2 2 x 10 20 30 40 50 Instrument status Idle Embedded system version 210 0 77 17 2 Click Firmware in the upper right hand corner of the home screen in ISQ Manual Tune 3 Anew 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 Thermo Scientific ISO User Guide 109 8 Troubleshooting Checking the ISQ System Firmware Figure 94 Determining the F

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