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1 - Institute of Chemical Process Fundamentals of the CAS, vvi

1. Burn Hazard A The oven and transfer line may be hot Allow them to cool to room temperature before touching them Do not touch the hot injector b Unwind about one turn of the Column from the end of the Column Outlet User s Guide Revision B 41 www thermo com Chapter 1 Getting Connected 1 7 Installing the Mass Spectrometer TRACE DSQ or FOCUS DSQ 1 2 3 4 i 270 mm 5 1 Column Measuring Tool 4 Column 2 Transfer Line Ferrule 5 Septum 3 Transfer Line Nut Figure 1 10 Column Measuring Tool and Transfer Line c Wipe about 300 mm 12 in of the Column 4 with a tissue soaked in methanol d Insert the Column 4 through the Septum 5 Transfer Line Nut 3 and Ferrule 2 Wipe the Column 4 again with a tissue soaked in methanol e Screw the Transfer Line Nut 3 onto the Column Measuring Tool 1 f Push the Column 4 passed the end of the Column Measuring Tool 1 then score and break the end of the Column 4 with a Scoring Wafer Using a magnifying glass check for an even flat cut Repeat if necessary g Pull the Column 4 back so that it is flush with the end of the Column Measuring Tool 1 h Tighten the Transfer Line Nut 3 i Slide the Septum 5 up to the back of the Transfer Line Nut 3 j Remove the Column 4 Transfer Line Nut 3 and Ferrule 2 from the Column Measuring Tool 1
2. Post Acceleration 10 kV Conversion Dynode Xcalibur Ver 1 4 Running Under Microsoft Windows XP Professional with Office XP User s Guide Revision B 15 www thermo com Read Me Safety Information TRACE DSO or FOCUS DSQ Safety Information Read each instruction carefully before using the procedure Follow all instructions marked on the product and in the manuals Contact Tech Support to enroll in Instrument Training to prevent accidents and to get maximum use of the instrument Look for safety alerts see the following placed in this manual and on the instrument to protect you from injury and the instrument from damage CAUTION Instrument Damage Aa This safety alert contains information to prevent instrument w a damage or alert against practices that could possibly void the manufacturer s warranty CAUTION Personal Injury A CAUTION safety alert indicates a potential hazard exists that MAY result in minor or moderate personal injury These safety alerts also warn against unsafe practices WARNING Personal Injury that COULD result in death or serious personal injury DANGER Personal Injury A DANGER safety alert indicates a potential hazard exists that WILL result in death or serious personal injury 4 A WARNING safety alert indicates a potential hazard exists 16 User s Guide Revision B TRACE DSQ or FOCUS DSO Read Me Safety Information S
3. Post Acceleration 10 kV Conversion Dynode Turbomolecular Pumps 250 L s or 200 200 L s Split Flow Xcalibur Ver 1 4 Running Under Microsoft Windows XP Professional with Office XP lon Gauge with internal vacuum protection safety 14 User s Guide Revision B Read Me TRACE DSO or FOCUS DSO About Your TRACE DSQ or FOCUS DSO System Table i 2 Focus DSQ System Specifications FOCUS DSQ FOCUS Gas Data System Mass Spectrometer Chromatograph Wall Wall Outlet Outlet 2 Phone Jack OLD Rotary Vane f Pump fiL Specifications Features Options Certification Electromagnetic Compatibility Electron lonization El with Autosamplers Liquid or EMC and FCC Class A exchangeable lon Volumes Headspace Dimensions 68 cm x w 33 cm x h 44 cm 70 L s Turbomolecular Pump Data System Software Options NIST Wiley or PtlegerMaurerWeber Library EnviroLab Forms ToxLab 2 0 Space Requirements 2 m 6 ft RFOnly Curved Quadrupole Prefilter Direct Probes System DEP or DIP Weight 45 kg 98 Ibs lon Source Temperature up to Inlet Valve 300 C and GC Interface Temperature up to 350 C Power 120 V ac or 230 V ac 50 60 Hz Mass Range 1 1050 u Unit Mass lon Gauge with internal Resolution vacuum protection safety Temperature 15 31 C 59 88 F Scan Rate up to 10 000 u s Humidity 40 80 Full Scan SIM and Simultaneous Full Scan SIM
4. User s Guide Revision B 73 www thermo com Chapter 1 Getting Connected 1 18 Running CI Qualification Tests TRACE DSQ or FOCUS DSQ g Archive the Calibration Gas Spectrum h Close the Tune window Perform the PICI Installation Qualification test a Go to Xcalibur Sequence Setup and open the preset method PClI meth b Inject 1 uL of a 10 pg uL solution of benzophenone using the preset instrument method PCI meth c Go to Qual Browser to review the results by looking at the background subtracted spectrum d Archive the chromatogram and spectrum e Select the Signal to noise Calculator accessible from a shortcut on the desktop to display a mass chromatogram for the range 182 5 183 5 The minimum Signal to Noise Ratio should be 10 1 f Archive the signal to noise ratio g Repeat the benzophenone injection Begin Negative CI Installation Qualification tests a Go to the Tune window and open the autotune dsqtune file b Select the negative ion button to change to negative ion mode You can confirm this by viewing the Tune window 74 User s Guide Revision B NOTE To add tools to the Home Page select Tools Add Tools The location is XcalibunSystem Programs SigNoise exe TRACE DSQ or FOCUS DSQ Chapter 1 Getting Connected 1 18 Running CI Qualification Tests A autotune dsqtune Trace DSQ Tune cag Fie View Instrument Experiment Tune Diagnostics Help osa aloa
5. e Demonstration Mode is used to start the instrument in demonstration mode This mode is useful if no instrument is connected but you would like to demonstrate the software But don t select this to run your first sample e Specify the Pressure Units to display in the Tune window and the Status tab e Specify the Tune Path for Xcalibur to automatically retrieve stored tune files Use the Browse button to quickly navigate to the folder storing your tune files The factory default is Xealibur System DSQ Tune p Optional Configure CI Gas tab options if you have the CI option installed Instrument Configuration General Cl gas Prinict Source Saver Service M Cl gas option Gas type Methane z Action when software is closed and CI gas is on Prompt user C Turn off Cl gas C Leave CI gas on Figure 2 3 Instrument Configuration CI Gas User s Guide Revision B 85 www thermo com Chapter 2 Getting Started 2 2 Configuring Instruments for Use TRACE DSO or FOCUS DSQ e CI Gas option check to activate CI gas options e Cl Gas Type select a gas type Select this option to activate chemical ionization gas controls Options include Ammonia CO Isobutane Methane and Other Other refers to any gas type not listed in this list When Other is selected the flow module is set to a pressure of 0 3 7 4 psig against a fixed flow restrictor If a specific gas is selected the Cl flow module output
6. www thermo com Appendix B Additional Helps B 5 Adjusting the RF Dip Calibration TRACE DSQ or FOCUS DSQ B 5 Adjusting the RF Dip Calibration Use this instruction to adjust the RF Dip Calibration readback however make sure you run this calibration after the heaters and vacuum have stabilized Make sure the heaters and vacuum status readbacks have stabilized Open the Automatic Tune screen from the Tune window a Select Tune Automatic Tune to display the Automatic Tune screen Automatic Tune a Calibration OK emea M RF Frequency Calibration Eo J Detector Gain Calibration Resolution Calibration I Positivelons Negative lons J Mass Calibration Tune C Full Automatic Tune o Maintenance Uses Current Tune File Leak Check Close Tune when Automatic Tune successfully finished Figure B 7 Xcalibur 1 4 Automatic Tune Screen b Select the RF Frequency Calibration option c Select the Maintenance option d Uncheck all other options e Click OK to adjust the RF Dip Calibration automatically and return to the Tune window 142 User s Guide Revision B Appendix B Additional Helps TRACE DSO or FOCUS DSQ B 6 Reinstalling the Data System B 6 Reinstalling the Data System Use this procedure only if installing a new computer or replacing a hard drive Follow the instructions on the Xcalibur CD a Insert the Xcalibur CD into your computer This should automa
7. 1 Sliding a Septum on the Column before the Transfer Line Nut will help you measure the proper distance between the nut and the end of the column If you want to remove it later cut the Septum from the center to the edge 42 User s Guide Revision B NOTE Wear clean lint and powder free gloves when you handle the Column and Transfer Line Ferrule TRACE DSQ or FOCUS DSO Chapter 1 Getting Connected 1 7 Installing the Mass Spectrometer l o ooo O mo000 mm mm Ol Septum 3 Transfer Line Union Transfer Line Nut 4 Transfer Line Figure 1 11 Transfer Line Front k Insert the Column into the Transfer Line 4 Be careful not to move the Septum 1 For proper operation the Column must extend approximately 1 mm passed the end of the Transfer Line l Tighten the Transfer Line Nut 2 and the Transfer Line Union 3 Condition the Transfer Line Ferrule Graphite Vespel ferrules like the Transfer Line Ferrule require conditioning to insure a leak tight seal a Raise the oven temperature to 300 C b Wait for 10 min c Lower the oven temperature to 30 C and allow it to cool before continuing CAUTION Personal Injury Burn Hazard The oven may be hot Allow it to cool to room temperature before opening it The injector will still be hot so don t touch it User s Guide Revision B 43 w
8. Io Sold L lxl Status Lenses Filament Vacuum Heaters Power Status Ready E Mode SIM lon Source a lon Polarity NEG ear el p Detect Gai T ov10 S Matin 1000 peal OPER enn k iplier fon F 3 100 1 4140 4640 5020 100 150 250 350 400 450 500 550 600 Ready Source 33 C Fore pressure 10 mTorr Ton Gauge N A Figure 1 32 Tune Window Negative CI Mode c Select Instrument CI Reagent Gas to display the CI Reagent Gas screen d Select the option CI Reagent Gas On to turn the CI reagent gas on e Select Tune Automatic Tune to display the Automatic Tune CI screen and enter the Prefilter settings displayed in Figure 1 33 Automatic Tuning Negative CI Tests f Select the Change Masses button to enter these m z values 282 9855 311 9871 413 9775 451 9743 into the Calibration Masses screen Automatic Tune CI X Fv Mate calibration Calibration Masses User masses 283 312 414 452 Cancel Enter up to 5 masses for mass calibration Leave entries blank for Restore default masses unused masses Cancel 282 9855 M Tune 311 9871 Prefilter Offset and Lens 2 mass 283 Resolution and lon Offset masses 219 414 413 9775 451 9744 Close Tune when Automatic Tune successfully finished Print tune report automatically Figure 1 33 Automatic Tuning Negative Cl Tests g Save
9. a Select Instrument Setup from the Xcalibur Home Page to display Instrument Setup window b Select File Open and navigate to Xcalibur Methods Alternatively navigate to Examples Methods and then the folder matching your GC instrument configuration Cc Choose an _El_ FullScan meth This is the full scan method file that was used to validate that your instrument met factory specifications and saved for you to acquire a test sample Review MS method parameters by selecting the MS instrument icon from the Instrument Setup window somen f smmm po Detactr gan I0 2 X 105 putter votage 110V H i f Total scantme st 09 i f sj c C senmo C rason C sm Pa f Mauga 200 200 f pi Iwe F rome C nope Tine tie Er sf F ve tor orie sagnant FT Use tet entre sagnant View Figure 3 4 Trace DSQ Right_PTV_EI_FullScan meth Parameters 1 In this example we went to Xcalibur Examples Methods Trace Right PTV Methods and selected RIGHT_PTV_EI_Fullscan meth 98 User s Guide Revision B TRACE DSQ or FOCUS DSO Chapter 3 Running Your 1 Sample 3 2 Setting Up Methods This method acquires m z 200 300 It starts 2 5 min after the GC injection to allow the solvent to elute from the GC column Review the GC method parameters by selecting the GC instrument icon from the Instrument Setup window 7 8 8 OH 293 4 HS GY T Post Run Conditions Oven Tengashas CE q F Ente Cro Tene innt MaxTero ti z0 P
10. www thermo com Chapter 1 Getting Connected 1 15 Checking the Initial Tune a Run an Automatic Tune by selecting Tune Automatic Tune to display the Automatic Tune screen Select these options Automatic Tune Calibration IV RF Frequency Calibration IV Detector Gain Calibration Resolution Calibration Positivelons V Negative lons r Tune Full Automatic Tune Optimal Sensitivity C Classical lon Ratios Maintenance Uses Current Tune File IV Leak Check 7 Close Tune when Automatic Tune successfully finished Figure 1 26 Automatic Tune Full b Select the options indicated in Figure 1 26 Automatic Tune Full Except select the Resolution Calibration option for Negative lons only if the instrument will be used for negative chemical ionization This calibration may require that the mass spectrometer gain be increased from 1 x 10 to 3 x 10 in order to pass Only increase the mass spectrometer gain if the calibration fails on the first attempt The tune report will display m z 452 when this calibration has been run It is normal for this ion to display poor resolution The resolution for negative ions can be tuned once the instrument is switched to Negative Chemical lonization mode c Press the Advanced button to access the Advanced Calibration screen Using the Advanced Calibration Screen lets you compensate for a dirty instrument by adjusting the lens values while still allowing you
11. 1984 Level 2 EN 50082 1 1992 IEC 801 4 1988 Level 2 EN 50082 1 1992 IEC 801 5 1993 Class 3 User s Guide RevisionB 3 www thermo com Important Information TRACE DSQ or FOCUS DSQ CAUTION Instrument Damage pa Please be aware that any changes you make to your system Oe may void compliance with one of more of these EMC or safety standards or warranty To ensure compliance with EMC and safety standards order replacement parts from only Thermo Electron factory trained representatives If you make any changes to your system you may void compliance with one or more of these EMC or safety standards or warranty Changes to your system include replacing a part Safety Compliance m EN 61010 1 1993 plus Amendment 2 1995 Standard Warranty This standard warranty covers all products manufactured by Thermo Electron hereinafter referred to as the Seller WARRANTY AND LIMITATIONS Seller warrants that the products to be delivered hereunder products are free from defects in material and workmanship and meet Seller s field performance specifications as published by the Seller provided however that 1 Seller s liability under this warranty is at the discretion of the Seller limited to repairing or replacing or issuing a credit for any product delivered hereunder not conforming to this warranty 2 The alternative remedies provided for herein are Buyer s sole and exclusive remedies 3 Except
12. Running Your 1 Sample 3 3 Running Methods TRACE DSO or FOCUS DSQ c Begin entering the sample information for the file name and path right click in the field to display the drop down menu choose Browse to select the file untitled Open Saep m 0M Or ae e io Me zuei osas heo TASS ple m Sample lype File Sample iD Paths teat een Prec Meth Pesition nj Val Level vere merar aor 1 www thermo com Figure 3 8 Sequence Setup Sample Information e To insert a row within a list of samples you nent How EZ NOTE Press F2 on your have already entered right click anywhere computer to edit text in the row below which the new sample is Insert above line 3 already in a cell Press F2 to be inserted and choose Edit Insert two times to see an edit Row to display the Insert Row screen No dialog box Save the sequence by selecting File Save Enter an appropriate name such as OFN sld Run the sequence by clicking on the row number you wish to run this highlights the row ee Sequence Setup Fie Edit Change Actions View GoTo Help gt HASEN Sele gt mia __ Sample Type Sample ID Path 1 J ngE a ee FRU This SANO me wy Check Disk Space Al Ai e 8 Unknown lt calibur Dats C lt caliburmethods RIGHT S51 Status Acquisition Batch Reprocess E Run Manager Ready Tol Open File Sequence Sain Sample Nar Poe Working Or St
13. Buyer s premises Before any products are returned for repair and or adjustment written authorization from Seller for the return and instructions as to how and where the product should be shipped must be obtained When any product Is returned for examination and inspection or for any other reason Buyer shall be responsible for all damage resulting from improper packing or handling and for loss in transit notwithstanding any defect or nonconformity in the product User s Guide RevisionB 5 www thermo com Important Information 12 13 14 15 If it is found that the defective product returned to Seller has been caused by the fault of the Buyer or has been returned without cause and is still serviceable Seller shall notify Buyer and shall return such product to Buyer at Buyer s expense in addition a charge for testing and examination may at Seller s discretion be made on products so returned Seller will not authorize return or repair or replacement at Buyer s lab of defective products that have been used for the analysis of toxic carcinogenic mutagenic or corrosive irritant chemicals until said products are certified to have been decontaminated by Buyer Seller shall not warranty products that have not been decontaminated and Seller shall have no obligation to repair or replace such products Any products returned to Seller for examination shall be sent prepaid via the means of transportation indicated
14. DIP or DEP User s Guide Revision B 77 www thermo com Chapter 1 Getting Connected 1 20 Providing Basic Training TRACE DSQ or FOCUS DSQ 1 20 Providing Basic Training Tools Needed A None sats Frequency Day 2 Now that the system is running to factory specifications show the customer how to use the Xcalibur software Demonstrate Instrument Configuration a Start Instrument Configuration from the desktop b Show how to add configure and delete components Demonstrate the Roadmap View in the Xcalibur Home Page a Start the Xcalibur Home Page from the desktop b Show how to use the Roadmap View Cc Show how to view the instrument status Demonstrate Instrument Setup a Start Instrument Setup from the Home Page b Show how to setup a GC method Cc Show how to setup a Mass Spectrometer method d Show how to setup an autosampler method if applicable Demonstrate the TRACE DSQ Tune window a Start Tune from Instrument Setup b Show how to open Tune files 78 User s Guide Revision B TRACE DSQ or FOCUS DSO Chapter 1 Getting Connected 1 20 Providing Basic Training Cc Show how to look at an air water spectrum d Show how to look at a calibration gas spectrum e Show how to run an Automatic Tune f Show how to run Diagnostics Demonstrate the Sequence View in the Xcalibur Home Page a Set up a new sequence b Run a sample Demonstrate the Qual Br
15. Devices Configured Devices ASBO0 LC Autosampler m a A AS9000 Autosampler p AI AS 3000 as 3 jaj ws fl U HP7673A Autosampler 452000 Autosampler A HS2000 Autosampler 4S800 Autosampler x x come ooe Done Help A2005 Autosampler A Figure 2 8 AS Instrument Configuration b Double click the AS icon in the Configured Devices panel then click the Configure button to display the autosampler Configuration screen c Enter autosampler parameters in the AS Configuration screen The autosampler is usually connected to a COM port on the computer with a Focus GC or through the GC with a TRACE GC and an AI AS 3000 or AS 2000 A 10 uL syringe is standard User s Guide Revision B 89 www thermo com Chapter 2 Getting Started 2 2 Configuring Instruments for Use 5 Set up the GC handshaking parameters by referring to the GC manuals for configuration instructions Table 2 1 GC Handshaking Parameters Remote Start In High to Low Inhibit Ready In When High End of Run Out High to Low Start of Run Out High to Low GC Ready Out When Low Prep Run Out When Low 6 Click the BXA windows desktop short cut to display the Xcalibur Xcalibur home page Figure 2 9 Xcalibur Home Page 7 Test the AS GC and MS communication to Xcalibur a Check the Ins
16. Gas LINES 0 ccc ccceccecceeseeeeececcsseseeeecesteeeeessntsaaeees 26 1 5 Installing the Data System ccccccccececceccseeseeeeeseseeeeecestseeeeseenteaeees 31 1 6 Installing the Gas Chromatograph ccccccceccccecssssseeeeesteeeesenseeeees 33 1 7 Installing the Mass Spectrometer cccccccccecccceesssseeeeessseeeeeensseeees 38 1 8 Starting Up the System oo cc ccceeecececssseeeeeeeesseeeeecstsseeeesttneaeeees 45 1 9 Confirming REAADAGCKS sieeiniccissensccsiaeesnncndsveenniocserenhacdsanennnacsieeenncnsns 47 1 10 Running Diagnostics 20 00 00 ceecccceccceececeeeceeceeeeeeeeeceeeecensneeaeeeeeeeeeeeees 49 1 11 Checking the RF Dip Calibration ccccceccccccceesseceeeseseeeeessneeeees 51 1 12 Checking the RF Gain Calibration oo ccecceccccccseeseeceesseteeeeessnsaeeees 53 1 13 Checking the Air Water SpectrUM 0 ccccccccccccteceeeeestteeeeseeseeeeenes 56 1 14 Leak CHECKING ccccccccecccccccsseececeecsseseececsseseeeeccstseeeesesssseeesentnsaeeees 59 1 15 Checking the Initial TUNG oo cc cceccecceeseeeeeeceseeeeeecstsseeesenensaeeees 60 1 16 Stabilizing the Instrument c cc cece ccceeeeeeeeecstseeeeecnssseeeesentaaeens 64 1 17 Running El Qualification Tests sossrussrisorrsrii urcoaren 66 1 18 Running Cl Qualification Tests ccc cc cceecccccesseseeeecseteeeeeesseaeeees 70 1 19 Installing Upgrade Options oo cece cccceescececesseseeeescsstseeeeesstaeeees 77 1 20 Providing Basic Training cc
17. Plugs 11 On Off Switch 5 Outlet Port 12 Handle 6 MAX maximum level mark 13 Voltage Indicator 7 Oil Level Sight glass 14 Electrical Inlet Connector Figure 1 8 Rotary Vane Pump b Check the Voltage Indicator 13 to verify the Rotary Vane Pump is configured for the same voltage as the Mass Spectrometer c Remove one of the Oil Filler Plugs 4 d Add oil to the Oil Filler Plug 4 opening half way between the MIN 9 and MAX 6 level marks e If the oil level goes above the MAX 6 level mark remove the Drain Plug 8 and drain the excess oil from the pump f Replace the Oil Filler Plug 4 g Connect the Foreline Vacuum Hose 1 h Connect the Outlet Port 5 to a suitable exhaust User s Guide Revision B 39 www thermo com Chapter 1 Getting Connected 1 7 Installing the Mass Spectrometer Rotary Vane Figure 1 9 Rotary Vane Pump Power Connection Back View i Plug the power cord into the Mech Pump plug located on the back of the Mass Spectrometer Upgrade Option Repeat this procedure for a second Rotary Vane Pump which is included with the Sample Probe upgrade option a Plug the second pump into the Accessory plug on the back of the Mass Spectrometer b Make sure the Inlet Valve Vacuum Hose exits the Mass Spectrometer just above the Foreline Vacuum Hose Connect the transfer line Ethernet and remote start cables a Confirm the Transfer Line Cable is p
18. Revision B 121 Chapter 3 Running Your 1 Sample 3 6 Analyzing the Data Peak Height and Area TRACE DSO or FOCUS DSQ www thermo com 122 3 6 Analyzing the Data Peak Height and Area In a chromatogram the area of an isolated peak is directly proportional to the amount of material present for peaks that overlap height may give a more accurate determination Determining the area and or height of a peak is therefore an important feature of quantitation Zoom in on the part of the chromatogram that is of particular interest 3 4 4 0 min a Right click on the chromatogram and choose Peak Detection Toggle Detection in All Plots from the context menu Individual peaks are shown shaded and the extent of each peak shown by blocks on the baseline 3 5 5 5 1 eT De to me mee Oe cee fan ee ae mieis spo aj minioj s ixiefE fS rispis xiiten Ei cmri az sey t maaa yii ee AA Heme Ln ater poet ne Figure 3 23 Qual Browser Peak Detection b Right click on the chromatogram and choose Display Options to display the Display Options screen User s Guide Revision B TRACE DSQ or FOCUS DSQ Chapter 3 Running Your 1 Sample 3 6 Analyzing the Data Peak Height and Area Display Options Figure 3 24 Qual Browser Labels Select the Labels tab Select both the Area and Height check boxes Click on OK to return to the chromatogram User s Guide Revision B 123 www thermo c
19. Tune Report a Select Tune View Tune Report to view the last tune report and determine when the instrument was last calibrated Select the Print button if you want to have hard copy handy User s Guide Revision B 95 www thermo com Chapter 3 Running Your 1 Sample 3 1 Calibrating and Tuning the Instrument TRACE DSQ or FOCUS DSQ b Close the Tune Report Optional Perform a Full Automatic Tune if you have just performed maintenance or your standard operating procedure requires it It s not necessary to calibrate and tune the instrument more than once every week However the number and type of samples you run determine how often you must tune your instrument a Select Tune Automatic Tune to display the Automatic Tune screen E m Calibration IV RF Frequency Calibration Canal I Detector Gain Calibration Resolution Calibration I Positivelons JV Negative lons I Mass Calibration m Tune Full Automatic Tune Optimal Sensitivity Classical lon Ratios Maintenance Uses Current Tune File I Leak Check T Close Tune when Automatic Tune successfully finished gt Print tune report automatically Figure 3 2 Automatic Tune Screen Full 96 User s Guide Revision B NOTE How often you tune your instrument is determined by the number and type of samples you run Please refer to 8 4 Automatic Tune Flow Chart pp 141 TRACE DSQ or FOCUS DSQ Chapter 3 Running
20. and technical reports by completing and returning this card by mail E mail techoubsaustin thermo com or Fax to Tech Pubs Austin 512 251 1547 Reader Survey Trace DSO amp Focus DSO User s Guide PN 120156 0003 Revision B Help us improve the quality of our manuals by circling one number for each statement Syongl agree Disagree tondly 2 4 5 The manual ts clearly written 1 2 4 5 The manual contains all the information need 1 2 4 5 The instructions are easy to follow 1 2 4 5 The instructions are complete 1 2 4 5 The technical information is easy to understand 1 2 4 5 Examples of operation are clear and useful 1 2 4 5 The figures are helpful 1 2 4 5 was able to operate the system using this manual If not 1 2 4 5 l l l l l l l l l l l l l l The manual is well organized 1 l l l l l l l l l l please comment below l l Additional Comments Attach additional sheets if necessary fold Customer Registration MY ORGANIZATION IS Check only one MY PRIMARY APPLICATION IS Check only one System Type Serial Number Date purchased O Commercial for profit lab O Analytical O Government lab O Biomedical O Hospital Clinic O Clinical Toxicology O Industrial lab O Energy O Research Institute O Environmental O University College O Food Agricultural O Veterinary O Forensic Toxicology O Other O Pharmaceu
21. at the starting time you are interested in at a position close to or on the baseline Click and drag the cursor parallel to the time axis to the end of the period required Notice that a line is drawn on the screen as you do this As the cell redisplays notice only that part of the chromatogram within the line you have just drawn Lee aiin SBS aj Melo M ef FS risia ia I mr Aa Fy j 2 ae vie Figure 3 16 Chromatogram Using Mouse Functions 114 User s Guide Revision B Chapter 3 Running Your 1 Sample TRACE DSO or FOCUS DSQ 3 4 Analyzing the Data Compounds With a Known Retention Time Using Range Functions lt Right click on the chromatogram to display the context sensitive menu and choose Ranges to display the Chromatogram Ranges screen a Enter the time range of interested in the Time Range field such 3 4 to 4 0 min x Ranges Automatic processing Range Time range minutes T Fixed scale Type Range Scan fiter Delay min Scale Raw fle tc 2 0 00 z C AXcalbur y o r 3 3 s O o o oO o o 4 2 Plot properties Raw fle c xcalbur data 1 00pgei raw z Detector ms J Scan fiter Peak aloothm ficis Plat type TIC Iz z Delay min 0 00 angels ix scale to f1000000 0 Range s Fi to fi000000 00 Cancel Help Figure 3 17 Chromatogram Ranges Screen Using Range Functions Click OK to return to Q
22. b Select the Acquisition Queue tab to view the list of the samples you have selected to run Green items mean the sequence is running 108 User s Guide Revision B TRACE DSQ or FOCUS DSO Chapter 3 Running Your 1 Sample 3 4 Analyzing the Data Compounds With a Known Retention Time NOTE See the online Help for additional instruction or see Getting Productive Qualitative Analysis Getting Productive Quantitative Analysis Getting Productive Processing Setup and Analysis of Quantitation Data Getting Productive Creating and Searching Libraries and Getting Productive Designing and Generating Custom Reports with Merlin 3 4 Analyzing the Data Compounds With a Known Retention Time When you re ready to analyze your data use the Xcalibur browsers Qual Quan and Library to view the data file results Reviewing Cursor Actions in Browsers Before you begin using the Browsers let s review some of the cursor actions and effects within the chromatogram and spectrum cells A e A click picks a point on the cell A se A line dragged parallel to any axis picks a range A A line dragged in any diagonal direction selects an area The effect of these actions depends on one of these cell states Inactive Active and unpinned each cell has a pin icon in its top right corner Only one of the cells can be active at any one time The active cell is highlighted with a gray border Active and pi
23. forming a safe and leak free seal between the tubing and the inlet body Place a Swagelok nut on the end of the tubing The threads on the nut should face the open end of the tubing as shown in Figure B 1 Swagelok Ferrule and Nut Assembly Swagelok Nut Front Ferrule Inlet Body Y Tubing Back Ferrule Figure B 1 Swagelok Ferrule and Nut Assembly Place a Swagelok back ferrule over the tubing with the smaller side NOTE Do not put tape on facing the open end of the tubing the threads of a Swagelok fitting 134 User s Guide Revision B Appendix B Additional Helps TRACE DSO or FOCUS DSQ B 1 Assembling Swagelok Fittings Place a Swagelok front ferrule over the tubing with the smaller side facing the open end of the tubing Push the ferrules down into the Swagelok nut Insert the tubing into the Swagelok inlet as far as it will go as shown in Figure B 2 Swagelok and Inlet Connection Inlet Body Tubing Ferrule and Nut Assembly Figure B 2 Swagelok and Inlet Connection Slide the nut over the inlet and tighten until fingertight Pull the tubing out from the nut very slightly 1 16 in User s Guide Revision B 135 www thermo com Appendix B Additional Helps B 1 Assembling Swagelok Fittings TRACE DSO or FOCUS DSQ While holding the inlet tight with a backup wrench tighten the nut 3 4 turn past finger tight as shown in Figure 5 3 Tightening Swagelok Fittings You can make a mark on the nut before y
24. from the Standard Warranty and service contract coverage Copyright Under the copyright laws this publication may not reproduced or transmitted in any form electronic or mechanical including photocopying recording storing in an information retrieval system or translating in whole or in part without the prior written consent of Thermo Electron FCC Compliance FCC part 15 Class A This equipment has been tested and found to comply with the limits for a Class A digital device pursuant to part 15 of the FCC rules These limits are designed to provide reasonable protection against harmful interference when the equipment is operated in a commercial environment This equipment generates uses and can radiate radio frequency energy If it is not installed and used in accordance with the instruction manual it may cause harmful interference to radio communication Operation of this equipment in a residential area is likely to cause harmful interference In this case users will be required to correct the interference at their own expense Regulatory Compliance Thermo Electron thoroughly tests and evaluates its products to ensure full regulatory compliance with applicable domestic and international regulations Your system instruments and software is CE compliant and meets Electromagnetic Compatibility EMC and safety standards EN 55011 1991 Group 1 Class A EN 50082 1 1992 IEC 801 2 1991 Level 3 EN 50082 1 1992 IEC 801 3
25. gas turning on 61 El Qualification Test 66 68 El DSO Tune 68 electron lens hole 72 Enable Cal Gas Source Saver 87 Enable DC RF Gain Adjustment 88 Enable Manual Calibration 62 87 Ethernet cable 32 Experiment Full Scan 71 F features 14 15 Ferrule 42 Fil Mult Dyn Off 63 filament 60 63 72 Trace DSQ and Focus DSQ Index Focus GC 89 Focus GC 15 Focus GC User s Manual 35 Fore Pressure 47 Full Automatic Tune 61 G gas chromatograph configuration 88 gas connections carrier 27 gas lines 30 GC 66 Column Eval column characterization column characterization 36 leak check 37 64 setup 33 GC Column 41 GC injection 99 GC instrument configuration 98 GC parameters setting up 90 GC serial cable 32 GC MS Test Kit 106 107 General tab 85 88 H heaters readback 142 heaters status readback 142 heatsink 138 139 Height 123 Hit List Cell 117 I I R Tool 70 In Use field 106 107 Injector connection 34 Inlet Valve 70 Insert Cells 112 Inst Meth 103 Installation Qualification test 73 75 installation spec El 66 Instructions doc 143 Instrument Cl Reagent Gas 70 Instrument Fil Mult Dyn On 60 Instrument System On 60 Instrument Configuration 62 143 Instrument Configuration screen 84 89 Instrument method 70 instrument method 101 Instrument Setup 70 98 Instrument Setup window 98 Instrument Status Tabs 47 lon Gauge 47 lon Offset 62 lon Source 65 ion source dirty 124 lon Source Temperature 65
26. gives time for the needle to heat up in the injector before the sample is injected This hot needle injection helps all analytes to vaporize at the same time Post injection dwell time 1 s Also called the Pull Out Delay This time allows residual solvent in and on the needle to evaporate If set too long chromatographic peak tailing can result Pre Injection Washes A 2 cycles This will wash the syringe with solvent vial A before drawing the sample for the injection This makes sure the syringe is wet and it is clean prior to drawing up the sample If required the volume should be set to the size of the syringe 10 uL Sample Rinses 1 Also called Sample Cleans This is how many times your sample is drawn into the syringe and discarded before the injection is made Using at least one means the syringe will be rinsed once with your sample Post Injection Washes B 6 cycles This will wash the syringe with solvent vial B after the injection is made This will remove any residual analytes or solvent from the syringe It is a good idea to use a different vial for pre and post injection washes This way the pre injection solvent vial A will stay cleaner 100 User s Guide Revision B TRACE DSQ or FOCUS DSQ Chapter 3 Running Your 15 Sample TRACE DSO or FOCUS DSQ 3 2 Setting Up Methods Figure 3 6 Al AS 3000 Method Parameters This method injects 1 uL of Iso octane d Fill the AS solvent vials A and B with a su
27. helpful information about the current topic Changes to the Manual Your comments and suggestions help us to correct errors and improve the documentation Please send your suggestions and comments to Editor Technical Publications Thermo Electron Corporation 2215 Grand Avenue Parkway Austin TX 78728 FAX 512 251 1547 E mail techpubsaustin thermo com View and Download Manuals http www tmaaustin com fr_manuals htm 18 User s Guide Revision B Getting Connected In This Chapter 1 1 Getting the Right Tools pp 21 1 2 Verifying Site Preparation pp 23 1 3 Unpacking the Instruments pp 24 1 4 Connecting the Gas Lines pp 26 1 5 Installing the Data System pp 31 1 6 Installing the Gas Chromatograph pp 33 1 7 Installing the Mass Spectrometer pp 38 1 8 Starting Up the System pp 45 1 9 Confirming Readbacks pp 47 1 10 Running Diagnostics pp 49 1 11 Checking the RF Dip Calibration pp 51 1 12 Checking the RF Gain Calibration pp 53 1 13 Checking the Air Water Spectrum pp 56 1 14 Leak Checking pp 59 1 15 Checking the Initial Tune pp 60 1 16 Stabilizing the Instrument pp 64 1 17 Running El Qualification Tests pp 66 1 18 Running CI Qualification Tests pp 70 1 19 Installing Upgrade Options pp 77 1 20 Providing Basic Training pp 78 Measure Control User s Guide Revision B 19 www thermo com Chapter 1 Getting Connected This chapter contains step by
28. lon Volume 41 71 lon Volume Tool 41 Isobutane 86 Iso octane 101 K Keypad button 34 K factor 36 L Labels tab 123 124 Leak check carrier gas supply line 30 reagent gas supply line 30 leak check 56 gas lines 30 leak check GC 37 64 leaks troubleshooting 56 library Qual Browser 116 Library Options 118 Library Search 116 Library Spectrum Cell 117 User s Guide Revision B 147 www thermo com Index Trace DSQ and Focus DSQ M Manual Calibration 62 Manual Calibration menu item 87 Manual Calibration screen 62 manual injections 105 Manual Noise Region 125 Mass Range 120 Mass Range Chromatogram 121 Mass Spectrum 112 Methane 28 86 methane Cl spectrum typical 71 missing items 24 Mouse functions 113 114 MS covers 44 MS method editor 95 MS Transfer Line 41 89 N NCI Installation Qualification test 76 NCI method 76 Negative Cl Installation Qualification test 74 negative ion Cl 70 Negative lons 62 negative ion button 74 noise range 125 O octafluoronaphthalene 76 106 107 108 octafluoronaphthalene OFN 68 76 octafluoronaphthalene injection 76 optional software 143 options 14 15 Oven temperature 37 41 65 P path 103 peak 116 peak detection signal to noise ratio 124 Peak Detection Settings 124 148 User s Guide Revision B Peaks eluting 116 heights areas 122 PICI Calibration Gas 72 PICI Installation Qualification test 74 PICI tests 73 PICI dsqtune 73 pin
29. procedure should only be performed by factory trained Field Engineers WARNING Personal Injury Electrical Shock Hazard A This procedure requires the safety covers to be removed and an adjustment made inside while the instrument is running This procedure should only be performed by factory trained Field Engineers CAUTION Instrument Damage Improperly adjusting the RF Null will permanently damage the RF system This procedure should only be performed by factory trained Field Engineers Run the Rod DC Test in continuous mode a Open the Tune window Diagnostic screen by selecting Tune Diagnostics Run Tests to display the Diagnostics screen Diagnostics Diagnostic Tests Host MS Interface Test not tested Automatic Testing Repeat Count 1 a Power Supply Test not tested I Stop on Error r Vacuum System Test not tested a Run Selected Tests r Heater System Test not tested r lonization Lens Test not tested r Detector Test not tested Vv Rod DE Test Passed Print Diagnostic Report RF Dip Calibration RF Gain Calibration Close Help Figure B 4 Tune Diagnostic Screen b Uncheck all options except the Rod DC Test 138 User s Guide Revision B TRACE DSQ or FOCUS DSQ TRACE DSQ or FOCUS DSQ Appendix B Additional Helps B 3 Adjusting the RF Null c Select the Rod DC Test button to display the Rod DC Test screen i E Rod DC Test Setpoint Readb
30. pump down In the Tune window select the Vacuum tab to validate the Fore Pressure Turbo Pump status and lon Gauge status a Verify that the Fore Pressure is less than 300 mTorr Status Lenses Filament Vacuum Heaters Power Pump Switch ON Turbo Pump OK Turbo Pump RPM OK Yacuum OK lon Gauge ON Fore Pressure 39 mTorr lon Gauge Pressure 4 0e 006 Torr Cl Reagent Flow OFF Figure 1 13 TRACE DSO Vacuum Status It should reach this level within 5 min after turning on the system If it doesn t there is a large leak which must be fixed immediately Consult the TRACE DSQ or FOCUS DSQ Hardware Manual PN 120156 0002 for troubleshooting a large leak b Make sure the turbomolecular Pump Switch is ON Within 5 min after turning the turbomolecular pump the readback for the Turbo Pump should be OK indicating it has reached operating speed User s Guide Revision B 47 Chapter 1 Getting Connected 1 9 Confirming Readbacks TRACE DSO or FOCUS DSQ c Wait until the lon Gauge Pressure is less than 1 x 10 Torr If the system is not equipped with an ion gauge wait at least 15 min Select the Heaters tab to confirm the lon Source Temp to 200 C www thermo com Status Lenses Filament Vacuum Heaters Power Setpoint Actual lon Source Temp 200 C 200 C Internal Ambient Temp 36 C RF Generator Temp 30 C Figure 1 14 Mass Spectrometer Heaters Readbacks Use this tab to view t
31. s Guide Revision B TRACE DSQ or FOCUS DSO Chapter 3 Running Your 1 Sample 3 7 Analyzing the Data Signal to Noise Ratio Pin the chromatogram cell by clicking in the top right corner Click on the chromatogram plot on which you wish to measure the Signal to noise It will turn grey Check Manual Noise Region in the Info bar Enter a noise range near the peak such 4 0 5 0 min Avoid choosing a region with a peak in it Choose Apply The RMS root mean square Signal to noise is calculated and displayed The noise range you chose is shown by a red line in the chromatogram Using the Signal to Noise Calculator Use the Signal to noise Calculator Alternatively you can use the Signal to noise calculator which is provided with all versions of Xcalibur a Run the Signal to noise Calculator by double clicking the icon the desktop You can also run it from Xcalibur System Programs Signoise exe if the icon is not available Choose File Open and select the 100pgEIl raw file Select Chromatogram Ranges x r Plot Properties Time Range minutes f 30399 060 Noise Range minutes asso Scan Filter a Se Plot Type MassRange Rangefs Jer20000 0 6 Smoothing I Enable Type E oxcar 7 Paints 3 7 r Automatic Noise Range Offset After Base Peak minutes jos Data Points in Range scans 100 Coret Figure 3 25 Signal
32. to noise Calculator Select Mass Range for Plot Type User s Guide Revision B 125 Chapter 3 Running Your 1 Sample 3 7 Analyzing the Data Signal to Noise Ratio e Enter 272 for Range s f Select OK to display the Signal to noise ratio www thermo com Figure 3 26 Signal to noise Calculator g Select different regions of the baseline for the noise range if necessary Choose Chromatogram Automatic Noise Range to disable the automatic range made Choose Chromatogram Specify Noise Range and click and drag the noise range you want for example 4 0 5 0 min Avoid choosing a region with a peak in it 126 User s Guide Revision B TRACE DSQ or FOCUS DSQ Chapter 3 Running Your 1 Sample TRACE DSQ or FOCUS DSQ 3 8 Automating Processing 3 8 Automating Processing When you re ready to automate your processing please read the following Xcalibur books for instructions Getting Productive Quantitative Analysis Getting Productive Processing Setup and the Analysis Of Quantitation Data Getting Productive Creating and Generating Custom Reports with Merlin User s Guide Revision B 127 www thermo com Chapter 3 Running Your 1 Sample 3 8 Automating Processing 128 User s Guide Revision B TRACE DSQ or FOCUS DSQ Appendix A Preinstallation Checklists In This Chapter A 1 Preinstallation Checklist pp 130 A 2 Installation Checklist pp 131 This appendix provides checklis
33. to use full tuning options For example if you adjust the lenses by resetting the Prefilter Offset and lon Offset values you can save these values to the Cal_tune dsqtune file And then after getting a successful tune return to the Advanced Calibration screen to press the Restore button which restores the factory default tuning factors which are optimal for a clean instrument Run a Manual Calibration if ions are further away by selecting Tune Manual Calibration to display the Manual Calibration screen However this option is only available if you selected Enable manual calibration located on the Service tab during Instrument 62 User s Guide Revision B TRACE DSQ or FOCUS DSQ TRACE DSQ or FOCUS DSQ Chapter 1 Getting Connected 1 15 Checking the Initial Tune Configuration See the June Help Topic Manual Calibration Screen for detailed information Press OK to return to the Tune window Turn the filament off by selecting Instrument Fil Mult Dyn Off User s Guide Revision B 63 www thermo com Chapter 1 Getting Connected 1 16 Stabilizing the Instrument 1 16 Stabilizing the Instrument y Tools Needed None JARS Frequency End of Day 1 Once the initial tune looks good allow the system to bake out the vacuum to stabilize and allow the gas lines to purge before performing the installation qualification tests tomorrow Replace any covers that were removed Se
34. 0 C Start Xealibur to establish communication and initialize each instrument configured for use a Wait about 60 seconds for the Mass Spectrometer to initialize b Then look for Xcalibur to display a screen There is not sufficient vacuum Cc Choose Ignore so you can continue to monitor the instrument status User s Guide Revision B 45 www thermo com Chapter 1 Getting Connected 1 8 Starting Up the System d If you see any other error messages check that all instruments are connected and turned on Also consult the Troubleshooting section of the TRACE DSO or FOCUS DSQ Hardware Manual PN 120156 0002 Start Tune Click the Instrument Tune desktop icon 2 pare the Windows desktop 46 User s Guide Revision B TRACE DSQ or FOCUS DSQ TRACE DSQ or FOCUS DSQ Chapter 1 Getting Connected 1 9 Confirming Readbacks NOTE If the fore pressure is not less than 300 mTorr within 5 min there is a large leak which must be fixed immediately 1 9 Confirming Readbacks Tools Needed None Frequency uA Day 1 Once the instruments have been initialized check the Mass Spectrometer Instrument Status Tabs to confirm the vacuum and heater readbacks are OK before running diagnostics Otherwise improper vacuum will cause damage to the filament during the lonization Lens Test Information contained in the Instrument status tabs let you watch the Mass Spectrometer heat up and
35. 30 go 30 Figure 1 23 Air Water Spectrum Large Leak 58 User s Guide Revision B TRACE DSQ or FOCUS DSO Chapter 1 Getting Connected 1 14 Leak Checking 1 14 Leak Checking y Tools Needed e Dusting spray containing tetrafluoroethane Falcon Dust Off MicroCare MicroBlast or equivalent e Leak detector GL Sciences Inc Model LD 228 or equivalent uA Frequency When the Air Water spectrum indicates m z 28 ion is larger than m z 18 Check for external leaks a Use the leak detector to check all gas fittings for leaks These include the carrier gas and Cl reagent gas lines Also check the capillary column connection to the injector Even a small leak in a gas line can allow air to enter Use the leak detector to check the septum for a leak Replace if necessary Check for vacuum leaks Scan from m z 50 to 100 by selecting Experiment Full Scan Spray dusting spray near the suspected leak while monitoring for an increase in m z 69 and 83 Common leaks occur at the transfer line capillary column connection and the vacuum manifold cover User s Guide Revision B 59 www thermo com Chapter 1 Getting Connected 1 15 Checking the Initial Tune 1 15 Checking the Initial Tune y Tools Needed None JAR Frequency Day 1 After a successful Air Water check check the initial tune of the system Make sure the instrument is on selec
36. Positive lon CI Spectrum 2 5 mL min Methane Scan 8430 TIC 1 8e 8 8 3e 7 100 50 29 0 10 OO anrr PT 15 20 25 30 35 40 45 50 55 60 65 70 75 80 85 90 Figure 1 29 Positive lon Cl Spectrum 2 5 mL min Methane User s Guide Revision B 71 www thermo com Chapter 1 Getting Connected 1 18 Running CI Qualification Tests Cc If it doesn t see if the lon Volume is inserted correctly adjust it with the I R Tool or if the filament is properly aligned with the electron lens hole shut down the instrument and use a needle to bend the filament wire to the center of the electron lens hole d Archive the Reagent Gas spectrum Check the Calibration Gas Spectrum a Select Experiment Full Scan and scan from m z 60 to 700 b Select Instrument Calibration PICI to turn the PICI Calibration Gas on Cc Verify that the Calibration Gas Spectrum is similar to Figure 1 30 Positive lon Calibration Gas Cl Spectrum 2 5 mL min Methane Scan 8589 TIC 5 4e 6 1 3e 6 100 414 219 504 69 502 131 169 614 434 464 576 652 A A A A n OE PPP PR eee PPP MADA ADANA PE PPT Said LALA 100 150 200 250 300 350 400 450 500 550 600 650 700 20 264 i 364 Figure 1 30 Positive lon Calibration Gas CI Spectrum 2 5 mL min Methane d If it doesn t see if the lon Volume is inserted correctly adjust it with the I R Tool or if the filament is properly aligned with th
37. TRACE DSQ and FOCUS DSO User s Guide PN 120156 0003 Revision B www thermo com Technical Support Thermo Electron Corporation offers Technical Support via phone Monday through Friday 9 00 AM to 6 00 PM Eastern US time Our staff of certified professionals will answer your technical questions regarding all Thermo Electron Corporation product lines Please contact us by phone fax or mail at Thermo Electron Corporation Technical Support 1400 Northpoint Parkway Suite 10 West Palm Beach FL 33407 Phone 800 685 9535 Fax 561 688 8736 E mail techsupport thermo com Thermo Electron Corporation products are produced under ISO 9001 accredited quality management systems Publication Info TRACE DSO or FOCUS DSO User s Guide PN 120156 0003 Revision B Printed October 2003 Software Xcalibur Data System Ver 1 4 Technical Content B Guckenberger S Quarmby Technical Publications K Johns Xcalibur TRACE DSO and PolarisO FOCUS DSO FOCUS GC TRACE GC are trademarks and or product names of Thermo Electron Corporation Microsoft and Windows are registered trademarks of Microsoft Corporation Technical information contained in this publication is for reference purposes only and is subject to change without notice Every effort has been made to supply complete and accurate information however Thermo Electron assumes no responsibility and will not be liable for any errors omissions damage or loss that might resul
38. Your 15t Sample 3 1 Calibrating and Tuning the Instrument Optional Perform a manual Tune if needed for other applications The tuning parameters generated during automatic tune work well for most applications but you may find the Manual Tune options suitable for other applications a Select Tune Show Manual Tune View to manually set the tune parameters in the tabs indicated in Figure 3 3 dsqtune Trace DSQ Tune aax trument Experiment Tune Diagnostics Help S BJ fF S d _ Dx 2 Flament Lenses Reschiion Seain Manual Tune Tabs 1 Electron energy eV 70 a Electron ens v 15 B ae a ae Emission curet uA 100 H 9 f _ 850 0 130 ae th fF eg 0 0e 0 Figure 3 3 Tune Show Manual Tune Tabs b Select File Exit to close the Tune window User s Guide Revision B 97 www thermo com Chapter 3 Running Your 1 Sample 3 2 Setting Up Methods TRACE DSQ or FOCUS DSQ 3 2 Setting Up Methods After your instrument is calibrated and tuned you re ready to set up the instrument methods using Instrument Setup Instrument methods are created and modified in the Instrument Setup window and saved as meth files Method files are stored in the Xcalibur Methods folder In this example you will enter the method parameters for the Mass Spectrometer GC and the AS Load an instrument method
39. ack Result Value Value A Rod DC V 50 50 Passed B Rod DC fV 50 50 Passed Average DC 50 50 Passed Rod DC A B Switch Passed Run Test Continuous Help Figure B 5 Rod DC Test d Select the Continuous button to run the test continuously Remove the Mass Spectrometer covers in this order front top and left Adjust the RF Null which is located behind the heatsink of the RF generator PCB a Insert the potentiometer adjustment tool into the slotted screw of the RF Null Adjustment b Slowly turn until the A and B Rod DC values are closest to the average Rod DC readback or 50 V User s Guide Revision B 139 www thermo com Appendix B Additional Helps B 3 Adjusting the RF Null TRACE DSQ or FOCUS DSQ Figure B 6 RF Null Position Replace the Mass Spectrometer covers in this order left top and front 140 User s Guide Revision B Appendix B Additional Helps B 4 Automatic Tune Flow Chart TRACE DSQ or FOCUS DSQ Tune Flow Chart B 4 Automatic Refer to this chart to determine when to use various tuning features gt gt L o sS S Ju wn ysu y Bues aojaq jem jyeq y YM paublje s dueIa 01NOS y pue ss qy pue snp Jo Bal yooyD ye 7 sun oewoyny N ase s jodnu penb pue 10 99 P ay SUO BANISO UOHeIqIeD UOYN OSaY a BoT oun JEU WUYUOD utu 00 Jo papd Arpeq uonesgjed ueg 10499420 Buljoejes aje
40. afety Alerts Found on Instruments Read Manual Please READ the manual before using to PREVENT an imminent or potential hazard Personal Injury Indicates imminent or a potential personal injury hazard exists Please use caution and consult the manual for details Burn Hazard Indicates a hot surface Make sure the part is room temperature before touching Explosion Hazard Indicates risk of explosion from flammable gas or liquid Use proper ventilation Shock Hazard Indicates risk of electrical shock Make sure the instrument is unplugged i Pe Material Hazard Wear impermeable laboratory gloves Eye Hazard Wear safety glasses X Lifting Hazard Use proper lifting technique User s Guide Revision B 17 www thermo com Read Me Typographical Conventions TRACE DSO or FOCUS DSQ Typographical Conventions Typographical conventions describe how information is presented to our readers For example some text is specially formatted to help you quickly find information contained in the document For example Bold is used for information required by or for the reader References are emphasized in talics Special terms are emphasized in bold and italic Notes provide important or helpful information about the current topic In NOTE Notes are addition notes can contain troubleshooting information contained in margin boxes like this They provide important or
41. al gas is not on source saver will not turn off the filament e Timeout minutes Enter the time in minutes that the instrument must wait after the last user action in tune before turning off the filament and cal gas Field Engineers Only Configure Service tab options Instrument Configuration General Cl gas PPINICI Source Saver Service I Enable manual calibration M Enable DC AF gain adjustment RodDe CA cB Figure 2 6 Instrument Configuration Service e Enable Manual Calibration Select this option to display the Manual Calibration menu item in Tune This allows the field engineer to manually calibrate the coarse mass calibration and resolution for troubleshooting We do not recommend using manual calibration values for normal operation because the calibration will not be accurate for changing scan rates and the manual resolution calibration makes resolution values in tune files meaningless User s Guide Revision B 87 www thermo com Chapter 2 Getting Started 2 2 Configuring Instruments for Use TRACE DSQ or FOCUS DSQ e Enable DC RF Gain Adjustment Select this option to display the DC RF Gain menu item in Tune e Rod DC Select A or B This should be set in the factory and never change unless the DC Driver PCB RF subsystem or quadrupole mass filter is changed If changed calibrations for both positive and negative ions must be performed The terms A and B refer to the selection of which DC pola
42. ap leak detectors may contaminate your system b Leak check the Carrier Gas Supply Line c Leak check the Reagent Gas Supply Line 30 User s Guide Revision B TRACE DSQ or FOCUS DSQ Chapter 1 Getting Connected TRACE DSO or FOCUS DSQ 1 5 Installing the Data System 1 5 Installing the Data System The data system is the computer and Xcalibur software Tools Needed A e Cable PC to Mass Spectrometer 15 ft Ethernet crossover PN 76396 0052 e Cable serial PC to GC PN 230 980 00 Frequency Day 1 Setup the Data System as demonstrated in Figure 1 4 Data System Rotary Vane Figure 1 4 Data System Power Connections Back View a Plug the power cords for the computer monitor and printer upgrade option into Wall Outlet 3 b Set up and connect the keyboard mouse monitor cable and printer cable if applicable User s Guide Revision B 31 www thermo com Chapter 1 Getting Connected 1 5 Installing the Data System TRACE DSQ or FOCUS DSO Connect the GC serial cable and the mass spectrometer s Ethernet cables a Connect the GC Serial Cable to the computer s COM1 port b Connect the Ethernet Cable which is supplied with the Mass NOTE Be sure you use Spectrometer to the computer s Ethernet port The the supplied shielded computer has two Ethernet ports The Ethernet port on a card crossover cable to connect is for the instrument whereas the Ethernet port
43. are is closed and Cl Gas is on 86 Actions Subtract Spectra 2 Ranges 116 adjusting RF dip 142 RF gain 138 Advanced 62 Advanced Calibration screen 62 Air Volume 100 air water check 56 air water spectrum typical 57 Ammonia 86 Apply button 71 Area 123 AS 2000 Communication 90 AS Configuration screen 89 AS instrument icon 100 automatic injections 105 automatic range disable 126 Automatic Tune 62 Automatic Tune Cl screen 73 Automatic Tune screen 62 96 142 Autosampler configuration 89 autosampler Configuration screen 89 autotune dsqtune 73 Aux 1 Present 89 Auxiliary and Oven Options tab 89 Available Devices 84 Available Devices panel 88 B Background Contamination 116 background spectrum 60 background spectrum typical 61 background subtracted spectrum 74 baseline noise range 124 benzophenone 74 Browse button 85 C cables remote start transfer line ethernet 40 Cal_tune dsqtune 62 calibration gas spectrum 54 61 67 72 74 79 calibration gas spectrum Cl 72 calibration gas spectrum El 61 Calibration Masses button 73 Calibration Masses screen 73 75 calibration RF dip 51 calibration RF gain 53 carrier gas quality 124 carrier gas connection 27 Carrier Gas Supply Line 30 Category 5 Ethernet cable 32 cell states 109 cells pinned 110 unpinned 109 Change Column Arrangement Comment 102 User s Guide Revision B 145 www thermo com Index Trace DSQ and Focus DSQ Change Instruments I
44. as acceptable to Seller Seller reserves the right to reject any warranty claim not made in accordance with the foregoing procedures or any warranty claim on any item that has been altered or has been shipped by non acceptable means of transportation Except as above expressly provided no warranty is made as to the merchant ability of the goods to be delivered nor is except as expressly provided above no warranty is made as to the fitness of such goods for any particular purpose Statements expressed or implied by any person including employees or factory trained representatives of Seller that are inconsistent or in conflict with this warranty shall not be binding upon Seller unless said statement is in writing and signed by an officer of Seller a Liability In no event shall Seller be liable to buyer or any other party for incidental consequential or special damages b Damages Seller s liability whether by reason of breach of warranty breach of contract tort or otherwise and irrespective of Seller s negligence for damages shall in no event exceed the payment if any received by seller for the unit or productor service furnished or to be furnished as the case may be which is the subject of claim or dispute August 1998 This warranty shall be governed by the laws of the State of California P N QSFPR 0012 Rev A 6 User s Guide Revision B TRACE DSQ or FOCUS DSQ Contact Us Receive a FREE gift application
45. as otherwise provided in this document Buyer s warranty on all products is limited to a period of ninety 90 days commencing with the date of acceptance of any such product or 120 days after shipment whichever occurs first 4 Minor deviations from specifications that do not affect performance of the products covered hereby are excluded from this warranty 5 Warranty on repaired or replaced parts is extended only to the expiration date of an issued standard warranty and only after receipt of written authorization from Seller 6 Seller makes no warranty as to expendable items including but not limited to electron multipliers filaments O rings vacuum gauge tubes fuses septa lamps sources reaction tubes and solvents 4 User s Guide Revision B TRACE DSQ or FOCUS DSO Important Information 7 10 11 Moreover after initial installation any readjustment recleaning or recalibration is expressly excluded from this warranty The warranty will be null and void and Seller will not be liable under this warranty upon the occurrence of the following events unless Seller s prior written consent to the continuation of this warranty is granted a Inthe event Buyer installs products or physically moves products from their position of installation at time of acceptance by Buyer or b Inthe event Buyer transfers ownership of products to third parties other than Buyer Seller will not be liable under this warran
46. averaged range ina mass spectrum from that retention time chromatogram cell range chromatogram Click ina spectrum The chromatogram cell displays the mass cell chromatogram of the selected mass If the Plot Type is TIC or Base Peak it is changed to Mass Range chromatogram Drag across an m z The chromatogram cell displays the mass range in a spectrum range chromatogram of the selected mass cell range If the Plot Type is TIC or Base Peak it is changed to Mass Range Important points to note are The cursor action is always applied to the pinned cell Within an active cell cursor actions rescale the plot 110 User s Guide Revision B TRACE DSQ or FOCUS DSQ Chapter 3 Running Your 1 Sample 3 4 Analyzing the Data Compounds With a Known Retention Time Using Qual Browser you can answer the question Does this sample contain compound X X being the octafluoronaphthalene OFN you used in the previous topic Then we will determine the peak height area and signal to noise ratio In this example we used the Xcalibur Data l00pgEI raw file you just acquired Step 6 Make the injection and start the GC pp 3 108 which has a retention time of approximately 3 7 min If you did not acquire this sample you can use the sample file located in Xcalibur Data Factory Test Data 100pgEl raw Let s assume that you have previously carried out a GC run with a pure sample of the compound you ar
47. built into the to the instrument If you motherboard may be used for a local area network need a longer cable you can connect a standard Category 5 Ethernet cable between the i computer and the supplied a Set the time and date cable Turn on the computer monitor and printer b Set up passwords if desired Cc Test the printer and install drivers as necessary Computers purchased from the Thermo Electron Corporation factory have been fully setup and tested with the Xcalibur 1 4 data system software However if you experience the rare situation where you need to reinstall software on a new computer or new hard drive follow these instructions B 6 Reinstalling the Data System pp 143 1 Tune reports will not display if a printer driver is not installed 32 User s Guide Revision B Chapter 1 Getting Connected TRACE DSO or FOCUS DSO 1 6 Installing the Gas Chromatograph 1 6 Installing the Gas Chromatograph Tools Needed fo e Capillary column 5MS 15 m 0 25 mm i d 0 25 um y PN 76317 3015 e Gloves clean lint and powder free e Injector ferrule for 0 25 mm column PN 290 134 88 e Leak detector GL Sciences Inc model LD 228 or equivalent e Magnifying glass e Methanol or other suitable solvent e Scoring wafer or sapphire scribe to cut capillary column e Tissue lint free e Wrench Open ended 6 mm Frequency JAKA Day 1 Check the GC configuration against the
48. calibur when to make the injection Change Instruments In Use x Al AS 3000 TRACE DSQ TRACE GC 2000 Figure 3 11 Sequence Setup Change Instruments In Use Screen automatic injections Configure the Change Instruments In Use screen for automatic injections a Make Yes display for each instrument AS GC MS listed in the In Use fields Fig 3 11 However if Yes is not listed then click on the blank field to toggle Yes on b Make Yes display in the Start Instrument field for the AS This makes the autosampler start as soon as all devices are ready Cc Select OK to return to the Run Sequence screen Prepare the injection a Open and transfer the 100 pg octafluoronaphthalene sample that is in the GC MS Test Kit PN 120150 TEST into an autosampler vial vials are supplied with the autosampler b Load the sample vial into position 1 of the autosampler 106 User s Guide Revision B TRACE DSQ or FOCUS DSQ Chapter 3 Running Your 1 Sample 3 3 Running Methods Start the Run by selecting OK from the Run Sequence screen Fig 3 10 If You re Doing Manual Injections Manual injections are necessary for those not having an autosampler or not wishing to use it to run this method Change Instruments In Use x TRACE DSQ TRACE GC 2000 Figure 3 12 Sequence Setup Change Instruments In Use Screen manual injections Configure the Change Instruments In Use screen for manual injecti
49. ccccccceceeeeeceeceeeeeeeeeeeceeceteeseeeteeeeeeeeees 78 User s Guide Revision B 9 www thermo com Contents TRACE DSQ or FOCUS DSQ Chapter 2 Chapter 3 Appendix A Appendix B 10 User s Guide Revision B Getting Started 81 2 1 Using Desktop ICONS 0 0 ceceeeeeeee eee ee eee eeee eee eaeeaeeeeeeeeeeeeeeeeeeea 83 2 2 Configuring Instruments for USE ou ccceeececcsteeeeeeesseeeesecseeeeeeees 84 Running Your 15 Sample 93 3 1 Calibrating and Tuning the Instrument cee ceeeeecceeseeeeeeetteeeeees 95 3 4 Setting Up Methods iscccicctscaacatssrhscctantenancsatantiacudmalasancvestabaarseenebants 98 3 3 Running Methods ccccceceeececceceeeeceecceeeeeeeeeeeeeeceeenseeeeeeeeseeees 102 3 4 Analyzing the Data Compounds With a Known Retention Time 109 3 5 Analyzing the Data Compounds With a Known lon Pattern 119 3 6 Analyzing the Data Peak Height and Area ccceeeeeeeeeeeeeeeeees 122 3 7 Analyzing the Data Signal to Noise Ratio cccccccceeeeseeeeeeestaees 124 3 8 Automating Processing ccccccccccceceteceeeeceeeeeeeteeecetesteeeeeeeeeeenens 127 Preinstallation Checklists 129 A 1 Preinstallation Checklist xiciccissscsecssesecisasocsenssiesadsverascasteetassnmensseeias 130 A 2 Installation Checklist oo cccccccccteccececstneeeeeccsseeeecessaeeesesssateeeeseaaees 131 Additional Helps 133 B 1 Assembling Swagelok Fittings ccccccceccsseeceeec
50. ctor temperature to 220 C User s Guide Revision B 37 www thermo com Chapter 1 Getting Connected 1 7 Installing the Mass Spectrometer 1 7 Installing the Mass Spectrometer f Tools Needed f e Cable GC to Mass Spectrometer remote start PN 76396 0050 e Column Measuring Tool PN 119640 0550 e Gloves clean lint and powder free e Leak detector hand held electronic GL Sciences Inc model LD 228 or equivalent e Magnifying glass e Methanol or other suitable solvent e Potentiometer adjustment tool e Scoring wafer or sapphire scribe to cut capillary column e Tissue lint free e Transfer line ferrule 0 4 mm i d PN A0101 18100 e Wrench Open ended 5 16 in e Wrench 2 Open ended 7 16 in Jak Frequency Day 1 Install the Rotary Vane Pump a Set the Rotary Vane Pump on the floor behind the system The pump should not be placed on the workbench as it produces excessive vibration that may affect the performance of the system 38 User s Guide Revision B TRACE DSQ or FOCUS DSQ TRACE DSQ or FOCUS DSO Chapter 1 Getting Connected 1 7 Installing the Mass Spectrometer 1 14 2 13 3 12 4 11 5 7 10 8 9 1 Foreline Vacuum Hose 8 Drain Plug 2 Inlet Port 9 MIN minimum level mark 3 Gas Ballast Control 10 Mode Selector 4 Oil Filler
51. e electron lens hole shut down the instrument and use a needle to bend the filament wire to the center of the electron lens hole 72 User s Guide Revision B TRACE DSQ or FOCUS DSQ Chapter 1 Getting Connected TRACE DSQ or FOCUS DSO 1 18 Running CI Qualification Tests Select File Open Tune and select the autotune dsqtune file Change the e Electron energy to 120 eV e Emission current to 50 pA e Lens 2 to approximately 2 V closer to 0 V Begin PICI tests a Select Tune Automatic Tune to display the Automatic Tune Cl screen b Make the selections illustrated in Figure 1 31 Cl Automatic Tune PICI Tests Automatic Tune Cl K MV Mass calibration Calibration Masses a User masses 219 414 502 aai Cancel Canca Enter up to 5 masses for mass calibration Leave entries blank for Restore default masses unused masses Cancel 218 986 M Tune 413 978 Prefilter Offset and Lens 2 mass 219 Resolution and lon Offset masses 219 414 501 971 V Close Tune when Automatic Tune successfully finished J Print tune report automatically Figure 1 31 Cl Automatic Tune PICI Tests c Select the Calibration Masses button to display the Calibration Masses screen d Enter these masses 218 986 413 978 and 501 971 for the mass calibration e Click OK to return to the Tune window f Save the PICI auto tune file as PICl dsqtune for the Installation Qualification test
52. e exe e 25 1 70 L s pump e 50 1 250 L s pump e 50 1 200 200 L s pump Archive the signal to noise result Repeat the octafluoronaphthalene injection If the instrument does not pass after several injections check for leaks especially at the transfer line union 68 User s Guide Revision B Chapter 1 Getting Connected TRACE DSO or FOCUS DSQ 1 17 Running El Qualification Tests Troubleshooting Tips Comparing the factory test RAW files to your files Look for any discrepancies in your methods or instrument readbacks by selecting View Report Status log Tune Method and Instrument Method in Qual Browser User s Guide Revision B 69 www thermo com Chapter 1 Getting Connected 1 18 Running CI Qualification Tests TRACE DSQ or FOCUS DSQ 1 18 Running CI Qualification Tests Tools Needed e Cl ion volume PN 119650 0230 e R tool and guide bar e Syringe 10 uL 70 mm needle PN 365 001 03 e Test mix octafluoronaphthalene and benzophenone PN 120150 TEST Frequency JA Day 2 If Applicable If the Mass Spectrometer has the Cl chemical ionization upgrade option you must run Cl Qualification Tests Load the appropriate Cl method a Select Instrument Setup from the Xcalibur home page b Select File Open to load the appropriate factory instrument method c Navigate to Xcalibur Examples Methods Method files are organized by several GC configurations so you can c
53. e interested in compound X and consequently you know the retention time Open Qual Browser and select the raw file that contains the data for the sample you want to work on a Select Qual Browser from the Home page b Choose File Open and navigate to Xealibur Data and open the sample file 100pgEl raw or a raw file containing the data you re interested in T aigixi Pe Ci ven Copley Gat ame b Window ee aleixi SBS aj Belo ixe fF rya E Kc sll ciel t eeann osa DIN ee es Nase 88 sg sa aw te I a en a ee bk ne ee Tee 0 20 Peeraty 3 900007 Scan Pm inana Ha Figure 3 13 100pgEl raw Don t be surprised if the Qual Browser window looks different than Figure 3 13 The default layout can be changed and saved User s Guide Revision B 111 www thermo com Chapter 3 Running Your 1 Sample 3 4 Analyzing the Data Compounds With a Known Retention Time TRACE DSQ or FOCUS DSQ Display a Chromatogram and a Mass Spectrum in the same window If you want to identify the compound that is eluting at approximately 3 69 min look at the mass spectrum recorded at that time in the chromatogram aH a Click the Insert con Ell toolbar button to display a new cell containing the same information as the existing cell Ss nor PS aj anl sie lio fs FS rise as xinea j ner Sie sc 9 w 3 As T on PED Figure 3 14 Displaying Two Chromatograms 112 User s Gu
54. e mass spectrum cell is pinned b Choose Actions Subtract Spectra 2 Ranges You can choose between subtracting the background from either one side of the peak you are interested in or from both sides To get the best results you will usually want to subtract from both sides so choose two Ranges Cc Move the cursor into the chromatogram cell and position it slightly to one side of the peak you are interested in d Click and drag the cursor away from the peak making sure to stop before reaching the next discernible peak on the chromatogram Notice a line drawn on the screen as you do this e Repeat to mark the opposite side of the peak In general after background subtraction most of the larger mass peaks in the mass spectrum will be unchanged these are true peaks due to the sample compound Common contamination peaks are at m z 207 and 281 The removal of such contamination peaks will help you to obtain a more accurate result from a library search Use the spectrum to perform a Library Search When you have a clean mass spectrum you can use it to search the NIST library to determine the nature of the compound a Right click in the mass spectrum cell and choose Library Search from the context menu 116 User s Guide Revision B TRACE DSQ or FOCUS DSQ Chapter 3 Running Your 1 Sample 3 4 Analyzing the Data Compounds With a Known Retention Time E a a Sis aj sleir lo icf FS cima xtian
55. e or corrosive You must vent the gas to a fume hood or other suitable exhaust The Cl reagent gas supply line must be leak tight Prepare the Reagent Gas Supply Line a Run a Supply Line from the Reagent Gas Regulator to the Cl Reagent Gas Input located on the Mass Spectrometer Do not connect it yet Include a Shock Loop to isolate vibration and allow enough tubing to move the Mass Spectrometer at least 40 cm 16 in Purge the Supply Line a Route the Supply Line to a vent hood or other suitable exhaust Turn on the Reagent Gas supply and set the Regulator to 30 psi 200 kPa Purge the line for about 15 seconds to remove air and debris Set the Reagent Gas Regulator to 5 10 psi 35 70 kPa Lower supply pressures produce more stable Cl reagent gas flows Turn off the Reagent Gas supply Attach the Supply Line to the CI Reagent Gas Input on the Mass Spectrometer Turn on the Reagent Gas supply CAUTION Instrument Damage Do not exceed 35 psi 240 kPa or damage to the Cl Reagent Gas Flow Module results User s Guide RevisionB 29 www thermo com Chapter 1 Getting Connected 1 4 Connecting the Gas Lines Leak check all the gas lines a Use an electronic hand held leak detector sensitivity helium 0 01 mL min to check all gas fittings for leaks CAUTION Instrument Damage fe Do not use liquid soap leak detectors such as Snoop to Oe check for leaks Liquid so
56. evision B 13 www thermo com Read Me About Your TRACE DSQ or FOCUS DSO System TRACE DSQ or FOCUS DSQ Table i 1 TRACE DSO System Specifications TRACE DSQ Mass Spectrometer TRACE Gas Chromatograph Data System Specifications Rotary Vane Pump m Certification Electromagnetic Compatibility EMC and FCC Class A Phone Jack Features Electron lonization El with Exchangeable lon Volumes Options Autosamplers Liquid or Headspace Dimensions 68 cm x w 33 cm x h 44 cm 70 L s Turbomolecular Pump Chemical lonization Cl Space Requirements 2 m 6 ft RFOnly Curved Quadrupole Prefilter Data System Software Options NIST Wiley or PflegerMaurerWeber Library EnviroLab Forms ToxLab 2 0 Weight 45 kg 98 Ibs lon Source Temperature up to 300 C and GC Interface Temperature up to 350 C Direct Probes System DIP or DEP Power 120 V ac or 230 V ac 50 60 Hz Mass Range 1 1050 u Unit Mass Resolution Inlet valve Temperature 15 31 C 59 88 F Scan Rate up to 10 000 U s PPINICI Pulsed Positive lon Negative lon Cl Humidity 40 80 Full Scan SIM and Simultaneous Full Scan SIM Programmable Temperature Vaporizer or Cold On Column Injector
57. h for El Set the lon Source Temperature to 200 C Set the GC Oven Temperature to 40 C Turn off the Cl Reagent Gas Wait at least 30 min for the system to stabilize Check Air Water Spectrum a Scan from m z 10 to 90 by selecting Experiment Full Scan b Turn instrument on by selecting Instrument Fil Mult Dyn On c Compare the Air Water Spectrum with those in Figure 1 21 through Figure 1 23 to determine whether or not you have a 66 User s Guide Revision B TRACE DSQ or FOCUS DSQ Chapter 1 Getting Connected 1 17 Running El Qualification Tests NOTE When archiving data include the Mass Spectrometer serial number and sales order number leak Usually if m z 28 is larger than m z 18 there is a leak go to procedure 1 14 Leak Checking pp 59 d Archive the Air Water Spectrum Check Background Spectrum a Scan from m z 10 to 650 by selecting Experiment Full Scan b Verify that the Background Spectrum is similar to Figure 1 24 Background Spectrum m z 10 650 c Archive the Background Spectrum Check the Calibration Gas Spectrum a Scan from m z 50 to 650 by selecting Experiment Full Scan b Turn the El Calibration Gas On c Verify that all peaks are present m z 69 131 264 414 and 502 as in Figure 1 25 Calibration Gas Spectrum m z 50 650 Run a Full Automatic Tune a Runa full automatic tune by selecting Tune Automatic Tune to display the Automatic Tune Scree
58. he temperature To set the temperature go to Tune Instrument Set Temperatures to display the Temperature Settings screen Then Set the lon to 200 and select OK to return to the Tune window 48 User s Guide Revision B Chapter 1 Getting Connected TRACE DSO or FOCUS DSQ 1 10 Running Diagnostics 1 10 Running Diagnostics Tools Needed None sas Frequency Day 1 After confirming that the heaters and vacuum readbacks are OK run Xcalibur diagnostics to test other internal components for functionality CAUTION Instrument Damage aa Make sure the vacuum readbacks are OK before running 4 rN diagnostics Otherwise improper vacuum will cause damage to the filament during the lonization Lens Test Open the Tune window Diagnostic screen Select Tune Diagnostics Run Tests to display the Diagnostics screen Tests Calibration Diagnostic Tests u ARF Automatic Testing Repeat Count 1 M Power Supply Test not tested a I Stop on Error Vv Vacuum System Test not tested o Bun Selected Tests Vv Heater System Test not tested SSS M lonization Lens Test not tested M Detector Test not tested RF Dip Calbrati Print Diagnostic Report ip Calibration RF Gain Calibration Close Help Figure 1 15 Tune Window Diagnostics Screen User s Guide Revision B 49 www thermo com Chapter 1 Getting Connected 1 10 Running Diagnostics Run each test listed in the Diagnostic Test
59. help you quickly get to where you want to go Instrument Configuration Desktop Icon What it Does Launches the Xcalibur Instrument Configuration program Use this program to set up and inform Xcalibur which devices are connected to the data system K Xcalibur Launches the Xcalibur Home Page program f DSQTune Launches the DSQ Tune Window HINT When running Xcalibur you can also use the Q icon located in your Windows task bar tuneedit Launches the DSQ Autotune Tune Edit program This program is a replicate of the Show Manual Tune View command which is located in the DSQ Tune Window Use this to create and edit tune files re Signal to Noise Calculator Launches the Xcalibur Signal to noise Calculator This program allows the Signal to Noise to be calculated for specific ranges within raw files 2 Signal to Noise Instructions Launches the MS Word based signal to noise Instructions Use this for help in using the Signal to noise Calculator te Merlin Launches a MS Word based document Merlin is a Microsoft Word Template designed to help you create reports It automatically loads the Merlin dot file and automatically applies the styles to your text User s Guide RevisionB 83 www thermo com Chapter 2 Getting Started 2 2 Configuring Instruments for Use TRACE DSO or FOCUS DSQ 2 2 Configuring Instruments for Use Select the Xcalibur Instrument Config
60. hoose either the PCl meth for positive ion CI or NCI meth for negative ion Cl Prepare for the instrument for Cl mode a Install a clean Cl lon Volume using the I R Tool and the Inlet Valve found on the Mass Spectrometer b Open the Tune window and select Instrument Cl Reagent Gas to display the Cl Reagent Gas Flow screen c Check the Reagent Gas On option d Enter 2 5 mL min in the Reagent Gas Flow box or use the slider to set the flow in the Reagent Gas Flow box 70 User s Guide Revision B TRACE DSQ or FOCUS DSO Chapter 1 Getting Connected 1 18 Running CI Qualification Tests e Click the Apply button and then the OK button to return to the Tune window Now you ll see the Automatic Tune window changed from El mode to Cl mode A cal_tune dsqtune Trace DSQ Tune Saz File View Instrument Experiment Tune Diagnostics Help Dart S GI O S JS _ Slll Status Lenses Filament Vacuum Heaters Power Setpoint Actual lon Source Temp 33 C 33 C Internal Ambient Temp orc j a 4 RF Generator Temp 273 C kip Ready Source 33 C Fore pressure 10 mTorr Ton Gauge N A Figure 1 28 Tune Window CI Mode f Wait at least 30 min for the lon Volume to heat up and bake out Check the Reagent Gas spectrum a Select Experiment Full Scan and scan from m z 10 to 90 b Verify that the Reagent Gas spectrum is similar to Figure 1 29
61. iagnostic Tests Vv Host MS Interface Test not tested Automatic Testing Repeat Count fi Vv Power Supply Test not tested T Stop on Error Vv Vacuum System Test not tested Run Selected Tests Vv Heater System Test not tested Vv lonization Lens Test not tested K Detector Test not tested Vv Rod DC Test not tested Print Diagnostic Report FF Dip Calibration RF Gain Calibration Close Help Figure 1 18 Tune Diagnostic Screen User s Guide Revision B 53 www thermo com Chapter 1 Getting Connected 1 12 Checking the RF Gain Calibration Select the RF Gain Calibration button to display the RF Gain Calibration screen and run the RF Gain Calibration test RF Gain Calibration 1 Target RF blue line 3 RF Modulation white line 2 Detected RF yellow line 4 m z 1050 red purple vertical line Figure 1 19 RF Gain Calibration Screen This screen plots these values versus m z e Target RF 1 ramp is linear and corresponds to the ramp used to scan the quadrupole to produce a mass spectrum e Detected RF 2 measures the actual RF applied to the quadrupole It must be a linear ramp all the way to the m z 1050 line 4 e RF Modulation 3 measures the power output of the RF generator It is usually slightly curved a Allow the display to stabilize for approximately 15 seconds b Verify that the Detected RF is linear
62. ide Revision B TRACE DSQ or FOCUS DSQ Chapter 3 Running Your 1 Sample 3 4 Analyzing the Data Compounds With a Known Retention Time b Select the lower cell and then right click your mouse to display the context sensitive menu Eme ba ves oiy Grd Actions Toos Window Help le x SBZ S Belo gt Riche 5 glaa REE E r aaae 2 3 sie FILI PM PRRPEEE i i Figure 3 15 Qual Browser Chromatogram Context Menu c Choose View Spectrum from this menu to change the view from chromatogram to spectrum The lower cell now displays spectral data Notice that the lower cell now displays a graph of Relative Abundance vs m z that is a mass spectrum Initially you ll see the first mass spectrum Zoom in on the Time Period of Interest Although the full TIC chromatogram is currently displayed in the upper cell only the retention time around three or four minutes is of particular interest Therefore zoom in on that part of the chromatogram and view it in more detail There are two ways of doing this using Mouse functions or using Range functions User s Guide Revision B 113 www thermo com Chapter 3 Running Your 1 Sample 3 4 Analyzing the Data Compounds With a Known Retention Time TRACE DSQ or FOCUS DSQ Using Mouse Functions Click the pin icon that is located in the top right corner of the chromatogram cell so it is green pinned Position the cursor
63. instrument as your test compound NOTE These instructions are written with Trace GC and AI AS 3000 assumptions However making the necessary modifications and or omissions will still help you accomplish each step 94 User s Guide Revision B Chapter 3 Running Your 1 Sample TRACE DSO or FOCUS DSQ 3 1 Calibrating and Tuning the Instrument 3 1 Calibrating and Tuning the Instrument Before you run a sample it s wise to calibrate and tune the instrument using the Tune window Open the Tune program using one of these methods NOTE Select online help e Click the fall from the MS method editor or for Tune Window information e Select the fd shortcut from the Windows desktop DSQTune Check the instrument s basic operation by selecting Diagnostics Run Test to display the Diagnostics screen Tests Calibration Diagnostic Tests mE p Automatic Testing Repeat Count 1 Vv Power Supply Test not tested T Stop on Error K Vacuum System Test not tested Run Selected Tests Vv Heater System Test not tested Jea T v lonization Lens Test not tested La Detector Test not tested PF Dip Calibration Brint Diagnostic Report PF Gain Calibration Close Help Figure 3 1 Tune Window Diagnostic Screen a Click on the Test buttons to run each test b Select the Print Diagnostics Report button to print the results from all the tests you ran Cc Close the Diagnostics Check the last
64. itable rinse solvent such as so octane 5 Save the instrument method for use in the next step Method files have the meth extension and are by default saved to the Xcalibur Methods folder But you can save method files to any folder you prefer User s Guide Revision B 101 www thermo com Chapter 3 Running Your 1 Sample 3 3 Running Methods TRACE DSQ or FOCUS DSQ 3 3 Running Methods After setting up the methods in Instrument Setup you re ready to run the method in Sequence Setup Create a sequence to run in the Sequence Setup window to record sample details and determine how you want to acquire the data a Select diji or wy from the home page to display the Sequence Setup window Pa Et Owo anws We Gie Het fa af piaia ej TASHE DHE lm uj Per tote rom rt Wm Ua S26 Figure 3 7 Sequence Setup Window Untitled Sequence Setup works just like a spreadsheet with each row representing a single sample and each column an item of information required for a sample Column descriptions are in Table 3 1 Sequence Setup Columns pp 103 Additional columns are available by choosing Change Column Arrangement such as Comment 102 User s Guide Revision B TRACE DSQ or FOCUS DSO Chapter 3 Running Your 15 Table 3 1 Sequence Setup Columns Sample 3 3 Running Methods Item Description Sample Type Type of sample selected from the following e Unknown the no
65. ith no condensation c Install a temperature and humidity monitor d Particulate Matter air quality is free of excess particulate matter _ e Electrostatic Discharge work area is free of electrostatic discharge _ f Exhaust System suitable exhaust system available l 7 Gas Equipment Requirements is the necessary gas equipment available _j 8 Solvent Requirements are the recommended solvents available _j 9 Telephone Requirements a telephone is located near the workbench 130 User s Guide Revision B Appendix A Preinstallation Checklists TRACE DSO or FOCUS DSQ A 2 Installation Checklist A 2 Installation Checklist Two Day Schedule At A Glance way 30 Days before _ Call customer _j Is Preinstallation checklist complete _ Are there any questions Is there anything additional need to bring l Step 1 1 Get the right tools uai Day 1 Morning l Step 1 2 Verify site conforms to specifications l Step 1 3 Unpack the instruments Afternoon Step 1 4 Connect the Gas lines Step 1 5 Install the Data System Step 1 6 Install the GC Step 1 7 Install the Mass Spectrometer Step 1 8 Start the Instrument Step 1 9 Confirm Readbacks Step 1 10 Run Diagnostics Step 1 11 Check RF DIP Calibration Step 1 12 Check RF Gain Calibration Step 1 13 Check Air Water Spectrum Step 1 14 Leak check Step 1 15 Check the Initial Tune DOWUUUOOUUOUUL Step 1 16 Stabilize the instruments oA Da
66. lugged into the left side of the GC b Carefully push the GC next to the Mass Spectrometer making sure the Transfer Line extends into the GC c Connect the Ethernet cable leading from the computer to the back of the Mass Spectrometer d Connect the Remote Start Cable to the GENERIC H S port located on the GC to the GC START port located on the Mass Spectrometer 40 User s Guide Revision B TRACE DSQ or FOCUS DSQ TRACE DSQ or FOCUS DSO Chapter 1 Getting Connected 1 7 Installing the Mass Spectrometer Inspect the Mass Spectrometer a Remove the covers front top and left side from the Mass Spectrometer Detailed instructions for removing covers are in the TRACE DSQ Hardware Manual PN 120156 0002 Remove the shipping foam that secures the Vacuum Manifold Cover Store the foam with the Mass Spectrometer accessories in case the instrument needs to be moved in the future Check the Mass Spectrometer configuration against the sales order Look for anything that might have come loose during shipping Verify that the lon Volume is fully inserted You can use the lon Volume Tool to push on the lon Volume The lon Volume is held loosely in the lon Source at room temperature so that it does not seize when the source lon Volume heats to 300 C Connect the GC Column to the MS Transfer Line a Lower the oven temperature to 30 C and allow it to cool before continuing CAUTION Personal Injury
67. meter ADM 1000 or equivalent Forceps PN 76360 0400 Gas filter helium PN A0950 01600 Gloves clean lint and powder free medium PN 23827 0008 large PN 23827 0009 Hex nut driver 5 5 mm User s Guide Revision B 21 www thermo com Chapter 1 Getting Connected 1 1 Getting the Right Tools TRACE DSO or FOCUS DSQ Table 1 1 Required Tools Continued e Injector ferrule for 0 25 mm column PN 290 134 88 e lon volume tool PN 119270 0001 e R tool and guide bar if applicable e Leak detector GL Sciences Inc Model LD 228 or equivalent e Magnifying glass e Methanol or other suitable solvent e Potentiometer adjustment tool e Power cords with appropriate plugs e Preinstallation Guide PN 120156 0001 e Scoring wafer or sapphire scribe to cut capillary column e Screwdriver flat blade e Screwdriver phillips 1 e Screwdriver phillips 2 e Syringe 10 uL 70 mm needle PN 365 001 03 e Tape measure e Teflon thread tape e Tissue lint free e Tubing cutter e Test mix octafluoronaphthalene and benzophenone PN 120150 TEST e Transfer line ferrule 0 4 mm i d PN A0101 18100 e Wrench set Allen 1 5 2 2 5 3 4 5 mm PN 3812 0100 e Wrench set Open ended 5 17 mm e Wrench Adjustable 12 in e Wrench Allen 1 16 in e Wrench set Open ended 1 4 in 5 16 i
68. n Automatic Tune Calibration IV RF Frequency Calibration Detector Gain Calibration Resolution Calibration IV Positivelons V Negative lons r Tune Full Automatic Tune Optimal Sensitivity C Classical lon Ratios C Maintenance Uses Current Tune File Leak Check I7 Close Tune when Automatic Tune successfully finished r Figure 1 27 Automatic Tune Full User s Guide Revision B 67 www thermo com Chapter 1 Getting Connected 1 17 Running El Qualification Tests TRACE DSO or FOCUS DSQ b Check the tests indicated in Figure 1 27 Automatic Tune Full and select OK c When finished archive the Tune Report d Turn the instrument off by selecting Instrument Fil Mult Dyn Off e Save the tune file for the El Qualification Test by changing the emission current to 350 pA in the AutoTune tune file and save it as El dsqtune f Select OK to return to the Tune window Inject 1 uL of a 1 pg uL solution of octafluoronaphthalene using El meth as the instrument method Review the results a b c Look at the background subtracted spectrum in Qual Browser Archive the chromatogram and spectrum NOTE To add Tools to the Home Page select Use the Signal to noise Calculator accessible from a Tools Add Tools The shortcut on the desktop to display a mass chromatogram for location IS the range 271 5 272 5 The minimum Signal to Noise Ratio Xcalibur System Programs should be SigNois
69. n 7 16 in 2 9 16 in 1 2 in 22 User s Guide Revision B Chapter 1 Getting Connected TRACE DSO or FOCUS DSO 1 2 Verifying Site Preparation 1 2 Verifying Site Preparation Tools Needed 74 e Digital voltmeter Fluke model 77 or equivalent e Preinstallation checklist from customer e Preinstallation Guide PN 120156 0001 e Tape measure Frequency JAK Day 1 Review the customer s Preinstallation Checklist keeping these items in mind The customer is responsible for providing a completed Preinstallation Checklist prior to the installation If the checklist is lost or unreadable you can make a copy of A 2 Installation Checklist pp 131 and determine if the installation can still be performed All preinstallation requirements are listed in the TRACE DSO Preinstallation Guide PN 120156 00071 so you only need to double check that the proper workbench power outlets power cords temperature and gases are available User s Guide RevisionB 23 www thermo com Chapter 1 Getting Connected 1 3 Unpacking the Instruments 1 3 Unpacking the Instruments Tools Needed 74 e Original purchase order A e Packing slip e Installation report supplied by service organization Frequency ATL Day 1 Unpack the instruments to confirm that each item the customer ordered arrived without incident WARNING Personal Injury al Lifting Hazard Use pro
70. n Outlet 5 in a small vial of methanol Bubbles indicate there is flow through the Column 4 e Allow the Column 4 to purge for at least 10 min Perform a Column Characterization a Raise the Oven and Injector temperatures to 50 C and allow them to stabilize b Run Column Eval key to characterize the column This takes several minutes Cc Expect a K factor of about 0 7 0 9 for a 15 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 36 User s Guide Revision B Chapter 1 Getting Connected TRACE DSO or FOCUS DSQ 1 6 Installing the Gas Chromatograph CAUTION Instrument Damage ge Do not raise the oven temperature until you are sure the ja system is leak free At temperatures above 100 C the column will be destroyed if exposed to oxygen d Raise the Oven temperature to 150 C and allow it to stabilize Perform a column Leak Check a Run the automated Leak Check on the GC b If the report indicates a leak look for and fix leaks at all the fittings in the GC using the leak detector Cc Repeat the Column Evaluation and Leak Check until no leaks are indicated d Raise the Inje
71. n Use screen 106 107 cursor Change Masses button 75 actions effects active inactive unpinned pinned chemical ionization 28 109 Chemical Structure Cell 117 ACUVe 109 Chromatogram 110 112 pinning 109 zooming in on period of interest 113 chromatogram 68 74 76 115 D Chromatogram Automatic Noise Range 126 damage 24 Chromatogram Ranges 125 Chromatogram Specify Noise Range 126 Chromatogram Ranges Screen 115 119 chromatography techniques 124 CI calibration gas spectrum 72 CI Gas 85 CO2 isobutane ammonia methane other 86 Type 86 CI Gas tab 85 CI lon Volume 70 CI Qualification Test 70 CI Reagent Gas connecting 28 CI Reagent Gas Flow 64 65 CI Reagent Gas Flow screen 70 CI Reagent Gas On 75 Cl spectrum typical 71 CO2 86 Column 42 43 column 99 installation 34 poor quality 124 Column Characterization 36 Column Measuring Tool 42 Compounds known ion pattern 119 Configuration screen 84 Configure button 84 Configured Devices 84 Configured Devices panel 88 Continuous button 139 conventions typographical 18 146 User s Guide Revision B data system setup 31 DC RF Gain menu item 88 Delete 119 Delete Grid Row 119 Demonstration Mode 85 Detected RF 54 Detectors and Data tab 89 Diagnostic screen 51 53 138 tune window 49 diagnostics 47 49 Diagnostics Run Test 95 Diagnostics screen 95 138 Difference Spectrum Cell 117 Display Options 122 124 Display Options screen 124 DSQ Features 13 E El calibration
72. ned 115 Plot Type 120 Plunger strokes 100 position 103 positive ion Cl 70 Post Injection Washes 100 Post injection dwell time 100 power data system 31 TRACE DSO 44 PPINICI tab 86 Pre Injection Washes 100 preferred pressure units 88 Prefilter 62 Pre injection dwell time 100 Pressure Units 85 Print Diagnostics Report button 95 Q Qual Browser 74 76 111 115 120 cursor actions table 110 determining peak areas 122 determining peak heights 122 library search 116 Library Search Results window figure 117 signal to noise ratio 124 subtracting background contamination from a spectrum 116 qualification test El 66 quantitation 122 R R5 138 Range functions 113 115 Trace DSQ and Focus DSQ Index Ranges 119 subtracting spectra 116 Read This First 11 Readme button 143 Reagent Gas Flow 70 Reagent Gas On 70 Reagent Gas spectrum 71 Reagent Gas Supply Line 30 recording samples 103 Relative Abundance vs m z 113 Remote Start Active High 85 Resolution Calibration 62 Restore button 62 retention 121 retention time 115 RF dip calibration setup RF dip 51 RF Dip Calibration readback 142 RF gain adjustment 138 RF gain calibration 53 RF Gain Calibration button 54 RF Gain Calibration screen 54 RF Gain Calibration Test 54 RF generator PCB 138 139 RF Modulation 54 RF Null adjustment 138 RIGHT_SSL_EI _Fullscan meth 98 RMS 125 Rod DC 88 Rod DC readback 139 Rod DC Test 138 Rod DC Test button 139 Rod DC Test Fail
73. ng ys eur sAebeN i a cri coral teagan S M y J zju wejy y Boe da ja ae Rete phd iy UNL OHeWO NY uny a ges 0 pue suo aanisog uoneiqes lng Suor ISOd UOHeIqIeD 41431A p l aunyesadwa 91NOS MO Y 80NOS uognjosay uonesgeo Aousnba 4 uolnjosay uoesqeg Aouanbal4 y UBBID JUSWNYSU BY UMOPINYS y Ul BLUNIOA UO Z uea e e SU 2 ace 4H a aS aUN ewozny uny JH 998g eUN deWO NY uny fo payjeysul Ayadoid SWINJOA UO 4 ueaJ e s 49949 N yee aun ajewoyny NJ suoj SOq UOHeIqIeD uognjosoy uoqeiqijeg uleg 10 99 9q Buljogjes aun oewoyny uny ID aAgeBen 104 pesn aq zu wnaysu BU IM paun yu wnysu ay SEM jenuey aJempIeH au Ul Sainpasoid Buyooys jqno pue o1jsoubelp ay MOJO Keme dwnd o sjueulwejuo0o JO pue aZi Iqe s 0 WNNILA pue mzes dw 8dJNOS Y JO YEM a qeyds00e s nsai y ay s s9 e ssed Sun dHeWONY Bu PI ss vong p ue jp Jo pue pajuan u q pu v 1 yu wn su y SeH y2 y49 yee pue vueu yueN uoneiqieg ueg 104994290 6up aj s aun oyewozny uny y99y49 yee pue vueuayuLeN Bunjogjas aun opewozny uny uonesado Jo 49am sed y uly m payeiqijeo u q ule 10 99 p 94 SEH payeiqijes jeadde mopuim aun 1 y u suo y 0q User s Guide Revision B 141
74. nned pinning fixes the active status of a cell Unpin an active cell by clicking once on the pin icon Make a cell active by clicking anywhere within the cell Xcalibur highlights the cell with a gray border Click on its pin icon if you want to fix it as the active cell Cursor actions in an active cell cause the cell to be scaled according to the dimensions of the dragged line or area see Table 3 2 Cursor Actions In Active and Unpinned Cells pp 110 User s Guide Revision B 109 www thermo com Chapter 3 Running Your 1 Sample 3 4 Analyzing the Data Compounds With a Known Retention Time TRACE DSQ or FOCUS DSQ Table 3 2 Cursor Actions In Active and Unpinned Cells Cursor Action Effect Drag parallel to X axis Rescale graph showing selected X range only same Y range Drag parallel to Y axis Rescale graph showing selected Y range only same X range Dragged area Rescale graph showing both the selected X and Y ranges The same actions in the unpinned or inactive cell have a very different effect In this case the cursor actions affect the active pinned cell see Table 3 3 Cursor Actions In An Inactive Or Unpinned Cell pp 110 Table 3 3 Cursor Actions In An Inactive Or Unpinned Cell Pinned cell Cursor action Effect spectrum Click in a The spectrum cell displays the mass chromatogram cell spectrum at that retention time spectrum Drag across a time The spectrum cell displays the
75. nut 134 plugs 137 Swagelok and inlet connection 135 T Target RF 54 Temperature Settings screen 48 TIC 121 Time Period of Interest 113 Time Range field 115 Timeout 87 tools adding 74 training 78 Transfer Line 43 Transfer Line Cable 33 Transfer Line Nut 42 transfer line union 68 troubleshooting 69 150 User s Guide Revision B Tune View Tune Report 95 Tune desktop icon 46 Tune Path 85 Tune Window 95 Tune window 56 63 68 73 74 76 85 97 142 Turbo Pump 47 Type 119 typographical conventions 18 U unpacking 24 unpinned 115 upgrades 82 V Vacuum Compensation 44 vacuum status readback 142 vial number 103 View Spectrum 113 W Waiting for Contact Closure 108 washes 100 website 82 X Xcalibur CD 143 Xcalibur Instrument Configuration icon 84 Xcalibur Setup screen 143 Xcalibur software training 78 XInstall exe 143 Z Zoom 122 Zoom Reset 119
76. om Chapter 3 Running Your 1 Sample 3 7 Analyzing the Data Signal to Noise Ratio TRACE DSO or FOCUS DSQ 3 7 Analyzing the Data Signal to Noise Ratio The signal to noise ratio is a good measure of the performance of the system because it defines the smallest amounts of compound that can be detected and quantified If the signal to noise ratio is low true peaks signals resulting from the presence of very small amounts of material can be lost in the background noise Low signal to noise ratios can result from Poor column quality A dirty ion source Poor quality carrier gas Inadequate sample cleanup extraction Poor chromatography techniques There are two ways to determine the Signal to noise ratio of a peak The first uses Qual Browser and the second uses the Signal to Noise Calculator Note that in Xcalibur version 1 3 and earlier the Qual Browser method is not always accurate This is because you cannot select the region of the chromatogram from which to calculate noise Using Qual Browser Display the Signal to noise label on the chromatogram a Using Xcalibur right click on the chromatogram and choose Display Options from the context menu to display the Display Options screen b Select the Labels tab Cc Select the Signal to noise checkbox d Click on OK to return to the chromatogram Choose the baseline noise range a Click on the Peak Detection Settings tab in the Info bar 124 User
77. on gift and complimentary application and technical reports Before shipping your system Thermo Electron Corporation installed the Xcalibur Data System Ver 1 4 on your computer s hard drive Where to Find More Information Look at your Xcalibur Installation CD for a complete set of hardware and software documentation z _ X Xcalibur 1 4 Setup X If some of the setup buttons are disabled it is because the fy TM required version of core for the devices has not been installed Installing the Core will enable those buttons y a l U y Note that you may be required to reboot after you install the core Installation Help Xcalibur 1 4 Core Readme Xcalibur 1 4 Core Patches Readme NIST Setup GC Devices Trace DSQ Readme Acrobat Reader 5 0 Xcalibur 1 4 Manuals e W Screen Saver m jE N E Library Browser Browser Browser Exit Figure i 1 Xcalibur 1 4 TRACE DSQ Installation CD Screen 12 User s Guide Revision B TRACE DSQ or FOCUS DSQ Read Me TRACE DSO or FOCUS DSQ About Your TRACE DSQ or FOCUS DSQ System X Roadmap Home Page Beles File Actions View Tools GoTo Help ae Py gt alae 2 Status Acquistion Queue Run Manager Ta R Ready To Download aa ae ON LINE Sample Name oom Working On posoj Position id Raw File Inst Method AIAS 3000 Not Connected TRACE DSQ Ready
78. ons a Make Yes display for the GC and MS instruments listed in the In Use fields However if Yes is not listed then click on the blank field to toggle Yes on b Make sure the GC and MS instruments Start Instrument fields are empty Fig 3 72 c Make sure the AS if listed does not say Yes in both the In Use or Start Instrument fields d Select OK to return to the Run Sequence screen Open the 100 pg octafluoronaphthalene sample that is in the GC MS Test Kit PN 120150 TEST User s Guide Revision B 107 www thermo com Chapter 3 Running Your 1 Sample 3 3 Running Methods TRACE DSQ or FOCUS DSO Select OK from the Run Sequence screen Fig 3 70 to start the run Monitor the Status View until the instrument is Waiting for Contact Closure Prepare the injection a Draw 1 uL of the 100 pg octafluoronaphthalene sample into the supplied syringe Be sure there are no bubbles in the syringe b Drawin 1 uL of air Make the injection and start the GC a Carefully insert the needle into the injector port b Wait one second and push the plunger Cc Quickly press the Start button located on the GC d Remove the syringe Watch the data while the sequence is running This is a good time to watch the data by selecting from one of the two views a Click the Real Time Plot icon to view the Chromatogram and Spectrum acquisition in real time When the run is finished this screen goes blank
79. op Analysis Position Pause Analysis Raw File Inst Metho AIAS 3000 Ready to D B TRACE DSQ Ready to D E TRACE GC 2000 Ready to Download Devices On Devices Standby Devices Off Automatic Devices On Reins Figure 3 9 Sequence Setup Running A Sequence 104 User s Guide Revision B TRACE DSQ or FOCUS DSQ Chapter 3 Running Your 1 Sample 3 3 Running Methods a Select Action Run Sequence to display the Run Sequence screen x Acquisition Options i SS Tratrurnent Stan irinen ee ae TRACE GC 2000 Winne ji I Prendy Sequence F Siet When eed Change Insinmerts Processing Actions Inctouraerd Method rigs Stat Up Biome Shat Down Browse w F Reor Progam r Port Acquitiion Biome N Run Sychnant F PreAcqusion Post Acquston Alter Sequence Set System C On C Story C on Daa ej Figure 3 10 Sequence Setup Run Sequence Screen b Select Start When Ready c Press the Change Instruments button to display the Change Instruments screen and set up your instruments for an automatic injection or a manual injection See the topic f You re Doing Automatic Injections pp 3 106 or topic If You re Doing Manual Injections pp 3 107 for instructions User s Guide Revision B 105 www thermo com Chapter 3 Running Your 1 Sample 3 3 Running Methods TRACE DSQ or FOCUS DSO If You re Doing Automatic Injections An autosampler performs automatic injections and you instruct X
80. ou tighten it This helps ensure that you have turned the nut a 3 4 turn Figure B 3 Tightening Swagelok Fittings 136 User s Guide Revision B Appendix B Additional Helps TRACE DSQ or FOCUS DSO B 2 Using a Swagelok Tee or Cross B 2 Using a Swagelok Tee or Cross Tools Needed L e Ruler or measuring tape e Swagelok Fittings e Swagelok Plugs e Tubing Cutter Frequency sak Fixing leaks To use a single gas source for more than one inlet or detector module you must use a Swagelok tee or cross to properly split the gas flow Cut the tubing With a tubing cutter cut the tubing where the tee or cross will go Connect the tubing to the tee or cross with a Swagelok fitting Refer to instruction B 7 Assembling Swagelok Fittings pp 134 Measure and cut Measure the distance from the tee or cross to the inlets or detectors and cut the tubing in the appropriate lengths Connect the tubing to the tee or cross ends with Swagelok fittings Install Swagelok Plugs Install Swagelok Plugs instead of an Inlet Body on any open ends located on a tee or cross that are not connected with tubing User s Guide Revision B 137 www thermo com Appendix B Additional Helps B 3 Adjusting the RF Null B 3 Adjusting the RF Null Use this procedure only if an RF Null adjustment is necessary To adjust the RF Null you adjust the R5 potentiometer located behind the heatsink of the RF generator PCB This
81. ould affect instrument performance NOTE Install optional Inspect and store the shipping containers accessories for example the autosamplers after the a Carefully inspect ALL boxes and packing materials for missed installation and qualification tests are complete b items Put packing materials back into shipping crates and store the empty boxes User s Guide Revision B 25 www thermo com Chapter 1 Getting Connected 1 4 Connecting the Gas Lines 1 4 Connecting the Gas Lines Brass back ferrules Swagelok PN AQ101 02500 Tools Needed y e Brass front ferrules Swagelok PN A0101 08500 Brass nuts Swagelok PN A0101 15500 Copper tubing clean PN 76381 0041 or Mueller Industries refrigeration tubing 1 8 in o d 0 030 in wall Gas filter helium PN A0950 01600 Leak detector GL Sciences Inc Model LD 228 or equivalent Teflon thread tape Tubing cutter Wrench Adjustable 12 in Wrench Open ended 7 16 in 2 Wrench Open ended 1 2 in Wrench Open ended 9 16 in JAR Frequency Day 1 Assembly Tips To insure safe leak tight connections follow these instructions B 1 Assembling Swagelok Fittings pp 134 before assembling the swagelok fittings Leave enough slack in the tubing so the GC and mass spectrometer may be moved at least 40 cm 16 in away from each other This ensures that column connections and system maintenance are easily
82. owser a Opena raw file b Add a cell to view a spectrum c Explain how to use push pins d Explain background subtraction e Demonstrate how to change the chromatogram range and mass Remind the customer to use Chapter 2 Getting Started pp 81 to reinforce all that you have demonstrated today User s Guide Revision B 79 www thermo com Chapter 1 Getting Connected 1 20 Providing Basic Training 80 User s Guide Revision B TRACE DSQ or FOCUS DSQ Getting Started This chapter provides GC MS instructions using Xcalibur 1 4 software In This Chapter 2 1 Using Desktop Icons pp 83 2 2 Configuring Instruments for Use pp 84 Analyze Detect Measure Control User s Guide RevisionB 81 www thermo com Chapter 2 Getting Started Upgrades Periodically visit our website http www thermo com for the latest releases on application notes new manuals software and firmware updates and information on new features 82 User s Guide Revision B TRACE DSQ or FOCUS DSQ TRACE DSQ or FOCUS DSQ Chapter 2 Getting Started 2 1 Using Desktop Icons NOTE You might find it helpful to copy this page and keep it out to use as a quick reference template while you re getting used to Xcalibur 2 1 Using Desktop Icons After the instrument is connected it s a good idea to get acquainted with how your software is organized on the desktop Xcalibur desktop icons can
83. per lifting techniques as several items are heavy Check for damage a Check carefully for obvious damage tip indicators displaying a tipped condition or evidence of rough handling b If external damage is apparent note this fact on the installation report and describe briefly the extent of the damage Have the customer sign or initial next to your comments Confirm that the shipment is complete a Open and carefully remove all items from all shipping containers The packing list is located in the installation packet b Verify that each item listed on the customer s purchase order and packing list is included with the shipment If any items are missing make a note on the installation report and immediately contact the factory Quality Representative at 512 251 1400 24 User s Guide Revision B TRACE DSQ or FOCUS DSQ Chapter 1 Getting Connected TRACE DSO or FOCUS DSO 1 3 Unpacking the Instruments Set up the instruments TRACE DSQ TRACE Gas Mass Spectrometer Chromatograph Data System Wall Wail Outlet Outlet 1 2 m o Phones 1 Jack NS Rotary Vane Pump i O I Figure 1 1 TRACE DSQ System Layout Front a Place the instruments from left to right in this order Mass Spectrometer GC and the computer monitor with the mid tower CPU beside the monitor or under the bench b Place the rotary vane pump on the floor If placed on the bench excess vibration c
84. performed Forming Shock Loops with the tubing helps to dampen vibrations that can loosen the fittings 26 User s Guide Revision B TRACE DSQ or FOCUS DSQ Chapter 1 Getting Connected TRACE DSO or FOCUS DSO 1 4 Connecting the Gas Lines Connect the GC Carrier Gas Carrier Gas Regulator 80 psi 550 kPa Carrier Gas Input Helium Gas Figure 1 2 GC Carrier Gas Connections Back Install the Carrier Gas Regulator and Gas Filter a Connect the Carrier Gas Regulator b Set the Gas Filter as close as possible to the GC It should be easy to access since it must be changed regularly Do not put it behind the GC where hot air from the exhaust vents will hit the gas filter Mount it to the side of the GC or MS or on top CAUTION Instrument Damage ei Do not loosen or remove caps from the Gas Filter until lt PURGED lines are connected Loosening or removing caps early contaminates the filter Prepare the Supply Line a Runa Supply Line from the Carrier Gas Regulator to the Gas Filter but do not remove the Caps on the Gas Filter b Run a Supply Line from the Gas Filter to the Carrier Gas Input on the GC Do not connect it to the Gas Filter or GC yet Cc Include a Shock Loop to isolate vibration and allow enough tubing to move the GC at least 40 cm 16 in Purge the Supply Line User s Guide Revision B 27 www thermo com Chapter 1 Getting Connec
85. pj SI mi icicle t me r Figure 3 18 Library Search Pull down Menu b If you have the optional NIST library installed look for the results Chemical Structure Cell 3 Library Spectrum Cell Difference Spectrum Cell 4 Hit List Cell Figure 3 19 Library Search Results window c Look in the hit list cell 4 for the most likely compounds in decreasing order of match probability If octafluoronaphthalene is not one of the top hits you may not have the optional NIST User s Guide Revision B 117 www thermo com Chapter 3 Running Your 1 Sample 3 4 Analyzing the Data Compounds With a Known Retention Time library Check which libraries are available for search by selecting the Library Options pull down menu For each compound in the hit list Xcalibur displays a chemical structure 1 a library spectrum 3 to compare with your spectrum and a difference spectrum 2 that is the library spectrum subtracted from your spectrum 118 User s Guide Revision B TRACE DSQ or FOCUS DSQ TRACE DSQ or FOCUS DSO Chapter 3 Running Your 1 Sample 3 5 Analyzing the Data Compounds With a Known lon Pattern NOTE See the online Help for additional instruction or see Getting Productive Qualitative Analysis Getting Productive Quantitative Analysis Getting Productive Processing Setup and Analysis of Quantita
86. resnse Let PPa c Faemais 190 Eqaitvaten Prennze Right KPa L Tasers 010 Figure 3 5 Trace GC Method Parameters This method holds the GC at 40 C for 1 min ramps it at 30 C min to 250 C and holds it there for 10 min The injector is 220 C operated in splitless mode The column flow is 1 0 mL min The transfer line temperature is 250 C User s Guide Revision B 99 www thermo com Chapter 3 Running Your 1 Sample 3 2 Setting Up Methods Optional Review AS method parameters by selecting the AS instrument icon If you re using an Al AS 3000 you can enter the parameters shown in Figure 3 6 For other autosamplers there are several basic settings for all autosamplers for sampling injection and washes All other parameters can be left at their default values Sampling Injection Washes Sample Volume 1 uL This is the sample volume that will be injected Air Volume 1 uL Draw air after the sample volume to make sure no solvent is in the needle Having no solvent in the needle and using a pre injection dwell time of 1 second will give you a hot needle injection Al AS 3000 is always 1 uL Plunger strokes 10 Also called pull ups or bubble elimination strokes This is the number of times the plunger is pulled up and down while in the sample vial The plunger volume should be set larger than the sample volume to say 4 uL Pre injection dwell time 1 s Also called Injection Delay This
87. riment Tune Diagnostics Help ixl max Status Lenses Filament Vacuum Heaters Power Dsm S OO Ilo O19 A _I Turbo Pump OK Turbo Pump RPM OK OK Vacuum a lon Gauge N A Sem ee we Elt r T Pump Switch ON Fore Pressure 10 mT on lon Gauge Pressure N A 100 1 4140 a640 5020 100 50 250 350 400 450 500 Ready Source 33 C Fore pressure 10 mTorr Ton Gauge N A Figure 1 20 Tune Window Vacuum Tab a Verify that the Fore Pressure is less than 50 mTorr For some instruments that have been exposed to high humidity while vented for an extended period of time this may require several hours This is common for an instrument shipped with the 200 200 L s pumping option because the large surface of the turbomolecular pump requires time to outgas b If the system has an ion gauge verify that the lon Gauge Pressure is less than 7 x 10 Torr c If the pressure is too high there is a leak that must be fixed immediately Refer to the TRACE DSO or FOCUS DSQ Hardware Manual PN 120156 0002 for troubleshooting instructions 56 User s Guide Revision B TRACE DSQ or FOCUS DSQ TRACE DSQ or FOCUS DSO Chapter 1 Getting Connected 1 13 Checking the Air Water Spectrum NOTE Figure 1 21 through Figure 1 23 were acquired with a 250 L s turbomolecular pump system Relative abundance of air water ions can vary depending upon the pump op
88. rity is applied to each quadrupole rod pair for each ion polarity Configure the gas chromatograph GC a Move the GC from the Available Devices panel to the Configured Devices panel Instrument Configuration Device Types GC X Available Devices Configured Devices Finnigan Q GC lt lt Remove Configure Help Figure 2 7 GC Instrument Configuration b Select the GC icon in the Configured Devices panel then click the Configure button to display the GC Configuration screen Cc Make these selections on the General tab e Serial Port COM 1 e Set the preferred pressure units e Click the Get button to retrieve the GC configuration through the serial port to Xcalibur 88 User s Guide Revision B TRACE DSQ or FOCUS DSQ Chapter 2 Getting Started 2 2 Configuring Instruments for Use d Verify the settings on the Inlet tab match the GC configuration e Verify the settings on the Detectors and Data tab match the GC configuration f Verify the settings on the Auxiliary and Oven Options tab match the GC configuration and Aux 1 Present has the MS Transfer Line selected g Click OK if no problems are detected and return to the Instrument Configuration screen Configure the autosampler AS a Move the AS icon from the Available Devices panel to the Configured Devices panel instrument Configuration g Device Types as z Available
89. rmal choice for qualitative analysis all other types are only normally used for quantitative analysis e Blank e QC quality control e Standard Clear e Standard Update e Start Bracket e End Bracket e Standard Bracket File Name Name of the file where to save the sample data Sample ID An identifier unique to the sample This field can also be used to import a barcode identifier Path The path to the raw file that Xcalibur creates for the sample data Xcalibur creates this file with extension raw Double click on this field to select a directory Inst Meth The path and file name of the Instrument Method to be used for acquisition Proc Meth The path and file name of the processing method used to process the data after acquisition Position The sample s vial number The format of the entry depends on the configured autosampler Al AS 3000 and AS 2000 use simple integers Inj Vol Not used in this editor but used instead in the AS method editor Level Used with Standard and QC samples to enter the sample s concentration level 1 More information about recording samples are in the Xcalibur Online Help or the Xcalibur Getting Productive Qualitative Analysis manual or the Getting Productive Quantitative Analysis manual b Start entering information in the blank row at the bottom of the list to add a new sequence User s Guide Revision B 103 Chapter 3
90. rmo com Chapter 1 Getting Connected 1 11 Checking the RF Dip Calibration Select the RF Dip Calibration button to display the RF Dip Calibration screen RF Dip Calibration TART 1060 TRACE DSQ or FOCUS DSQ Eee 1140 Actual 1106 3 Figure 1 17 RF Dip Calibration Screen a Allow the display to stabilize for approximately 15 seconds b Verity that the Setpoint and Actual are within 0 2 kHz c If they are not follow these instructions B 5 Adjusting the RF Dip Calibration pp 142 Press Close to return to the Diagnostics screen 52 User s Guide Revision B NOTE The RF Dip Calibration looks different than the Polaris O RF Dip calibration This is normal as the TRACE DSO use a more comprehensive algorithm The RF frequency is set correctly if the Setpoint and Actual are within 0 2 kHz NOTE If the Rod DC Test Fails after the RF Dip Calibration and RF Gain Calibration pass follow the instructions in B 3 Adjusting the RF Null pp 138 Chapter 1 Getting Connected TRACE DSQ or FOCUS DSO 1 12 Checking the RF Gain Calibration 1 12 Checking the RF Gain Calibration Tools Needed e Potentiometer adjustment tool e Wrench Allen 3 mm Tals Frequency Day 1 After you see a successful RF Dip Calibration check the RF Gain Calibration Open the Tune window Diagnostic screen Select Tune Diagnostics Run Tests to display the Diagnostics screen E r D
91. s 52 Rod DC Test screen 139 Rod DC values 139 root mean square 125 Rotary Vane Pump 38 Run Sequence screen 105 106 107 108 Run Tests 49 51 53 138 S S N 76 sample ID 103 Sample Probe upgrade option 40 Sample Rinses 100 Sample Volume 100 Samples type 103 sampling injection 100 second Rotary Vane Pump 40 Septum 42 43 Sequence setup columns 103 sequence running 104 105 saving 104 Sequence Setup Inst Meth 103 path 103 position 103 sample type 103 sample ID 103 vial number 103 Sequence Setup window 102 Serial Port 88 Service Personnel 87 Service tab 87 setup check air water 56 check initial tune 60 data system 31 GC 33 RF gain 53 running diagnostics 49 starting up 45 training 78 unpacking 24 shipping damage 24 Show Manual Tune View 97 signal to noise low ratios 124 measurement 124 ratio 124 Signal to Noise Calculator 68 74 signal to noise ratio El 68 PCI 74 software training 78 User s Guide Revision B 1149 www thermo com Trace DSQ and Focus DSQ Index solvent Tune 83 87 95 elute 99 automatic full 96 solvents manual calibration 87 rinse 101 Source Saver tab 87 specifications 14 15 spectrum 68 74 76 110 air water 57 background 61 calibration gas Cl 72 calibration gas El 61 methane Cl 71 subtracting background contamination 116 Start Instrument field 107 starting up 45 Status tab 85 Subtract Background Contamination 116 Swagelok fittings inlet 135
92. s a calibrated flow for that gas in mL min e Action when Software is closed and Cl Gas is on When Xcalibur software is closed these options determine what happens if Cl gas is on You can choose to turn it off leave it on or receive a prompt at the time the software is closed asking if you want to turn the Cl gas off If you choose to leave the Cl gas on it remains on until you restart the software However as soon as you restart the software the Cl gas is turned off f Optional Configure PPINICI tab options Instrument Configuration General Cl gas PFINICI Source Saver Service M PPINICI option Figure 2 4 Instrument Configuration PPINICI e Check the PPINICI option if you have the PPINICI option installed on your mass spectrometer 86 User s Guide Revision B TRACE DSQ or FOCUS DSQ Chapter 2 Getting Started 2 2 Configuring Instruments for Use NOTE Please do not adjust these settings Only factory trained Field Engineers are qualified to set the options in the Instrument Configuration Service tab Configure Source Saver tab options Instrument Configuration General cl aas PPINIC Source Saver Service M Enable cal gas source saver Timeout minutes fi a Figure 2 5 Instrument Configuration Source Saver e Enable Cal Gas Source Saver Check this option to enable the instrument to turn off the filament and cal gas if left unattended with the cal gas on If the c
93. s group box individually so that you can closely monitor each test s readbacks and note any failures If a diagnostic fails then view the help topic for that diagnostic However don t run the RF Dip and RF Gain Calibrations tests until the next procedure 50 User s Guide Revision B TRACE DSQ or FOCUS DSQ Chapter 1 Getting Connected TRACE DSO or FOCUS DSO 1 11 Checking the RF Dip Calibration 1 11 Checking the RF Dip Calibration Tools Needed J None sas Frequency Day 1 NOTE Run this test After you have finished running the Xcalibur diagnostics from the Diagnostics only after the heaters Tests group box and they have all passed then it s time to check the RF Dip and vacuum have Calibration However run this test only after the heaters and vacuum have stabilized stabilized Open the Tune window Diagnostic screen Select Tune Diagnostics Run Tests to display the Diagnostics screen LM x r Diagnostic Tests Vv Host MS Interface Test not tested Automatic Testing Repeat Count fr K Power Supply Test not tested I Stop on Eror Vv Vacuum System Test not tested Run Selected Tests Vv Heater System Test not tested Vv lonization Lens Test not tested Vv Detector Test not tested Vv Rod DC Test not tested Print Diagnostic Report PF Dip Calibration RF Gain Calibration Close Help Figure 1 16 Tune Diagnostic Screen User s Guide Revision B 51 www the
94. s menu to display the Chromatogram Ranges screen c Add another plot by clicking the check box under Type User s Guide Revision B 119 www thermo com Chapter 3 Running Your 1 Sample 3 5 Analyzing the Data Compounds With a Known lon Pattern TRACE DSQ or FOCUS DSQ Figure 3 20 Qual Browser Chromatogram 1 d Select Mass Range from the Plot Type field Chromatogram Ranges Neutral Fragment Figure 3 21 Qual Browser Chromatogram 2 e Enter the mass range in the Range s field In this example enter 272 f Click OK to return to Qual Browser where the chromatogram cell now shows a mass TIC and a chromatogram for the selected mass m z 272 120 User s Guide Revision B TRACE DSQ or FOCUS DSO Chapter 3 Running Your 1 Sample 3 5 Analyzing the Data Compounds With a Known lon Pattern 2a aj Bele aeisiese FS pigivia 2j cjf Ser sei ej t J a8 DING aitizi f Figure 3 22 Displaying a TIC And Mass Range Chromatogram The result in this example shows that the peak at retention time 3 69 min is of particular interest because it includes m z 272 the molecular ion from octafluoronaphthalene View the mass spectrum Having identified a particular retention time of interest you can investigate the peak further by looking at the mass spectrum Follow the same procedure you did in the previous section for adding a spectrum cell User s Guide
95. sales order Connect the Transfer Line Cable to the left of the GC User s Guide Revision B 33 Chapter 1 Getting Connected 1 6 Installing the Gas Chromatograph TRACE DSQ or FOCUS DSQ www thermo com gz Figure 1 5 Power Connections Back View 3 Plug the power cord into the back of the GC and then into Wall Outlet 2 4 Connect the Column to the Injector The test column is conditioned at the factory and requires no additional conditioning Focus GC users must set up instrument parameters using the virtual Keypad button located on the Xcalibur Home Page E ween Hil win Stans Accpsstion Qun Aun Manager Figure 1 6 Focus GC Instrument Status View 34 User s Guide Revision B Chapter 1 Getting Connected TRACE DSO or FOCUS DSO 1 6 Installing the Gas Chromatograph Refer to the Focus GC User s Manual for instructions on using the keypad The arrow in Figure 1 7 points to an exploded view of the injector AE y LA Cea 6 SRERRE pooo 5 805 o 000 E a poa 4 1 Injector 4 Column 2 Injector Ferrule 5 Column Outlet 3 Injector Nut 6 Transfer Line Figure 1 7 GC Injector Front View NOTE Wear clean lint a Unwind the Column 4 about a half turn and powder free gloves when you handle the b Wipe abo
96. ssteeeeescseeeeeeenaees 134 B 2 Using a Swagelok Tee Or CroSS wiccccccccccceecsteeeeeessseeeeeessseesesensaees 137 B 3 Adjusting the RF Null cdseicsatn cc dcsesacasndeansanbddadassuvsdisannsasdacshacabadeiiausendes 138 B 4 Automatic Tune Flow Chart cccccccccccececssseeeeeessaeeeeeessseeeeeseaees 141 B 5 Adjusting the RF Dip Calibration ccccccccccceccssteeeeesetseeeeeensaees 142 B 6 Reinstalling the Data System ceccccccecccsteeeeeeesseeeeeeseaeeeeeeeeaaes 143 Index 145 Read Me In This Chapter Where to Find More Information pp 12 Typographical Conventions pp 18 Changes to the Manual pp 18 Analyze Detect Measure Control User s Guide Revision B 11 www thermo com Read Me Where to Find More Information This chapter explains how this book is organized and designed specifications about your system and where to find more information about your system Be sure to tear out the Contact Us card located at the front of this book and return it to us after filling out the Reader Survey and the Customer Registration forms The Reader Survey allows you to give us feedback which helps us to improve the quality of our documentation The Customer Registration Card allows you to register your product to receive all the privileges associated with being a Thermo Electron Corporation product user After we receive your Contact Us card we ll send you a FREE Thermo Electron Corporati
97. step instructions for factory trained Field Engineers installing the TRACE DSO or FOCUS DSO system and for experienced users finding it necessary to re setup the instrument 20 User s Guide Revision B TRACE DSQ or FOCUS DSQ NOTE This chapter is primarily written for factory trained Field Engineers TRACE DSQ or FOCUS DSQ Chapter 1 Getting Connected 1 1 Getting the Right Tools 1 1 Getting the Right Tools Use this table to determine the tools and parts you will need to take with you to the installation However keep in mind some items are included with the system Table 1 1 Required Tools L Tools Needed Brass back ferrules Swagelok PN A0101 02500 Brass front ferrules Swagelok PN A0101 08500 Brass nuts Swagelok PN A0101 15500 Cable PC to mass spectrometer 15 ft Ethernet crossover PN 76396 0052 Cable PC to GC PN 230 980 00 Cable GC to mass spectrometer remote start PN 76396 0050 Capillary column 5MS 15 m 0 25 mm i d 0 25 um PN 76317 3015 Column Measuring Tool PN 119640 0550 Copper tubing clean PN 76381 0041 or Mueller Industries refrigeration tubing 1 8 in o d 0 030 in wall CI ion volume PN 119650 0230 if applicable Digital voltmeter Fluke model 77 or equivalent Dusting spray containing tetrafluoroethane Falcon Dust Off MicroCare MicroBlast or equivalent Flashlight small hand held Flow
98. t Instrument System On Make sure the filament is on select Instrument Fil Mult Dyn On Check the background spectrum Select Experiment Full Scan and scan from m z 10 to 650 Verify that the background spectrum is similar to Figure 1 24 The background may be higher the first day after being pumped down 60 User s Guide Revision B TRACE DSQ or FOCUS DSQ Chapter 1 Getting Connected TRACE DSO or FOCUS DSO 1 15 Checking the Initial Tune Sean 313 TIC 1 2e 6 5 3e 5 1004 18 50 55 PEPTIC TIIE PT TTT TTT TTT TPT TT PT TIT PTT TTT PTT TP TTT PT TT 50 100 150 200 250 300 350 400 450 500 550 B00 B50 Figure 1 24 Background Spectrum m z 10 650 Check the calibration gas spectrum a Select Experiment Full Scan and scan from m z 50 to 650 b Select Instrument Calibration Gas EI NICI to turn the El Calibration Gas on c Verify that all peaks are present m z 69 131 264 414 and 502 as in Figure 1 25 Scan 161 TIC 8 2e 5 68 9 2 2e 5 100 219 0 504 99 9 131 0 169 0 264 0 502 0 AJ 352 0 ri ADAMAM AMAMMA BA MLA LL Ld ML Ld DL MM 50 100 150 200 250 300 350 400 450 500 550 600 650 413 9 0 j Figure 1 25 Calibration Gas Spectrum m z 50 650 Run a Full Automatic Tune if ions are within 12 5 or 20 m z units whichever is smaller then run a full automatic tune to calibrate the instrument User s Guide Revision B 61
99. t from any use of this manual or the information contained therein even if this information is properly followed and problems still arise This publication is not part of the Agreement of Sale between Thermo Electron Corporation and the purchaser of a GC MS system In the event of any conflict between the provisions of this document and those contained in Thermo Electron Corporation s Terms and Conditions the provisions of the Terms and Conditions shall govern System Configurations and Specifications supersede all previous information and are subject to change without notice Information in this book may refer to the continental USA exclusively Assurances and specifications might differ in other locations Specific details are available from the Thermo Electron Corporation Tech Support office However if you are unsure whom to call contact the Thermo Electron Corporation Customer Service office assigned to your area Published by Thermo Electron Corporation Technical Publications Austin Texas Contact Editor at techpubsaustin thermo com Copyright 2003 Thermo Electron Corporation All rights reserved Printed in the United States of America Important Information NOTE TRACE DSO or FOCUS DSO systems operate reliably under carefully controlled environmental conditions If you maintain a system outside the specifications listed in this guide failures of many types may occur The repair of such failures is specifically excluded
100. t the CI Reagent Gas Flow to 2 5 mL min Perform a column leak check a Run the automated Leak check on the GC b If the report indicates a leak then look for and fix leaks at all the fittings in the GC using the leak detector c Repeat this step until no leaks are indicated CAUTION Instrument Damage Do not raise the oven temperature until you are sure the system is leak free At temperatures above 100 C the column will be destroyed if exposed to oxygen 64 User s Guide Revision B TRACE DSQ or FOCUS DSQ Chapter 1 Getting Connected TRACE DSO or FOCUS DSO 1 16 Stabilizing the Instrument Set the GC Oven Temperature to 250 C Set the lon Source Temperature to 250 C Allow the Cl Reagent Gas Flow to purge Allow the lon Source and Oven to bake out overnight User s Guide Revision B 65 www thermo com Chapter 1 Getting Connected 1 17 Running El Qualification Tests TRACE DSO or FOCUS DSQ 1 17 Running EI Qualification Tests Tools Needed f e Syringe 10 uL 70 mm needle PN 365 001 03 e Test mix octafluoronaphthalene and benzophenone PN 120150 TEST Frequency JAR Beginning of Day 2 Instrument Methods are already loaded inside the computer for use in running the qualification tests These methods were used during the factory qualification tests They can be found in xcalibur Examples Methods and are organized by GC configuration Choose the El met
101. ted 1 4 Connecting the Gas Lines TRACE DSO or FOCUS DSQ a Turn on the Carrier Gas supply and set the Regulator to 5 psi 35 kPa b Purge the line for 2 min to remove air and debris Without turning off the Carrier Gas quickly remove the Inlet Cap from the Gas Filter and attach the Supply Line d Remove the Outlet Cap from the Gas Filter and attach the Supply Line e Before attaching the Supply Line to the GC purge it for 10 min f Attach the Supply Line to the Carrier Gas Input on the GC If the GC is equipped with an additional inlet you can use a Swagelok tee union to connect the Supply Line to the second Carrier Gas Input Set the Carrier Gas Regulator to 80 psi 550 kPa Upgrade Option Connect the CI Reagent Gas otherwise proceed to Step 10 Leak check all the gas lines pp 30 If the system is equipped with the chemical ionization upgrade option you must connect CI Reagent Gas Methane is the most common CI Reagent Gas Reagent Gas Regulator 10 psi 70 kPa CI Reagent Gas Input Reagent Gas Methane Isobutane or Ammonia Supply Line Figure 1 3 CI Reagent Gas Connections Back Install the Reagent Gas Regulator to the Reagent Gas Cylinder 28 User s Guide Revision B TRACE DSQ or FOCUS DSO Chapter 1 Getting Connected 1 4 Connecting the Gas Lines WARNING Personal Injury A Explosive or Corrosive Gas Hazard Cl reagent gases are often flammabl
102. the NICI auto tune file as NCI dsqtune for the Installation Qualification test User s Guide Revision B 75 www thermo com Chapter 1 Getting Connected 1 18 Running CI Qualification Tests TRACE DSO or FOCUS DSQ h Close the Tune window Perform the NCI Installation Qualification test a Inject1 uL of a1 pg uL solution of octafluoronaphthalene using the preset NCl meth instrument method b Go to Qual Browser to review the results by looking at background subtracted spectrum c Archive the chromatogram and spectrum d Use the Signal to noise Calculator accessible from a shortcut on the desktop to display a mass chromatogram for the range 271 5 272 5 The minimum S N should be 500 1 e Archive the signal to noise ratio f Repeat the octafluoronaphthalene injection 76 User s Guide Revision B Chapter 1 Getting Connected TRACE DSQ or FOCUS DSO 1 19 Installing Upgrade Options 1 19 Installing Upgrade Options i Tools Needed J Option dependent Frequency uA Installation Day 2 Once you have finished installing and testing the basic TRACE DSO or FOCUS DSO system install any additional options Upgrade options may include am Autosampler s With a TRACE GC the serial connection to the AI AS 3000 or AS 2000 should be connected to the GC With a Focus GC or other type of autosampler connect the serial connection to COM 2 on the computer Direct Sample Probe
103. tical l O Research Education O Other Job Function is Check one only O Administration O Operator I O Lab management O Other Name Title Company Address City State Postal Code l Country Telephone Ext I From Editor Technical Publications THERMO ELECTRON Corporation 2215 GRAND AVENUE PKWY AUSTIN TX 78728 3812 UNITED STATES OF AMERICA Chapter 1 Contents Important Information 3 Contact US cccccccccccccceccssnececescsneeeeescesseeeeessseeesesssaeeeeeesseeeeessseeeeeeneaas 7 REAGESE SUVEN sea iredi EEANN EO 7 Customer Registration oc ccccccccccccccceceecssteceeescseeeeeescsseeesessaeeeesetseeeeeneaas 7 Read Me 11 Where to Find More Information cccccceccsceceeesseeeeeeesseeeeeeeseeeeeseteaes 12 About Your TRACE DSO or FOCUS DSO System cecccccccectteeeeeeeteeeees 13 Sate ty IATOP MATION seas sonasdioncemesadanicessaatiesBeaddaansnien Senanideschanamiohiteneiaimae nessa 16 Typographical CONVENONS sica sincescdesbasedeantiledaimesdceaahsonpdaawaeoehiGunsbagaoneaes 18 Changes to the Manual ccccccccccscccccsseecececcsseeeeescssaeeeeescsaeeeeessneeeeeneeea 18 Getting Connected 19 1 1 Getting the Right TOONS sci acswesnanactidiuncdnsuaetaheaebaantaddiaeinncddbaaneananses 21 1 2 Verifying Site Preparation cccccccceeccecccsseseececseeeeeeeessseeesenstaeeees 23 1 3 Unpacking the Instruments 20 2 2 ccc ee ceeeeeeee ce eeeee tects teecnteeeeeeeeeeeees 24 1 4 Connecting the
104. tically display the Xcalibur Setup screen Figure B 8 If it doesn t use windows to run the XInstall exe from the CD f If some of the setup buttons are disabled it is because the required version of core for the devices has not been installed Installing the Core will enable those buttons Note that you may be required to reboot after you install the core Installation Help Xcalibur 1 4 Core Readme Xcalibur 1 4 Core Patches Readme NIST Setup GC Devices Trace DSQ Readme Acrobat Reader 5 0 Xcalibur 1 4 Manuals Screen Saver Browser Exit Figure B 8 Xcalibur Data System Setup Screen b Select the Installation Help button file to display the Instructions doc file and then send it to your printer Follow the instructions to install the data system software NOTE Click the Readme button located on the Setup Screen to read l Install any optional upgrade software You should now install any important new information optional software like libraries Follow the instructions provided with about this option these options Configure the instruments Follow the instructions listed in 2 2 Configuring Instruments for Use pp 84 User s Guide Revision B 143 www thermo com Appendix B Additional Helps B 6 Reinstalling the Data System 144 User s Guide Revision B TRACE DSQ or FOCUS DSQ Index A Accessory plug 40 Action when Softw
105. tion Data Getting Productive Creating and Searching Libraries and Getting Productive Designing and Generating Custom Reports with Merlin 3 5 Analyzing the Data Compounds With a Known Ion Pattern Using Qual Browser you can answer the question Does this sample contain compound x X being the octafluoronaphthalene OFN you used in the 3 3 Running Methods pp 102 Then we will determine the peak height area and signal to noise ratio In this example we used the Xcalibur Data l00pgEL raw file you just acquired Step 6 Make the injection and start the GC pp 3 108 which has a retention time of approximately 3 7 min In this example let s assume that you already have some knowledge of the mass spectrum of the compound of interest compound X and consequently you know the characteristic ions present in its mass spectrum For the purposes of this example m z 272 represents an ion perhaps the molecular ion of the compound and therefore this ion represents a marker for the compound Open Qual Browser a Setup the cells so you have only one cell a chromatogram You can delete other cells by pinning them and selecting Delete Grid Row zx from the toolbar b Reset the time range to the full range by selecting Zoom Reset ig from the toolbar Add a mass range chromatogram a Select the chromatogram cell and then right click your mouse to display the context sensitive menu b Choose Ranges from thi
106. tion and the amount of air in the helium supply Nitrogen is typically the most abundant contaminant in any helium supply Make sure the calibration gas has been off for at least 5 min Because the calibration gas flow module introduces air into the instrument Check the Air Water Spectrum a Open the autotune dsqtune tune file by selecting File Open autotune dsqtune Select Experiment Full Scan and scan from m z 10 to 90 Select Instrument Fil Mult Dyn On to turn the instrument on Compare the Air Water Spectrum with those in Figure 1 21 through Figure 1 23to determine whether or not you have a leak Usually if m z 28 is larger than m z 18 there is a leak refer to procedure 1 14 Leak Checking pp 59 Scan 174 TIC 1 1e 6 5 3e 5 100 18 50 28 o no ka 32 aq A 30 3 40 45 10 15 20 25 Figure 1 21 Air Water Spectrum No Leak 50 55 E0 Bo 70 75 80 85 30 User s Guide Revision B 57 www thermo com Chapter 1 Getting Connected 1 13 Checking the Air Water Spectrum TRACE DSO or FOCUS DSQ Scan 670 TIC 1 0e 8 5 9e 7 100 z 50 32 40 i i4 16 A 10 15 20 25 30 35 40 45 50 55 E0 E5 70 75 80 85 30 Figure 1 22 Air Water Spectrum Small Leak Scan 283 TIC 1 0e 9 25e 8 100 27 9 32 0 50 40 1 141 6 0 0 FITTV TTT TTT Try rir fi riry iri ryt itty trity ti itytiitytiitytiti titi iiit 10 15 20 25 30 3 40 45 50 5 60 65 70 45
107. to Download m For Help press F1 N 10 5 2003 11 51 am Figure i 2 Xcalibur 1 4 Home Page Xcalibur software provides you with Instrument Configuration after installation access to this module is outside the Xcalibur home page and located as a Windows desktop icon Use this module to configure your instruments for use with Xcalibur Instrument Setup use this module to set up instrument methods and as quick access to the Tune program for calibrating your instrument for sensitivity and mass assignments The remaining Xcalibur modules fulfill your data acquisition and data processing needs Data Acquisition store mass spectra peaks as they evolve and monitor the total ion chromatogram TIC or the intensity of a selected ion Data Processing integrate chromatograms view mass spectral data compare spectra to reference libraries quantify and qualify data and customize and automate reports About Your TRACE DSO or FOCUS DSO System The TRACE DSO or FOCUS DSQ is a powerful quadrupole mass spectrometer MS mass spectrometer with features benefiting those in the chemical science industry analysts technicians and chemists The TRACE DSO system includes the TRACE DSO mass spectrometer the TRACE GC and the Xcalibur Ver 1 4 or higher software on a computer The FOCUS DSO system includes the FOCUS DSO mass spectrometer the Focus GC the Xcalibur Ver 1 4 or higher software on a computer User s Guide R
108. to the m z 1050 If the Detected RF is not linear to the m z 1050 the mass calibration may be incorrect At this point check the mass calibration by viewing the calibration gas spectrum detailed instructions are in Step 4 Check the calibration gas spectrum pp 61 If the masses are not within 2 m z of the theoretical m z wait until the automatic tune calibration is finished to pass the RF Gain Calibration Diagnostic 54 User s Guide Revision B TRACE DSQ or FOCUS DSQ TRACE DSQ or FOCUS DSO Chapter 1 Getting Connected 1 12 Checking the RF Gain Calibration If the Detected RF shows noise or spikes shut down the instrument and check for dust or fibers on the quadrupole and prefilter or check for loose connections between the RF Coil Low Pass Filter and Quadrupoles Select the Close button to return to the Diagnostics screen Press Close to return to the Tune window Proceed to step 7 73 Checking the Air Water Spectrum pp 56 User s Guide Revision B 55 www thermo com Chapter 1 Getting Connected 1 13 Checking the Air Water Spectrum 1 13 Checking the Air Water Spectrum Tools Needed A None sats Frequency Day 1 After successfully completing the RF Gain Calibration test it s a good time to check the air water spectrum to look for leaks In the Tune window select the Vacuum tab from the Status display A autotune dsqtune Trace DSQ Tune File View Instrument Expe
109. trument Status in the Status tab of the Info View All instruments should report Ready to Download If not 90 User s Guide Revision B TRACE DSQ or FOCUS DSQ TRACE DSQ or FOCUS DSO Chapter 2 Getting Started 2 2 Configuring Instruments for Use NOTE The MS may take up to 1 min to initialize consult the troubleshooting section of the instrument s appropriate manual Okay if you re ready to run your first sample go to Chapter 3 Running Your 15t Sample pp 93 User s Guide Revision B 91 www thermo com Chapter 2 Getting Started 2 2 Configuring Instruments for Use 92 User s Guide Revision B TRACE DSQ or FOCUS DSQ Running Your 1 Sample In This Chapter 3 1 Calibrating and Tuning the Instrument pp 95 3 2 Setting Up Methods pp 98 3 3 Running Methods pp 102 3 4 Analyzing the Data Compounds With a Known Retention Time pp 109 3 5 Analyzing the Data Compounds With a Known lon Pattern pp 119 3 6 Analyzing the Data Peak Height and Area pp 122 3 7 Analyzing the Data Signal to Noise Ratio pp 124 Analyze Detect Measure Control User s Guide Revision B 93 www thermo com Chapter 3 Running Your 15 Sample TRACE DSQ or FOCUS DSQ After your instruments are configured for use with Xcalibur you re ready to run your first sample In just three easy steps you ll be running your first sample using octafluoronaphthalene which comes with your
110. ts for both the TRACE DSQ or FOCUS DSO preinstallation and the field service installation Do not write on the copies presented in this chapter Rather make duplicate copies whenever you need a checklist or report Analyze Detect Measure Control User s Guide Revision B 129 www thermo com Appendix A Preinstallation Checklists A 1 Preinstallation Checklist TRACE DSQ or FOCUS DSQ A 1 Preinstallation Checklist The customer should have met all the requirements listed on this checklist prior to your arrival Ask the customer to give you their copy of the Preinstallation Checklist and check each item Detailed information matching the items on this checklist are in your Preinstallation Guide Preinstallation Guides are given to the customer by the sales person taking the order _j 1 Entrance Requirements delivery doors are at least 102 cm 40 in wide 2 Workbench Space Weight and Stability Requirements workbench is at least 2 m 6 ft across supports a 119 kg 262 Ib load and is sturdy and free from vibration _j 3 Lighting Requirements work area is properly lit l 4 Power Requirements acceptable power source available and nearby l 5 Wall Outlets amp Voltage Requirements wall outlets meet system voltage current specifications 6 Environment Requirements LI 1 a Temperature room temperature is 15 31 C 59 88 F _ b Humidity relative humidity is between 40 and 80 w
111. ty unless i Seller is promptly notified in writing by Buyer upon discovery of the failure of any products to conform to this warranty ii when possible such product is returned to Seller with Seller s written approval transportation charges prepaid by Buyer iii such product is received by Seller not more than ten 10 days after the last day of the applicable warranty period iv Seller s examination of such product shall disclose to Seller s reasonable satisfaction that such defects or failures have not been caused by misuse neglect improper installation by Buyer repair alteration or accident including but not limited to failure of electric power excessive or erratic power failure of environmental control equipment as defined in Seller s published specifications failure of Buyer s self maintenance program or failure of Buyer to maintain product in accordance with Seller s manual or instructions All claims under warranty must be made promptly after occurrence of circumstances giving rise thereto and must be received within the applicable warranty period by Seller or its factory trained representative Such claims should include the product type and serial numbers and a full description of the circumstances giving rise to the claim At it discretion Seller may authorize the prepaid return to Seller s plant or designated repair center of products or parts that prove to be defective or Seller may repair or replace at
112. ual Browser View the mass spectrum for a specific chromatogram retention time Currently a selected chromatogram time period is displayed in one cell and a mass spectrum in another cell This step describes how to select a particular retention time on the chromatogram and view the corresponding mass spectrum a Locate the pin icon shown in the top right corner of the mass spectrum cell and click on it The icon changes from unpinned lt to pinned eo b Move the cursor over the chromatogram until it is positioned at the retention time you are interested in and click on it to view the mass spectrum for the desired retention time User s Guide Revision B 115 www thermo com Chapter 3 Running Your 1 Sample 3 4 Analyzing the Data Compounds With a Known Retention Time TRACE DSO or FOCUS DSQ Subtract the Background Contamination from the spectrum Peaks eluting from a GC column can contain low levels of contamination due to material bleeding from the matrix of the column This material will have its own mass spectrum that will be superimposed on that of the sample compound The mass spectrum of a chromatogram peak can therefore be made up of mass peaks resulting from the sample compound plus mass peaks resulting from background contamination Therefore to obtain a mass spectrum for the compound alone that can be used in a library search subtract the mass spectrum of the background contamination a Make sure that th
113. uration icon co from the Instrument Windows desktop configuration Configure the mass spectrometer MS NOTE Select the Help button to use the online help for more detailed a Double click the TRACE DSQ icon located in the Available instructions Devices column to move it to the Configured Devices panel Select the TRACE DSO even if you have a FOCUS DSO Instrument Configuration Device Types MS x Available Devices Configured Devices TRACE DSO TRACE DSQ Add gt gt lt lt Remove Configure Figure 2 1 MS Instrument Configuration b Double click the TRACE DSQ icon from in the Configured Devices panel or click the Configure button to display the Instrument Configuration screen Cc Use the tabs on the Instrument Configuration screen to select options to display on the Instrument Setup and Tune windows 84 User s Guide Revision B TRACE DSQ or FOCUS DSQ Chapter 2 Getting Started 2 2 Configuring Instruments for Use d Configure General tab options Instrument Configuration General Ja gas PPINICI Source Saver Service I Remote start active high I Demonstration mode Pressure units Ton z Tune path E Xcalibur System dsq tune Browse Figure 2 2 Instrument Configuration General e The default setting for Remote Start Active High is unchecked This starts the GC with an active high signal instead of active low
114. ut 100 mm 4 in of the Column 4 with a tissue Column and Injector soaked in methanol Ferrule c Insert the Column 4 through the Injector Nut 3 and Ferrule 2 open end up d Wipe the Column 4 again with a tissue soaked in methanol User s Guide Revision B 35 www thermo com Chapter 1 Getting Connected 1 6 Installing the Gas Chromatograph TRACE DSQ or FOCUS DSO e Score and then break the Column 4 about 2 5 cm 1 in from the end with a Scoring Wafer With the magnifying glass check for an even flat cut Repeat if necessary f Insert the Column 4 into the Injector 1 so that the end of NOTE Sliding a Septum the Column 4 is the proper distance from the back of the on the Column before the Injector Nut 3 Proper distances are as follows splitless Injector Nut will help you 64 mm split 40 mm PTV 30 mm measure the proper distance between the Nut and the end of the Column If you want to remove it later cut the Septum from the center to the edge g Fingertighten the Injector Nut 3 and then give it an additional 1 4 turn with the wrench h Score and then break the Column Outlet 5 about 2 5 cm 1 in from the end with a Scoring Wafer i Turn on the GC Setup the GC a Set the Oven Injector and Transfer Line temperatures to 30 C b Set the Injector flow to 1 0 mL min Turn the Vacuum Compensation Off under the Right or Left Carrier menu d Dip the Colum
115. ww thermo com Chapter 1 Getting Connected 1 7 Installing the Mass Spectrometer TRACE DSQ or FOCUS DSQ d Re tighten the Transfer Line Nut 2 and the Transfer Line Union 3 Setup the GC a Make sure the Column does not have any sharp bends and that it does not touch any metal objects or walls inside the Oven b Raise the Oven temperature to 40 C Cc Turn the Vacuum Compensation On under the Right or Left Carrier menu Replace the covers to the MS in this order left top and front Plug the power cord for the Mass Spectrometer into Wall Outlet 1 Data System Rotary Vane Figure 1 12 Mass Spectrometer Power Connection Back Double check all vacuum gas and electrical connections 44 User s Guide Revision B Chapter 1 Getting Connected TRACE DSO or FOCUS DSO 1 8 Starting Up the System 1 8 Starting Up the System f Tools Needed None SARS Frequency Day 1 Turn the Mass Spectrometer on by setting the Main Circuit Breaker to ON I to e Turn on the Rotary Vane Pump e Allow the Fore pressure to reach the proper operating pressure e Turn on the Turbomolecular Pump CAUTION Instrument Damage Damage occurs if you turn on the mass spectrometer without column flow This forces air to be drawn through the column damaging it This large air leak into the mass spectrometer will also cause the ion source to require cleaning Set the Transfer Line to 25
116. y 2 Morning _ Repeat steps 1 8 to 1 14 Afternoon Step 1 17 Run an El Qualification Test Step 1 18 Run a Cl Qualification Test Step 1 19 Install Upgrade Options L L Step 1 20 Provide basic training User s Guide Revision B 131 www thermo com Appendix A Preinstallation Checklists A 2 Installation Checklist 132 User s Guide Revision B TRACE DSQ or FOCUS DSQ Appendix B Additional Helps In This Chapter B 1 Assembling Swagelok Fittings pp 134 B 2 Using a Swagelok Tee or Cross pp 137 B 3 Adjusting the RF Null pp 138 B 5 Adjusting the RF Dip Calibration pp 142 B 6 Reinstalling the Data System pp 143 Analyze Detect Measure Control User s Guide Revision B 133 www thermo com Appendix B Additional Helps B 1 Assembling Swagelok Fittings TRACE DSO or FOCUS DSQ B 1 Assembling Swagelok Fittings Tools Needed L e Swagelok Fitting e Wrench set open end 5 16 in 7 16 in 1 2 in 9 16 in Frequency JAR Fixing leaks Building Swagelok compression fittings and connecting tees and crossings are essential to a leak free system A Swagelok Fitting is a compression fitting that has four components a Swagelok Nut a Back Ferrule a Front Ferrule and an Inlet The completed assembly is comprised of five pieces when the Swagelok Ferrule and Nut assembly is affixed to Tubing Two ferrules merge when the nut is tightened

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