PerkinElmer TORION T-9 User Manual Download Page 8

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4 . Torion T-9 User’s Guide

Peak Details .............................................................................................. 206

Library Search ................................................................................................ 208

NIST .............................................................................................................. 209

Mass Spectrometer .............................................................................................. 212

Mass Spectrometer Mini Toolbar ................................................................. 212

MS Parameters Tab ........................................................................................ 214

MS Calibrations Tab ........................................................................................ 216

File Manager ....................................................................................................... 217

File Manager Mini Toolbar .......................................................................... 217

Computer Section – Right click functionality ................................................ 218

SD Card Section – Right click functionality ................................................... 220

Supported File Types ................................................................................. 222

Library Editor ...................................................................................................... 223

Library Editor Mini Toolbar ......................................................................... 224

Real Time Plots ................................................................................................... 231

Real Time Plots Mini Toolbar ...................................................................... 231

TIC Graph Tab .......................................................................................... 232

Spectra Graph Tab ..................................................................................... 233

Data Logger Tab........................................................................................ 233

Logging..................................................................................................... 234

Edit Data Logger Item List ......................................................................... 234

Clear Chart ................................................................................................ 236

Desorption .......................................................................................................... 237

Desorption Mini Toolbar ............................................................................. 238

Log Data Tab ............................................................................................ 240

Batch Processing ................................................................................................. 242

Batch Processing Mini Toolbar .................................................................... 242

Reports .............................................................................................................. 244

Reports Mini Toolbar ...................................................................................... 244

Creating a Report ........................................................................................... 244

Header Information ................................................................................... 246

Report Data .............................................................................................. 246

TightVNC Viewer ................................................................................................. 251

NIST .................................................................................................................. 252

Advanced Operations ....................................................................................... 253

Loading Operational Settings when Running an Analysis ........................................ 254

Reset and Restart Buttons on the Instrument ................................................... 254

Deleting Sample Data from the SD Card .......................................................... 255

Maintenance .................................................................................................... 257

GC Injection Port Maintenance ............................................................................. 258

Accessing the GC Injection Port ....................................................................... 258

Septum Replacement ...................................................................................... 258

Injection Liner and Seal Cleaning or Replacement ............................................ 259

How to “Bake Out” the GC Injection Port and Column ........................................... 260

Changing the Battery ........................................................................................... 261

Changing the Carrier Gas Cartridge ...................................................................... 262

Removing/Replacing the SD Card ......................................................................... 263

Troubleshooting ............................................................................................... 265

Troubleshooting Guide......................................................................................... 266

Torion T-9 GC/MS will not turn on ................................................................... 266

Torion T-9 GC/MS will not turn off ................................................................... 266

Torion T-9 GC/MS cannot maintain vacuum ..................................................... 266

GC baseline is noisy, or drifts upward .............................................................. 266

Summary of Contents for TORION T-9

Page 1: ...TORION T 9 Gas Chromatograph Mass Spectrometer GC MS User s Guide GC MS...

Page 2: ...ith regard to this document including but not limited to the implied warranties of merchantability and fitness for a particular purpose PerkinElmer shall not be liable for errors contained herein for...

Page 3: ...cil Directive 2006 42 EC May 17 2006 on the Approximation of the Laws of the Member States Relating to Machinery Council Directive 2004 108 EC December 15 2004 on Electromagnetic Compatibility Standar...

Page 4: ...iv Torion T 9 User s Guide...

Page 5: ...s for PerkinElmer Products 25 Decontamination 26 Cleaning the Instrument 26 3 System Overview 27 What is solid phase microextraction SPME 28 What is the Torion T 9 GC MS 29 About the Power Supply and...

Page 6: ...93 Mass Spectrometry Tab 93 Versions Tab 94 Status Tab 94 Edit Tab 95 Current Problems Tab 98 Performance Validation 98 Manage Files 99 Methods 100 System Settings 103 Setting the Date and Time 103 Pa...

Page 7: ...s List 157 Deconvolution Parameters Tab Target Library Editor 162 Deconvolution Parameters Mini Toolbar 162 Target List Search 163 Unknown Identification 164 Unknown Libraries 165 Quant Overrides Tab...

Page 8: ...cessing Mini Toolbar 242 Reports 244 Reports Mini Toolbar 244 Creating a Report 244 Header Information 246 Report Data 246 TightVNC Viewer 251 NIST 252 7 Advanced Operations 253 Loading Operational Se...

Page 9: ...instrument signal 270 Acquired mass spectra are not correct 270 SPME fiber came off inside the GC inlet 271 Torion T 9 GC MS fails to identify a compound 271 Torion T 9 GC MS falsely identified a comp...

Page 10: ...6 Torion T 9 User s Guide...

Page 11: ...1 Introduction...

Page 12: ...into the Torion T 9 GC MS After injecting a sample into the Torion T 9 GC MS it is separated into its chemical components Resolved components are characterized by retention time from the gas chromato...

Page 13: ...adros ste se proporciona informaci n sobre este tipo de circunstancias F Caution Attention Nous utilisons le terme CAUTION ATTENTION pour signaler les situations susceptibles de provoquer de graves d...

Page 14: ...En los recuadros como ste se proporciona informaci n sobre este tipo de circunstancias F Warning Danger Nous utilisons la formule WARNING DANGER pour avertir des situations pouvant occasionner des do...

Page 15: ...2 Safety Practices...

Page 16: ...should be practiced Ultimately maintenance of a safe laboratory environment is the responsibility of the analyst and the analyst s organization Please consult all manuals supplied with the T 9 and ac...

Page 17: ...ustments replacements or repairs to this instrument except as described in the accompanying user documentation N essayez pas de faire des ajustements des remplacements ou des r parations cet instrumen...

Page 18: ...hat the side and top covers are closed If the instrument is being used in an area where there is the potential for exposure to chemical vapors make sure all of the covers are in place If the instrumen...

Page 19: ...g of any biohazardous materials and minimizing any biohazards before the equipment is removed from use transported or processed for disposal Le responsable du laboratoire est responsable de l liminati...

Page 20: ...perature 5 C to 45 C 41 F to 113 F Relative humidity 20 to 80 without condensation If possible avoid any adjustment maintenance and repair of the opened operating instrument If any adjustment maintena...

Page 21: ...nstrument est utilis d une mani re non sp cifi e ici la protection fournie par l instrument peut tre alt r e The instrument has been designed to be safe under the following conditions Safe operating t...

Page 22: ...e est interdite WARNING AVERTISSEMENT Grounding circuit continuity is vital for safe operation of the instrument Never operate the equipment with the grounding conductor disconnected La continuit du c...

Page 23: ...e correct cord Ne pas d brancher ou vaincre le sol de s curit sur le cordon d alimentation Le sol est n cessaire pour un fonctionnement s r de l instrument et le bon fonctionnement des circuits lectro...

Page 24: ...20 Torion T 9 User s Guide...

Page 25: ...e 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 frequ...

Page 26: ...re on the instrument Hot surface by injection port Emergency power off emergency reset SD card slot USB port and LAN port Located under the cover on top of the instrument Label on door cover located o...

Page 27: ...Warning Labels 23 Carrier gas vent helium inlet power connection and minim USB port located on back of instrument Product Label located on bottom of instrument...

Page 28: ...ates the ON position of the main power switch Indicates the protective conductor terminal Caution Risk of danger Documentation must be consulted to determine the nature of the potential hazard and any...

Page 29: ...e recycling and recovery programs vary by regulatory authority at your location Contact your local responsible body for example your laboratory manager or authorized representative for information reg...

Page 30: ...on Procedure and complete the Certificate of Decontamination These documents are available on the PerkinElmer public website http www perkinelmer com Content technicalinfo dts_instrumentdeconprocedure...

Page 31: ...3 System Overview...

Page 32: ...temperature and the volume of both the polymeric phase and the solvent Extraction can take under a minute depending on sample volume and concentration Equilibration of the fiber with its surrounding m...

Page 33: ...retention time to a library of retention times and mass spectra of known chemicals and indicates whether or not any of the target chemicals in the library are present in the sample In addition to kno...

Page 34: ...e on just simply plugged into line power The following image shows the battery indicator lights on the Torion T 9 GC MS If the top indicator light is lit the Torion T 9 GC MS is connected to line powe...

Page 35: ...designed for the Torion T 9 GC MS is called the Custodion The Custodion triggers the injection and analysis to start on the Torion T 9 GC MS without having to push a start analysis button The SPME syr...

Page 36: ...ical in the sample A chemical that is volatile within the temperature range of the GC method parameters will eventually exit the column assuming the compound is not irreversibly adsorbed to the capill...

Page 37: ...that rely on only a small amount of resolution and mass spectral finger print recognition can provide a way of identifying and quantifying analytes that co elute Low thermal mass LTM GC refers to a mi...

Page 38: ...n of the chemicals in the sample and the electrons in the electron beam creates charged fragments The ionized chemical fragments are separated by a mass analyzer before they are registered by the dete...

Page 39: ...ever few are available as portable instruments due to overall size and power requirements The latest advancement in miniaturization of mass spectrometers is the miniaturized TMS The miniaturized TMS r...

Page 40: ...36 Torion T 9 User s Guide...

Page 41: ...4 Basic Custodion Operations...

Page 42: ...ion syringe into the injection port of the Torion T 9 GC MS or other GC heated to at least 250 C 2 Depress the plunger to extend the SPME fiber and allow the fiber to desorb contaminants for 30 60 sec...

Page 43: ...ectrice avant de la percer travers le septum du flacon d chantillon CAUTION ATTENTION Be careful not to bend the flexible SPME needle when piercing the septum Veillez ne pas plier l aiguille SPACE fle...

Page 44: ...ample into a sample vial Add sufficient volume of liquid to completely immerse the SPME fiber when it is fully extended from the Custodion syringe needle 2 Cap the vial with a septum cap 3 Insert the...

Page 45: ...the SPME fiber out of the Custodion syringe needle and shake off residual sample droplets that may have been taken up in the syringe needle during sampling Sample Solids Always perform vapor headspace...

Page 46: ...or port Use a syringe to take the headspace and deliver it into another vial Take headspace of the transferred headspace Allow sample on S PME to evaporate before injection do this by exposing the S P...

Page 47: ...ke headspace with shorter exposure time R educe the time of exposure in injector port Use a syringe to take the headspace and deliver it into another vial Take headspace of the transferred headspace A...

Page 48: ...r until you hear or feel a click and then release the plunger Similar to using a ball point pen The following image shows a cutaway diagram of the SPME inside the GC injector port 3 Follow the on scre...

Page 49: ...5 Basic Operation...

Page 50: ...connected directly to the instrument The functionality of the touch screen is the same as for a mouse Touching the screen will select a button and activate the commands associated with the button Usi...

Page 51: ...al power from 100 250 volts 50 60 Hz AC The following figure shows the power supply connected to the back of the instrument 3 Connect the lab helium to the external helium port located at the rear of...

Page 52: ...onnection and 2 Helium external port CAUTION ATTENTION Prior to the next step regulate the external gas pressure to a minimum of 80 psi Avant l tape suivante r glez la pression de gaz externe un minim...

Page 53: ...t will enter the pump down state automatically Once a vacuum is established then the instrument will initialize the heated zones to the method set points The following screen shows the instrument scre...

Page 54: ...name in the status bar In this example the sample type is Sample 1 To view the status of the power helium and instrument touch any of the icons in the top right corner of the screen once with the sty...

Page 55: ...certain that the SPME fiber is retracted into the Custodion syringe needle before inserting the needle into the injection port Assurez vous que la fibre SPME est r tract e dans l aiguille de la serin...

Page 56: ...SPME syringe does not come in contact with the GC Injection Port Contacts 4 Follow the on screen instructions Immediately depress the plunger until you hear or feel a click then release the plunger W...

Page 57: ...so cause a helium leakage Assurez vous que la fibre SPME est compl tement retir e l int rieur de l aiguille de la seringue avant de retirer la Custodion du port de l injecteur Le non respect de cette...

Page 58: ...tification The name of the compound Alert The compound type of hazard level which is created in Chromion Match The statistical confidence of the assignment based on the parameters in the compound agen...

Page 59: ...l appear and the Start Run button will be gray while the column temperature is returning to the initial temperature setting in preparation for the next analysis 9 To run another sample press the Start...

Page 60: ...background subtraction by the Torion T 9 GC MS However the chromatographic and mass spectrometric data from a blank run may help identify contamination in the instrument or on the SPME fiber SPME Blan...

Page 61: ...e by entering text 2 Press the Start Run button The system will start to perform a blank run automatically During the run a screen similar to the following the will be displayed 3 After a run if there...

Page 62: ...e X axis If additional peaks are observed in the chromatogram and do not go away after 7 system blanks contact PerkinElmer Above is an image of a successful chromatogram of a System Blank run without...

Page 63: ...reen an actual System Blank was run but there were contaminant peaks The peaks were either identified or listed as unknown compounds by the library 4 Tapping the stylus on the X axis opens a pop up op...

Page 64: ...so before taking a Sample of an unknown substance NOTE For cleaning new SPME fibers refer to Prepare the Custodion SPME Syringe for Sampling on page 38 in Chapter 4 Basic Custodion Operations To confi...

Page 65: ...Custodion avant d ins rer l aiguille dans l orifice d injection Assurez vous que le visage de la seringue Custodion contacte compl tement les points de contact d s que la seringue est ins r e Assurez...

Page 66: ...splayed in the report a second blank analysis should be performed If there are still peaks after several injections and the system blank was clean then try using a new SPME fiber To thoroughly clean t...

Page 67: ...Compound identification GC retention time 1 Verify appropriate System and SPME blanks have been performed See the System Blank and SPME Blank sections of this chapter 2 On the home screen open the dr...

Page 68: ...es that can be used on the instrument SPME Liquid Inject Needle Trap The injection type on the Start Run button of the instrument can be changed using the Chromion software in the Gas Chromatograph wi...

Page 69: ...tact points 1 SPME syringe gold rings 2 GC injection port contacts NOTE It is important to be sure the plunger is not depressed until the SPME syringe is fully inserted However the time between the in...

Page 70: ...Validation PV runs 10 If the result is a PASS the following screen displays You can return to the home screen 11 If the result displays a FAIL as shown in the below screen re run the Performance Valid...

Page 71: ...minimum requirements for validating the performance of the instrument some routine maintenance may be required 13 To view and export the report press View Details then View Report 14 If you have not...

Page 72: ...data to a USB drive press the Export button 17 Insert a USB drive into the slot under the Utility Cover Press Export Files A window displays with the SD card file structure on the instrument 18 Select...

Page 73: ...ethod are used automatically Occasionally users may see samples with very low concentrations to very high concentrations where the split flow should change but the method does not need to be changed I...

Page 74: ...en 10 SVOC Low Concentration_Open 10 High Concentration_Closed 30 VOC Low Concentration_Closed 30 SVOC Low Concentration_Closed 30 Split 10 to 1 High Concentration_Open 0 VOC Low Concentration_Open 2...

Page 75: ...a File Name field to open the on screen keyboard and enter the changes NOTE An external keyboard may also be plugged into Torion T 9 GC MS s USB port for entering sample names 2 Choose Start Run to be...

Page 76: ...injection port The instrument will NOT start an analysis if the Custodion syringe does not come in contact with these contact points The following figure shows 1 SPME syringe gold rings 2 GC injectio...

Page 77: ...E syringe CAUTION ATTENTION Be sure the SPME fiber has been retracted into the syringe needle before removing the needle from the injection port Assurez vous que la fibre SPME a t r tract e dans l aig...

Page 78: ...st what is setup in the method to ensure enough peaks are displayed e The Stop Run button stops the analysis and the screen changes to an intermediate screen The intermediate screen is shown at the en...

Page 79: ...been defined in the Chromion software Red alerts indicate levels set above 50 and Yellow indicates levels below 50 Refer to the Analyzing a Sample section in this chapter for a detailed description of...

Page 80: ...d alert is identified with hazard levels 50 to 100 These user defined levels could be considered critical or life threatening An orange alert is identified with hazard levels 49 and below These levels...

Page 81: ...ws the spectra of the compound peak selected in the image 2 Clicking Split View displays the spectra of the selected scan in the lower pane 3 Click and drag the cursor to form a square around the peak...

Page 82: ...e spectra plot can now be viewed more clearly using the zoom functionality The following image shows the zoom functionality being used in the chromatogram section of the run results 4 Clicking on the...

Page 83: ...ng in on either the TIC plot or the spectra plot tap the bottom axis area of the plot with the stylus A popup box displays with the option to Zoom Normal or Zoom Out Zoom Normal restores the full view...

Page 84: ...ditional functions 8 Details When clicking Details for the selected compound in the results list information will be retrieved from the NIOSH database which is located on the SD card The image below i...

Page 85: ...ort Wireless Used to export a report containing the analysis report using the wireless modem to a remote PC that is equipped with a wireless modem View Report Displays the report in text view Switch V...

Page 86: ...GC MS More extensive libraries can be accessed for comparison when using the PC application software You may also add chemicals into the Torion T 9 GC MS library Viewing the Results on the Torion T 9...

Page 87: ...d folder A list of all the data files within the chosen folder will be displayed 3 Touch the data file to be viewed from the list You can move through the Results list by either using the arrows and s...

Page 88: ...ew button to view on the instrument the results of the data file The following screen is displayed while the instrument loads the data file After the data file has been loaded into the window the prev...

Page 89: ...elect a method that has been set up for quantitative analysis in the Chromion software 3 Press Activate 4 A screen prompt suggests you run a system blank select Yes or No The Home screen displays the...

Page 90: ...le collection of 1 0 L of air but you were only able to collect 0 5 L you would enter a multiplier of 2 00 1 0 L 0 5 L 6 Press the Start Run button and follow the on screen prompts The next screen sho...

Page 91: ...button and then select a file for exporting 2 Click the Export button A list from which to export the file now displays two additional files besides the RES file The report or TXT file and the CDF fi...

Page 92: ...igate to and highlight the location where the data files are to be exported 4 Click OK to export the data files When the data files have successfully been exported the following screen will be display...

Page 93: ...nformation cdf file and report file txt includes the summary of the Analysis report Export Report Wireless Used to export a report containing the Analysis Report Summary using the wireless modem to a...

Page 94: ...can be created for the Torion T 9 GC MS software Locked A locked Procedure forces you to perform operations such as running a System Blank or Performance Validation in the exact order programmed into...

Page 95: ...GC MS software excepting those that require a password 4 Pressing the View button allows you to view the contents of a Procedure If there is interest in creating proprietary custom Procedures based on...

Page 96: ...rrent Default Procedure Thus the prefix for the automatically generated Sample name changed to activated when this operation is used 5 Pressing Previous Results allows viewing of previously collected...

Page 97: ...us Edit and Current Problems Gas Chromatography Tab This tab shows the actual temperatures and pressures of the various components of the GC It also shows the Split Splitless Settings for the currentl...

Page 98: ...build numbers of software can be viewed This information is helpful when determining the correct control software has been activated on the instrument Status Tab This screen shows the percent of Batte...

Page 99: ...the mouse when using VNC a screen will open in which to enter the password which is required to make a change 4 Enter the password and then click Continue Contact a PerkinElmer Service Representative...

Page 100: ...e effect immediately even in the middle of a run and should only be adjusted by experienced users Ces changements entrent en vigueur imm diatement m me au milieu d une course et ne devraient tre ajust...

Page 101: ...ption will shutdown the pumps and the heaters After the pumps have completely stopped and the heat has reached an acceptable level the instrument will power off This process could take 5 minutes or mo...

Page 102: ...reported by a Warning or Error message that was displayed during operation of the instrument Performance Validation Pressing this button will start a Performance Validation run on the instrument Foll...

Page 103: ...lder is the SD card on the instrument in which all the data files are stored 3 Click the expand icon next to the Data folder These folders are auto created each day by the system and contain data file...

Page 104: ...ome button will return the display to the home screen Methods From the Methods screen users can select a method to activate or simply view the method parameters in a selected method To choose a method...

Page 105: ...the instrument for all runs until changed to a different method 4 Press the View button with a method selected to open a window that shows specific settings in the method Injection Parameters This scr...

Page 106: ...reen displays the name of the library that is part of the selected method Click on the Activate button to load the selected method which will be used by the instrument for future runs Click on the Bac...

Page 107: ...st any of the values in the Date Time field select the value to be changed and either use the left right arrows at the end of the field using the stylus or if connected by VNC use the keyboard to make...

Page 108: ...the New Password and then Confirm New Password by entering the new password again 4 Press Change Password A confirmation dialog displays notifying the user that the password was changed Network Connec...

Page 109: ...ough a network or through a direct connection to a PC If the Torion T 9 GC MS is going to be connected through a network the instrument can be set to either get its IP address from the network using t...

Page 110: ...desired IP address and Subnet Mask Use an IP address and Subnet Mask assigned by the network administrator or us a private IP address that matches the Chromion computer 192 168 x x is a typical priva...

Page 111: ...ours after the last button input was pressed CAUTION ATTENTION Setting the value to zero will disable the automatic shutdow n function of the T 9 This should only be used for troubleshooting and servi...

Page 112: ...e Shutdown cycle if needed NOTE The Vent Cartridge feature will empty most of the helium from the cartridge Perform this operation only if you need to remove the helium cartridge after the system is s...

Page 113: ...ome screen will display when the system is ready to run samples again Exiting the Software The second shutdown process is used to exit the current software that is being used in order to access additi...

Page 114: ...ch the system password must be entered Contact a PerkinElmer Service Representative for the T 9 password Using the stylus tap in the letters numbers in the Enter Password field and press Continue 5 Th...

Page 115: ...will be the same process as the first procedures discussed in this section Exit Now This option will exit the current GUI application and return the user to the desktop From here the user can access...

Page 116: ...112 Torion T 9 User s Guide...

Page 117: ...6 Software...

Page 118: ...mpound identification interface deconvolution unknown identification and creation of methods for use on the instrument The Chromion software is also used to view and work with chromatographic and mass...

Page 119: ...the Torion T 9 instrument To make them compatible open a method in Chromion and then open Performance Validation Unlock the form by entering the password Click the mini toolbar icon Reset Performance...

Page 120: ...vigate within Chromion The main functionality is accessible from the navigation pane on the left side of the window In addition to the navigation pane there are other functions available from the foll...

Page 121: ...vigation pane can be easily hidden and unhidden by clicking on the horizontal expand collapse arrows located in the orange bar at the top of the pane Many of the items in the Navigation pane will open...

Page 122: ...cking on the vertical expand collapse arrows located to the right of the Hardware category All of the instruments on the network will be visible in the Hardware section of the main window 2 To connect...

Page 123: ...on the instrument and will stay associated with the particular instrument until it is changed More Info displays various information about the selected instrument as in the image below a Instrument n...

Page 124: ...renamed by selecting the option Rename Instrument The message below is displayed when an attempt is made to connect to an instrument that is already connected to a different computer Chromion will onl...

Page 125: ...nstrument 4 By moving the cursor over the green icon a name will appear Add Instrument By clicking on the icon a dialog will be displayed in which the instrument name and IP address can be entered 5 C...

Page 126: ...7 When a static instrument is no longer required it can be deleted from the Instrument Setup dialog To open the dialog right click below the instrument names in the Hardware section 8 Select the instr...

Page 127: ...e done by using the Instrument Setup window for Static Instruments which is accessible from right clicking in the instruments blank space underneath the instruments list in Hardware A name change to a...

Page 128: ...rt of the software Not all netCDF files will open in Chromion RAW data file This is a Torion file that contains the unfiltered data from the instrument It can be useful for troubleshooting instrument...

Page 129: ...d Data Review deconvolution results A user can indicate the number of decimal places to display by changing the numeric value in the Decimal Display tab of Preferences The default setting is 3 decimal...

Page 130: ...tallest mass peak The Selected Ions option is a toggle between Summed default and Average of Summed for a selected range of scans in the TIC graph with the results appearing in the Summed graph of Dat...

Page 131: ...e selected mass in Mass Spectrometer When the Manual Peak Labeling option is enabled the retention time will appear along with the manual label added to a peak in the TIC graph With this option disabl...

Page 132: ...nown compound to user preference There are four display options available for the known and unknown compounds Do Not Display Peak labelling for the compounds in the TIC graph will not be automatic but...

Page 133: ...once data collection in the Real Time Plots window has been started it will continue to collect data until you stop the collection Collection of data from the instrument requires processing resources...

Page 134: ...an be used to tune the instrument using Chromion The Data folders store the files generated from the blank and sample runs on the instrument These files can be opened by Chromion in order to view the...

Page 135: ...vertent deletion of necessary files Notice in the image above the folder highlighted in blue The contents of the folder are displayed in the lower right quadrant Within this folder there are different...

Page 136: ...isplayed indicating that File Manager must first be closed and then reopened for the changes to take effect The second option in Preferences for File Manager is Display only results RES files When thi...

Page 137: ...ch Path When the system has located the latest NIST files an Update message will be displayed If by chance a NIST library cannot be located on the computer a different type of message will be displaye...

Page 138: ...netCDF file When enabling this report the generated results will show the Internal Standard in the target list that was not found in the netCDF of the RES file when running deconvolution as well as t...

Page 139: ...displayed on the Target List is the information contained in the Hazard Level Text column NOTE Any modification made to the Hazard Level List will result in the removal of the Hazard Level from the co...

Page 140: ...from the target list However if Target Library Editor is closed and when the Data Review window is active the available options will change relative to functionality used in Data Review Overlay Files...

Page 141: ...ment avec d importantes fonctions d instrument Veillez faire preuve de prudence lors de la modification de ces param tres op rationnels car des ajustements inappropri s entra neront une mauvaise perfo...

Page 142: ...y have been made to the current method Save As This option opens a dialog box that allows a new name to be given to the currently loaded method Rename This option opens a dialog box that allows you to...

Page 143: ...ave been loaded For Performance Validation to work correctly it may be necessary to adjust the mass and or the retention time calibration windows Click OK to dismiss the window 5 If the response is No...

Page 144: ...Load Delete option opens the method list The following image shows the method list These methods are in the database which means they have been previously loaded into the Chromion software and are ava...

Page 145: ...on the Import Method icon in the method toolbar the Import Method dialog will open The Import Method option opens the following dialog box This dialog box allows you to import a method into Chromion f...

Page 146: ...the Remote Files window Saving a Method The Save option allows for changes made to any of the three forms specific to a method Gas Chromatograph Target List Editor and Performance Validation using the...

Page 147: ...he browser s File name field The method name can be changed or exported with the current method name Upon selection of the location click Save which will close the browser window and save the method T...

Page 148: ...eed to select the option When selecting to send the unknown libraries additional time may be required The following dialog box opens to confirm that the method was successfully sent and activated If t...

Page 149: ...commands to enter Clicking on About from the Help menu displays the dialog CHROMION About with version numbers of software that is being run on Chromion and on the instrument Software version This is...

Page 150: ...omion Many of the parameters interact directly with important instrument functions NOTE Caution should be used when changing these operational parameters as making inappropriate adjustments will resul...

Page 151: ...ws for exporting of current GC parameters to a file so they can be imported into a different method This option is available for both tabs Refresh Auto Calibration Data Clicking on this icon will enab...

Page 152: ...temperature of the GC column The minimum starting temperature is 5 C In addition to the control limit the temperature is also limited by ambient conditions In order for the instrument to work well th...

Page 153: ...values open NOTE To introduce more sample into the GC column the valves should both be closed for 1 to 2 seconds To do this you would set the Split On time to 2 seconds telling the instrument to turn...

Page 154: ...eping the retention times more consistent The countdown time is activated when the start run button on the T 9 is pressed The timer counts down for 10 seconds and then the T 9 starts to run that analy...

Page 155: ...using similar columns but different oven programs One of the most common indexes is the Kovats index All straight chain hydrocarbon molecules are assigned an index value of 100 per carbon So a molecu...

Page 156: ...data How to enter data into and verify the correctness of the performance validation table will be discussed in the next section Use calibration sets the method to either use the retention index or no...

Page 157: ...ctly above the Method group title in the navigation pane Target Library Editor has a mini toolbar with icons which activate according to the selected tab and required functionality The mini toolbar is...

Page 158: ...bration data or Use AUTO calibration data The manual option is only available if Manual Calibration Data has been added to the Retention Time Calibrations tab in Gas Chromatograph The Use AUTO calibra...

Page 159: ...know that none of the changes are permanent until the library has been saved If a change has been made to a Target Library and later decided not to keep the change there are two options Either close t...

Page 160: ...ion Parameters tab to the instrument The libraries are loaded into the UnknownLibraries folder located on the Storage Card SD card This icon is only available on the Deconvolution Parameters tab Reset...

Page 161: ...ak and still be acceptable There are three options for the Type column They are Main Necessary and Unnecessary As described above there is only one Main mass peak and it is usually the largest peak in...

Page 162: ...anged version of the method 4 The Quant Select column in the Mass List allows the user to determine which masses to use for quantitation calculations This only sets which ions will be used if the comp...

Page 163: ...tention time for a compound If a method is using Retention Index then the column label will change to Retention Index and the retention index value is displayed instead of the retention time The Reten...

Page 164: ...be the target compound and then click on the name of the internal standard peak The following screen shows a drop down where Methyl Salicylate and Toluene d8 have been setup as internal standards By c...

Page 165: ...of a specific compound which can then be pasted into a different Target List d Paste Compound allows for pasting of a copied compound from one Target List to another Target List in a different method...

Page 166: ...they are stored in separate locations The following image shows the available icons for Deconvolution Parameters in the mini toolbar for Target Library Editor as well as three main areas of functional...

Page 167: ...a peak If the known peaks of interest are going to be very small these settings can be set to lower values The Minimum known compound correlation is used to reduce the chance of misidentification for...

Page 168: ...uce the chance of misidentification for unknown compounds The correlation value combines the retention index and mass spectral information into a value that indicates how closely a compound matches th...

Page 169: ...o be search The search will be conducted by looking in the first library then in each successive library until the best match is found These libraries will be stored on the Storage Card SD card on the...

Page 170: ...mass go to the Target List Setup tab and click on the Compound Name Then in the Mass List set Quant Select to Yes for the desired masses 4 Selected Height is the tallest scan in a deconvolved peak aft...

Page 171: ...the R2 value for the line Linear X2 force through zero derives the equation of the line by use of a modified linear regression through both the positive and negated coefficients of the data points tha...

Page 172: ...oncentration that fits into the middle of the curve To populate the table with data entered for the first compound in the list click the icon Copy Current Value to All Compounds in the mini toolbar as...

Page 173: ...text menu in which the following menu items are available Find files when selected a Windows file dialog box will open in which to search for files used for calibration curves Delete file used to remo...

Page 174: ...d a correction factor can be entered to adjust the calculated response It is always preferable to remedy the problem and recollect the sample and analyze the new sample This option is for situations w...

Page 175: ...n selected and the method saved the new curves can be sent to the instrument as part of the method The curve types that are available are Average Linear non weighted Linear force through zero Linear X...

Page 176: ...pounds that will need to be found in order to confirm the target chemical Maybe is the number of compounds that may be found in the substance 4 Click OK to save the dialog At the top of the Groups scr...

Page 177: ...n will appear as in the image below 6 If however while in Chromion the option Groups is selected on the Groups tab the view displayed after running a sample run will be the group view as seen in the i...

Page 178: ...The group can be edited by clicking Modify on the Groups tab The method must be saved and resent to the instrument before running the sample again 8 The group can be deleted simply by selecting it an...

Page 179: ...lected tab and required functionality The mini toolbar is to the right of the method toolbar Below are descriptions of the icon functionality appearing for Performance Validation in the mini toolbar A...

Page 180: ...o Default Values This option is disabled until the form has been unlocked This function provides a way to set the validation parameters to the default values This is useful for converting methods that...

Page 181: ...ration section of this manual Retention Time These values represent the time that the compound is expected to elute from the instrument If the Gas Chromatography method is changed then it is necessary...

Page 182: ...ties are a percentage of the main peak Peak 171 has an intensity of 41 024 percent of the main peak Confidence This value is used to set a window of the Intensity used during peak identification and i...

Page 183: ...bromoform there are 3 peaks so the Total peak count would be 3 Enabled By placing a checkmark in this column the auto calibration routine is set to use the specified mass Leaving the box unchecked al...

Page 184: ...sis runs to a higher temperature and takes about 130 seconds This setting can be adjusted to shorten the time it takes to run a performance validation This value must be manually entered The default v...

Page 185: ...the navigation pane is used to view data files which have been created by the Torion T 9 instrument Data Review Mini Toolbar Upon opening Data Review a mini toolbar displays to the right of the method...

Page 186: ...atogram and mass spectra in the correct format for peak identification 3 RAW is a format of data that is produced directly by the instrument The mass spectral data has not been calibrated and does not...

Page 187: ...to display data from a RES file When a data file is opened in Data Review there are two charts or graphs that will automatically display diagnostic data from the RES file Those two default graphs are...

Page 188: ...is activated and therefore is showing or open in the Data Review window If there is not a blue box around an icon it means that the chart or graph is hidden or closed Look at the Data Review mini tool...

Page 189: ...e summed graph It is called Set Mode to Summed Select Clicking on this icon places a blue box around it and removes the blue box from the zoom icon Using the cursor select a group of peaks in the TIC...

Page 190: ...und highlight is now ready for use The summed highlighter will no longer be active In the same TIC graph select a different range of peaks or scans Notice the range is highlighted in blue and the spec...

Page 191: ...e following image shows the TIC with summed yellow and background blue areas highlighted with the difference graph showing Diff The difference graph shows the background Bkgd subtracted from the summe...

Page 192: ...convolution Decon graph also displaying in that same color The deconvolved peaks are shown in different colors with the spectra appearing in the deconvolution graph when clicking on the peak in the TI...

Page 193: ...Data Review are used to set the cursor mode The following describes the different cursor modes Set Mode to Zoom When the cursor is set to the Zoom mode areas of any open graph can be enlarged To zoom...

Page 194: ...ll leave any other selected regions i e Background The All option clears all selections regardless of type The following image shows the right mouse click popup menu with the Clear Region menu option...

Page 195: ...IC chart then clicking this button will enable the option to show the RIC ions in the TIC graph or not show the RIC ions in the TIC graph RIC selection can be made by clicking on a mass of a specific...

Page 196: ...the same RIC information for each file Select Overlay File List When clicking this icon on the mini toolbar a box will open that allows selection of files that can be displayed in the overlay files g...

Page 197: ...to remove all files from the dialog except the first original file which is already opened in Data Review Also right clicking on a specific file will display a popup from which to choose Find File or...

Page 198: ...Erase All Deconvolution Data This icon is used to erase the data from the window Before the data is deleted a confirmation dialog will display requiring a user response of either Yes or No to save the...

Page 199: ...List will appear in the listing The reason the compounds were not found by the deconvolution process will be entered in the Response column Click again on the icon to turn off the functionality 5 Show...

Page 200: ...Setup When selecting this icon the following dialog will display When none of the compounds in deconvolution are selected the option will default to Replace retention time of all compounds This means...

Page 201: ...are five main menu items in which specific Data Review functionality becomes available when Data Review is opened a RES file has been loaded and the focus is on the Data Review window File The File m...

Page 202: ...lier If the sample contains a compound in which the volume is not as initially expected the volume of the data can be multiplied by whatever number is entered into the dialog The default setting is 0...

Page 203: ...rent file formats All four options on this main menu item are specific to Data Review functionality a Export Graphs This option opens a dialog box that can be used to select graphs or charts that are...

Page 204: ...ilename section is for browsing to a location in which to save the files Click the Find button to open a Windows browse dialog and select the location where the image files will be saved after they ar...

Page 205: ...RAW file to an Excel file If this option is select without a RAW file open in Data Review a popup will display indicating that a RAW file must be first be opened Deconvolution Window After opening a...

Page 206: ...unds listing When placing the cursor on the compound name the peak in the TIC graph will become highlighted The following image shows the available columns for Target List Compounds and Unknown Compou...

Page 207: ...ctor This is a factor that takes into consideration how well the peak matches the Target List or unknown library information A perfect match would be 100 CAS This is the CAS number of the compound Thi...

Page 208: ...ab of the Target Library Editor the number of unknown peaks to be displayed can be specified This is to maintain the speed of analyzing samples on the instrument If a complex sample is analyzed and it...

Page 209: ...s available after a deconvolution run which are used to test or control the spectra results These are accessed from the Data Review mini toolbar MS graph Summed graph Background graph Difference graph...

Page 210: ...pens in which to enter a compound name to find a possible CAS number for the compound The library that is searched is the AMDISNISTEPACW which is the default library in Library Editor Destination Ther...

Page 211: ...est peak having a value of 100 Exclude under 0 If a selected spectrum has a large number of small ions there is a good chance that they are not really part of the masses from the compound but are just...

Page 212: ...ses the calibration information that is stored in the data file Retention index from file uses the calibration information that is stored in the data file Manual calibration from method uses the reten...

Page 213: ...ssing the Start Search button will activate a search using the settings The following window shows the search results for a compound that has five possible matches Search Results This section contains...

Page 214: ...verwrite option replaces the file with the single spectra These options allow the user to send multiple or single spectra to the NIST spectrum file for viewing in the NIST MS Search software Ions This...

Page 215: ...Tools 211 3 Clicking the Launch NIST Search icon in the Data Review mini toolbar will open the NIST MS Search software and display the comparison of the saved spectra to the NIST database...

Page 216: ...Mini Toolbar Mass Spectrometer has its own mini toolbar that is specific to the functionality of the instrument parameters Below are descriptions of the icon functionality appearing for the mini toolb...

Page 217: ...ass Spec Parameter This option allows loading of previously saved settings into the Mass Spectrometer table It is also used to update the displayed data The following image shows the dialog box that o...

Page 218: ...bration Data grid The information in the Auto table is not actively updated Using the update button will force the software to retrieve the most current data from the Torion T 9 If Auto is checked the...

Page 219: ...ions in the trap This sets the target value for the number of ions and is not an indication of the actual number of ions but is a unit less value that represents the number of ions Typically this val...

Page 220: ...r the Auto Calibration Data is used when looking at the data in Data Review or on the instrument If this box is not checked then the data are viewed as uncalibrated data This means that the data are s...

Page 221: ...r with the right two sections representing the folders and associated files on the SD card in the instrument File Manager Mini Toolbar There are five icons in the mini toolbar that become active upon...

Page 222: ...ul information when troubleshooting problems on the instrument The name of the file is Guardion_Log txt If File Manager is connected to an instrument and a folder selected in which the file can be tra...

Page 223: ...nd choose Rename Folder A popup will open with the current filename appearing in the field Enter the new file name and click OK Refresh Folder After making changes to the contents of a folder either i...

Page 224: ...files in an extracted RES i e XML CAL CSV TLIB TRES file can be opened with WordPad Refresh Files Select a folder in which the files needs to be refreshed and select this option Rename File Select a f...

Page 225: ...firmation to the target folder on the computer A response of Yes or No is required Refresh Folder This option will refresh the contents of the highlighted folder The lower right section of File Manage...

Page 226: ...verted to usable searchable data This file is contained in the RES file RAW This is the unconverted data that is generated by the instrument This file is contained in the RES file TXT There are report...

Page 227: ...to the data is needed for future searches a copy can be created and then edited Be sure to name the copy with a name that does not contain AMDIS A file that contains the word AMDIS either as part of...

Page 228: ...lt library Import Library This option allows a library to be imported from the computer into Library Editor These can be libraries that are exported from the NIST database or that have been previously...

Page 229: ...ete the currently open library A first confirmation dialog box will open to confirm that the library should be deleted Upon clicking Yes a second confirmation dialog will open to indicate that deletio...

Page 230: ...to the currently open library When a library is open and additional compounds need to be added from another library click the Append to Library icon A dialog will open in which to browse for the libr...

Page 231: ...ons The first contains a Mass and Intensity list of the selected compound as well as the compound spectrum The second section is the Compound Name list containing various compound details Mass This is...

Page 232: ...to necessary functionality Many of the options on the right click are not available in the mini toolbar Add Compound from Default Library This option has the same functionality as the icon in the min...

Page 233: ...ry in which all the compounds were deleted a dialog would appear that indicates the library must be saved before switching libraries If an attempt is made to exit Library Editor before saving the modi...

Page 234: ...way around this is to go to the Target List and using the icon Convert Method to Retention Index change the retention mode on all the compounds to retention index then the compound in Library Editor...

Page 235: ...aying Idle This indicates that the Data Logger is not activated When clicking the icon Enable Disable Data Logger in the mini toolbar the functionality will become enabled A blue box will be placed ar...

Page 236: ...ble on the graph but there is no control over starting stopping or other aspects of collecting data from within Chromion To view the data analyzed upon completion of the run on the instrument the RES...

Page 237: ...ew Data Logger Tab As described above the Data Logger tab is used to log selected readings from the instrument It will run simultaneously with the TIC graph when it is enabled When an instrument is no...

Page 238: ...st The next option on the menu above is Edit Data Logger Item List From this list values can be selected which are then plotted in the Data Logger window In the Data Logger image above there are five...

Page 239: ...low voltage IonSource FilamentVoltage Filament voltage MassAnalyzer AmplitudeVoltage RF amplitude voltage MassAnalyzer DriveCurrent RF drive current MassAnalyzer DriveTemperature RF drive temperature...

Page 240: ...ell A PowerSystem RemainTimeB Remaining time left for battery cell B PowerSystem TemperatureA Battery cell A temperature PowerSystem TemperatureB Battery cell B temperature PowerSystem VoltageInMonito...

Page 241: ...hen a SPS 3 has been connected to the network or directly to a computer The following image shows the location of the LAN port for the cable connection on the back of the device Do not connect the Eth...

Page 242: ...the mini toolbar for Desorption which become active at different requests of functionality Rename Method This icon allows renaming of the selected method Retrieve Log Data from Device If Logging is en...

Page 243: ...dule parameters which have been previously set on the SPS 3 device for that method will be displayed Changes to the parameters can be made in Chromion and will be sent to the device Refer to the SPS 3...

Page 244: ...od used for the specific desorption run Date Time Stamp The date and time of the desorption run Temp C The temperature set in the method parameters Leak Check The response in this column is based on w...

Page 245: ...CSV format The files can be deleted from the SPS 3 device by clicking the icon Delete Log Files from Device A confirmation dialog will display requesting a response by the user to continue with the de...

Page 246: ...list of existing files which have been previously created for processing RES files in a batch mode Create New Batch Using this option a new batch file can be created for processing multiple RES files...

Page 247: ...of part of a batch of files without having to create a new batch file The files can then be viewed using Data Review Cancel Processing This option is only available during processing of files and allo...

Page 248: ...n Report When clicking this icon all compounds will be selected and appear in the report Deselect All Compounds When clicking this icon all compounds will be deselected and not appear in the report Ge...

Page 249: ...n the sample indicated by a calibration curve or peak Using the icons in the mini toolbar or the right click option mark the compounds which are to be included in the report 2 Click the Report Setup t...

Page 250: ...ing that the name is to be included in the report Operator This is the name of the person who requested the report Date Collected This is the date on which the sample was run on the instrument It s th...

Page 251: ...he deconvolution run Method Details Table This report displays in a table format the settings in Gas Chromatograph Mass Spec Settings Table This report displays in a table format the first five parame...

Page 252: ...as well as the spectrum for each compound Found Unknown Compounds This report displays the details of the unknown compounds found in the deconvolution run as well as the spectrum for each compound Not...

Page 253: ...ution Settings This report shows the settings for Deconvolution Parameters in the Target Library Editor of the method Compound Quant Review This report shows the Quant Concentrations settings in the T...

Page 254: ...250 Torion T 9 User s Guide Quantitative Calibration Table This report shows in table format the quantitative calibration results for the compounds with calibration curves and peaks...

Page 255: ...ys accept the TightVNC Viewer The following image shows the setup screen where you should select only the TightVNC Viewer option 1 Click Next on all screens until the installation process has complete...

Page 256: ...e Chromion software that use the NIST database require that the NIST software be installed To install the NIST library open the NIST folder and run the setup program then follow the on screen instruct...

Page 257: ...7 Advanced Operations...

Page 258: ...on of the sample run Reset and Restart Buttons on the Instrument There is a reset button and an emergency shutdown button on the Torion T 9 The reset button is used to restart the instrument s CPU wit...

Page 259: ...s from the SD card Refer to the File Manager section of the Software chapter of this manual for detailed instructions on deleting and moving files from the SD card It is also possible to remove the SD...

Page 260: ...256 Torion T 9 User s Guide...

Page 261: ...8 Maintenance...

Page 262: ...he GC injection port 1 Unscrew the plastic cover from the Universal Interface 2 Using the Ring Removal tool remove the stainless steel Interfacing Mounting Ring Nut 3 Pull the Universal Interface out...

Page 263: ...m from the old Liner and insert it into the new Liner There are two separate Liners that can be used in the Torion T 9 There is a liner for SPME type injections and a larger volume liner for small liq...

Page 264: ...urrently open methods name Use the Save as option under the Method menu to change the name of the method to Bake Out Send and make active the modified method to the instrument 3 Run a blank run This w...

Page 265: ...tment 3 After removing the battery insert the new battery into the battery compartment so the connector in the compartment aligns with the hole in the battery NOTE Push the battery into the compartmen...

Page 266: ...empty the Helium cartridge at the end of the Shutdown cycle as discussed in Basic Operation NOTE This would typically be done if you need to remove the helium cartridge before transporting the Torion...

Page 267: ...ikelyhood of data being written to the card If the Torion T 9 GC MS is completely turned off the SD card may be removed or inserted at any time Otherwise the best time to remove and replace a card is...

Page 268: ...264 Torion T 9 User s Guide...

Page 269: ...9 Troubleshooting...

Page 270: ...under Advanced Menu Status Diagnostics section for images of the screens 2 The turbo pump information is shown on the Mass Spectrometer tab 3 Verify that the frequency of the Turbo Pump is not increas...

Page 271: ...are generally detected as asymmetric peaks in which case the chemical agent library can be calibrated to compensate 3 Asymmetric peaks may indicate problems with sampling delivery separation or ioniza...

Page 272: ...ncentration low ionization yield incorrect detector voltage detector malfunction steep temperature gradient in the temperature program or rapid carrier gas flow rate 7 The following list provides addi...

Page 273: ...Chapter 8 Maintenance Acquired mass spectra are noisy 1 If the mass spectra are noisy the chromatogram will probably be noisy as well A noisy mass spectrum may result from some of the problems discuss...

Page 274: ...the new calibrations Evaluate the extraction procedure and eliminate any variations such as inconsistent extraction time temperature or agitation procedure There is no instrument signal Lack of signa...

Page 275: ...identify a compound that is actually present a false negative identification There are several reasons why the Torion T 9 GC MS would fail to identify the compound Address each of the possibilities l...

Page 276: ...r left to run the Torion T 9 GC MS If these remedies fail to resolve the problem contact your PerkinElmer Service Representative for help Torion T 9 GC MS suddenly powers down If the Torion T 9 GC MS...

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