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Ion Max APPI Source User Manual Version C

1. 2009 Thermo Fisher Scientific Inc All rights reserved TSQ is a registered trademark of Thermo Fisher Scientific Inc in the United States LCQ LTQ and Ion Max are trademarks of Thermo Fisher Scientific Inc PhotoMate is a trademark of Syagen Technology Inc Swagelok is a registered trademark of the Crawford Fitting Company Teflon is a registered trademark of E I du Pont de Nemours amp Co Thermo Fisher Scientific Inc provides this document to its customers with a product purchase to use in the product operation This document is copyright protected and any reproduction of the whole or any part of this document is strictly prohibited except with the written authorization of Thermo Fisher Scientific Inc The contents of this document are subject to change without notice All technical information in this document is for reference purposes only System configurations and specifications in this document supersede all previous information received by the purchaser Thermo Fisher Scientific Inc makes no representations that this document is complete accurate or error free and assumes no responsibility and will not be liable for any errors omissions damage or loss that might result from any use of this document even if the information in the document is followed properly This document is not part of any sales contract between Thermo Fisher Scientific Inc and a purchaser This document shall in no way govern or modify any Terms and
2. Ferrule Teflon Tube 00101 18196 00301 22915 Figure 35 Syringe and syringe adapter assembly 2 Remove the sample transfer line installed between the syringe adapter assembly and the APCI probe 3 Install a sample transfer line between the syringe adapter assembly and the divert inject valve a Connect an appropriate length of tubing to the LC union on the syringe adapter assembly b Connect the other end of the tubing fitted with a nut and a ferrule to port 5 of the divert inject valve Figure 36 From Syringe To lon Source To Waste From LC Figure 36 Divert inject valve showing plumbing for auto loop injection 68 APPI Souce User Manual Thermo Scientific 6 Optimizing the TSO Quantum Ultra Mass Spectrometer with Your Analyte Setting Up to Introduce Sample by Auto Loop Injection in APCI Mode Note To minimize the possibility of cross contamination use a different syringe and a different sample transfer line for your tuning and calibration solution than you do for your samples and compound optimization solution 4 Load a clean 500 uL Unimetrics syringe with 420 uL of the 2 pg uL reserpine sample solution Refer to Appendix B Reserpine Solution Formulations for the procedure for preparing the reserpine solution Note Be sure to wipe off the tip of the needle with a clean lint free tissue before reinserting it into the syringe adapter assembly to minimize the possibility of cross contami
3. a Clean the syringe with a solution of 5 formic acid in water b Rinse the syringe with a solution of 50 50 methanol water c Use acetone to rinse the syringe Repeat this step several times CAUTION AVOID BURNS The APCI vaporizer heater can reach temperatures of 600 xC Always allow the APCI probe to cool to ambient temperature for approximately 20 min before handling or removing the APCI probe from the APCI flange CAUTION AVOID INJURY The corona discharge needle is very sharp and can puncture your skin if you handle it without caution 4 Remove the Ion Max ion source housing as described in Removing the Ion Max Ion Source Housing on page 26 Thermo Scientific 6 Optimizing the TSO Quantum Ultra Mass Spectrometer with Your Analyte Cleaning the Mass Spectrometer After Tuning in APCI Mode 5 Flush the sample transfer line sample tube and APCI probe thoroughly with a solution of 5 formic acid in water or with another appropriate solvent Note The solvent that you use to flush the sample transfer line sample tube and APCI probe assembly depends on the solvent system you use to dissolve your samples For example if you are using a buffered solution of a high concentration an acidic solution is appropriate a Fill a clean 250 uL Unimetrics syringe with an appropriate solvent b While holding the plunger of the syringe in place carefully insert the needle of the syringe into the free end of the Tefl
4. 5 Optimizing the LTO MS Detector with Your Analyte Optimizing the Tune of the MS Detector Automatically in APCI APPI MS Mode C xcalibur methods APCIhighflow LTQTune Tune Plus 14008 IT 20 353 ST 0 08 uS 1 NL 7 93E4 Adjusting Front Lens F ITMS p APCI SIM ms 608 20 610 20 Relative Intensity TT A TST mE erar Tr al TTT a TT BE Te 0 608 612 613 15 44 13 12 11 10 9 8 Lens Voltage Figure 32 Tune Plus window with the Tune dialog box showing the Automatic tuning page 60 APPI Souce User Manual Thermo Scientific 5 Optimizing the LTO MS Detector with Your Analyte Saving the APCI APPI MS Tune Method Saving the You can save the settings you just obtained in a Tune Method specific to APCI APPI MS Tune you particular analyte and solvent flow rate in this case the settings Method obtained using reserpine You can recall the Tune Method and use it as a starting point for optimizing the MS detector on reserpine at a different flow rate Note Save the Tune Method while the MS detector is still On To save your APCI APPI MS Tune Method 1 Choose File gt Save As to display the Save As dialog box Figure 33 2 In the Save In list box select the C Xcalibur methods folder 3 Click on the File Name text box and then enter APPImyTune to name the Tune Method APPImy Tune LTQTune Save in lo methods Eh 4PCci LTATune BESI LTQTune BAPCIHighFlow LTQTune BESIHighFlow LTQTune AutoTu
5. Deca XP MAX MS detector in the APCI APPI MS high flow mode It is not necessary to recalibrate the MS detector when you switch to APCI APPI MS operation You can use the calibration settings you obtained from the successful automatic calibration procedure you performed in the ESI MS mode For APCI APPI MS operation you open a default tune method located in your C Xcalibur methods folder in this case APClhighflow LCQTune From this starting point you optimize automatically the tube lens offset voltage capillary voltage and ion transfer capillary temperature for your particular analyte Note The following procedures assume that you are familiar with your XP Plus instrument and the Tune Plus window If you need information refer to the LCQ Deca XP MAX online help LCQ Deca XP MAX Getting Connected or the LCQ Deca XP MAX Hardware Manual Ensure that you have completed the procedures in the sections that describe how to calibrate your instrument in ESI mode and have properly set up your APCI APPI source This chapter includes the following sections e Setting Up the Inlet for Tuning Using High Flow Infusion e Setting Up the MS Detector for APCI APPI MS Operation e Optimizing the Tune of the MS Detector Automatically in APCI APPI MS Mode e Saving the Tune Method e Cleaning the MS Detector After Tuning in APCI Mode Thermo Scientific APPI Souce User Manual 37 4 Optimizing the LCQ Deca XP MAX MS Detector with Your Analyte Sett
6. Removing the APCI Sample Tube To remove the APCI sample tube from the APCI manifold 1 With a 3 8 in open end wrench remove the sample tube inlet fitting P N 70005 20250 0 239 in ID O ring P N 00107 04000 and sample tube from the APCI manifold Figure 46 2 Remove the exit end nut P N 70005 20220 0 016 in ID PEEK ferrule P N 00101 18120 and sample tube from the sample tube inlet fitting 3 Discard the old sample tube Thermo Scientific APPI Souce User Manual 89 7 Maintenance Maintaining the APCI Probe 90 0 312 in ID O ring On in ID 1 16 Viton O Ring Oz APCI Nozzle Installing a New APCI Sample APPI Souce User Manual Tube Fused Silica Pr Sample Tube 10 32 PEEK Fitting oe 0 016 in ID PEEK Ferrule 0 239 in ID 1 16 Viton O Ring Ry Flange Fitting Figure 46 APCI sample tube connection To install a new APCI sample tube 1 Use a fused silica cutting tool to cut a piece of 100 um ID 390 um OD fused silica tubing P N 00106 10498 to a length of approximately 15 cm 6 in Ensure that you squarely cut the ends of the fused silica tubing Slide the PEEK fitting P N 70005 20220 and ferrule P N 00101 18120 onto the length of the fused silica tubing See Figure 46 Check the condition of the 0 239 in ID O ring P N 00107 04000 on the sample tube inlet fitting Replace it if necessary Insert the fused silica tubing into the sample tube inlet fitting Sli
7. e Reserpine Stock Solution e LCQ Deca XP MAX Reserpine Sample Solution e LTQ Reserpine Sample Solution e TSQ Quantum Ultra Reserpine Sample Solution CAUTION AVOID EXPOSURE TO POTENTIALLY HARMFUL MATERIALS Always wear protective gloves and safety glasses when you use solvents or corrosives Also contain waste streams and use proper ventilation Refer to your supplier s Material Safety Data Sheet MSDS for the proper handling of a particular solvent Always take safety precautions when you handle chemicals and unknown samples READ AND UNDERSTAND THE HAZARDS OF THE CHEMICALS USED IN THE FOLLOWING PREPARATIONS Dispose of all laboratory reagents by the appropriate method for a specific reagent or solvent Material Safety Data Sheets MSDS provide summarized information on the hazards and toxicity of specific chemical compounds MSDSs also provide information on the proper handling of compounds first aid for accidental exposure and procedures for the remedy of spills or leaks Producers and suppliers of chemical compounds are required by law to provide their customers with the most current health and safety information in the form of an MSDS Read the MSDSs for each chemical you use Examples of potentially hazardous chemicals used in procedures throughout this manual are as follows APPI Souce User Manual 109 B Reserpine Solution Formulations e Acetic acid e Methanol e Reserpine Follow the directions given below to prepare a st
8. plumbing for sample input Tee to LC 38 tuning procedure 38 APCI manifold location 15 APCI nozzle reinstalling 89 removing 89 APCI probe cleaning 89 corona discharge needle 15 description 14 disassembling 88 figure 14 maintenance 88 nozzle 14 reassembling 91 removing 88 vaporizer 14 vaporizer temperature 14 APCI sample tube connection 90 installation 91 installing 90 removing 89 replacing 88 APCI Source dialog box displaying 55 figure 56 APCI Source dialog box figure 43 APCI vaporizer avoiding burns from CAUTION 88 cross sectional view 15 reconditioning note 72 APCI MS compound optimization 65 setting up LTQ for 55 APPI discussed 6 molecular polarity range 2 Thermo Scientific molecular weight range 2 operating parameters 11 APPI APCI combination probe maintenance 87 atmospheric pressure chemical ionization See APCI atmospheric pressure photoionization See APPI auto loop injection APCI plumbing for 67 auxiliary gas settings for APPI and APCI 11 box fan description 20 location 19 buffers LC discussion 10 C CAUTIONS avoid sharp needle 92 avoiding burns from APCI vaporizer 49 63 84 88 avoiding injury from corona discharge needle 27 Ion Max ion source exposing to atmosphere 49 63 84 ion source exposing to oxygen 49 63 84 ion transfer capillary avoiding burns 88 Cautions changing API probes 20 disconnecting PhotoMate power cord 20 handling VUV lamp 93 95 96 solvent wa
9. she 606 607 608 609 610 61 75 Figure 25 Tune Plus window with the Tune dialog box showing the Automatic page 46 APPI Souce User Manual Thermo Scientific Saving the Tune Method Thermo Scientific 4 Optimizing the LCQ Deca XP MAX MS Detector with Your Analyte Saving the Tune Method You can save the settings you just obtained in a tune method specific to your particular analyte and solvent flow rate In this case you save settings obtained using reserpine You can recall the tune method and use it as a starting point for optimizing the MS detector on reserpine at a different flow rate Note Save the Tune Method while the MS detector is On To save the APCI APPI MS tune method 1 Choose File gt Save As to display the Save As dialog box See Figure 26 Save As x Save in methods Alprazolam LCQT une APCITune LCQTune AutoTune LCQTune P ESITune LCQTune File name arc myTune Save as type Tune Files LCQ Tune 7 Cancel r Header Information No file selected Figure 26 Save As dialog box showing files in the folder C Xcalibur methods 2 In the Save In list box select the C Xcalibur methods folder 3 Click on the File Name text box and then enter APCImyTune to name the Tune Method APClmy Tune LCQTune APPI Souce User Manual 47 4 Optimizing the LCQ Deca XP MAX MS Detector with Your Analyte Saving the Tune Method 4 Cli
10. 609 CE 38 ST 0 10 1005 TE a4 853 80 Relative Abundance a 3 1 Ready 194 0 194 5 195 0 miz 0200 100 00 Untitled 0 00 0 00 100 00 195 5 196 0 196 5 0 points NUM 04 27 2001 9 49 AM Figure 41 Compound Optimization workspace APCI mode 2 In the Compound Optimization view in the top left corner of the workspace ensure that the Single Sample page is displayed APPI Souce User Manual 77 6 Optimizing the TSO Quantum Ultra Mass Spectrometer with Your Analyte Optimizing in APCI APPI MS MS Mode Automatically with Your Compound 3 Set the optimization parameters for monitoring the reserpine transition from m z 609 281 to m z 195 066 a Select Optimization Modes SRM to optimize a selected reaction Figure 42 b Select Optimization Options Standard to tune the default selection of devices The tube lens offset and collision energy are the default compound sensitive devices that are optimized in this configuration c Inthe Optimization table enter the parent mass 609 281 to set the parent mass of the SRM reaction to the ion at m z 609 281 d Enter the product mass 195 066 to set the product mass of the SRM reaction to the ion at m z 195 066 Note You need to select inlet type option button appropriate to the inlet mode you use to introduce your sample into the mass spectrometer This procedure uses the Auto Loop Injection option e In the Inlet Types box select the
11. Auto Loop Injection option button to have the TSQ Quantum Ultra automatically inject the optimization solution Single Sample AutoQuan Optimization Modes MS Only MS MS MS SRM Optimization Options Standard Custom Parent Product Mass Mass 1 503 351 195 066 Status x 200 000 100 000 Inlet Types Manual Loop Injection Syringe Pump Infusion Auto Loop Injection Start Print Figure 42 Compound Optimization view 4 Click Start to start the automatic tuning procedure 78 APPI Souce User Manual Thermo Scientific 6 Optimizing the TSQ Quantum Ultra Mass Spectrometer with Your Analyte Optimizing in APCI APPI MS MS Mode Automatically with Your Compound Note If the syringe runs out of sample during the compound optimization procedure the instrument pauses the automatic tuning and displays the message Syringe out of sample Reload and click OK If this occurs reload the syringe and click on OK to continue the optimization The message Finish compound optimization is displayed in the Status box in the Compound Optimization view when the compound optimization has completed successfully Figure 43 e Ifthe compound optimization procedure finishes without errors and the breakdown curve of the 195 066 fragment is Gaussian shaped Figure 44 or is a smooth positive sloped curve go to step 6 e If errors occur during the compound optimization procedure or the breakdown curve of the 195 066 f
12. In the presence of protic solvents the analyte ion may extract a hydrogen to form an M H ion 6 M S gt M H S H 7 The analyte ions pass through the ion transfer capillary enter the mass spectrometer and are analyzed Molecules including steroids basic drug entities and pesticides have ionization potentials below the threshold and protonated molecules are generated in the LC MS experiment APPI reduces fragmentation because only a small amount of energy is deposited in the molecule Molecules such as the nitrogen sheath and auxiliary gas and the simple solvents used for LC MS are not ionized because their ionization potentials are greater than the photon energy The result is selective ionization of analyte versus background See Figure 2 and Figure 3 6 APPI Souce User Manual Thermo Scientific Thermo Scientific 1 Introduction Atmospheric Pressure Photoionization A Gases in air Ea nn solvent molecules Fragment ion a thresholds Molecular ion Energy thresholds ore and other compounds Photoionization Figure 3 Energetics of photoionization Not lonized lonized Threshold Figure 4 Illustration of selective photoionization The PhotoMate light source uses a krypton lamp that emits photons with energies of 10 0 and 10 6 eV Molecules with ionization potentials less than 10 eV ionize to form M or M H while those with greater ionization potentials do
13. MS Mode Automatically with Your Compound Optimize the mass spectrometer to maximize the ion transmission of your compound Optimization is performed to fine tune compound dependent parameters such as discharge current capillary temperature and tube lens offset It is recommended that you optimize the mass spectrometer after it has been successfully tuned and calibrated To automatically optimize the mass spectrometer in the APCI APPI MS MS mode for the reserpine transition from m z609 281 to m z 195 066 1 On the Control Scan Mode toolbar click Compound Optimization Workspace to display the Compound Optimization workspace Figure 41 AutoTune Quantum Tune Master APCI Compound Optimization Workspace AutoTune TSQCalib File Workspace View Control ScanParameters Display Setup Help A e 2a AUSLE RK Eee nA Ane cos S i Single Sample AutoQuan Optimization Modes MS Only MS MS MS SRM Device Value Readback Optimization Options Standard Custom Ov Ceann a0 ao Ou APC Vaporizer Tempera 500 499 Parent Product Ow Sheath Gas Pressure 30 30 Mass Mass Status Oy Aux Valve Flow 0 o 1 En N E o Oy Capillary Temperature 350 350 Bl Tube Lens Offset 160 159 Oy Source CID 0 0 bal Oy Collision Pressure 15 15 Inlet Types Mv Collision Energy 38 38 C Manual Loop Injection Mv Quad MS MS Bias 3 0 3 0 Syringe Pump Infusion a Discharge Current fe SEH Start Print S 29943 SRM
14. Quantum Ultra APCI Tune 65 optimizing APCI tune 58 preparing reserpine solutions 110 removing ESI source 24 saving Tune Method 47 61 80 82 setting up LCQ Deca XP MAX for APCI MS operation 42 inlet for APCI tuning 38 LTQ for APCI MS operation 55 TSQ Quantum Ultra for compound optimization 71 syringe pump for compound optimization 67 setting up hardware for tuning and calibrating 23 tuning LCQ Deca XP MAX automatically APCI MS mode 45 LTQ automatically in APCI MS mode 58 R regulatory compliance iii Remote LED description 21 replacement procedures sample tube APCI 88 reserpine preparing solutions 110 S safety interlocks description 20 safety standards iii sample solutions ESI reserpine 112 sample solutions reserpine preparing 113 sample tube APC installing 90 APCI removing 89 APCI replacing 88 Save As dialog box 47 61 82 saving files 47 82 saving Tune Method 47 sheath gas settings for APPland APCI 11 solutions preparing 118 APPI Souce User Manual reserpine 113 solvents note 50 64 85 status LEDs location 18 18 syringe adapter assembly 68 syringe pump installing syringe into 52 plumbing 52 54 removing syringe from 49 63 84 setting up for compound optimization 67 starting 58 stopping 49 63 84 system replaceable parts 99 T Tables corona discharge needle status 9 light source status 9 operation parameter guidelines 11 temperatures APCI vaporizer 14 TSQ Quantum Ultra cl
15. Remove the 4 Phillips screws that secure the box top to the light source c Remove the box top from the electronics PCB but keep the fan power cable connected 7 Insert an Allen key into the lamp hole in the electronics PCB See Figure 48 on page 94 Gently push out the VUV lamp with the Allen key Installing the New VUV Lamp To install the new VUV lamp CAUTION Always wear clean gloves when you are handling a functional VUV lamp Fingerprints on the lamp can cause the lamp to fail when it is in use 1 While wearing clean gloves install a new VUV lamp by pushing it all the way to the stopping position in the light source assembly 2 If necessary reinstall the box top a Tip the box top forward and make sure the lamp On Off switch passes through the hole in the box top Then push the box top down over the fan connector b Reinstall the four screws to secure the box top c Reconnect the light source power cord to the light source 3 Close and secure the lid of the APCI APPI combination probe housing 4 Place the lamp On Off switch in the On position 96 APPI Souce User Manual Thermo Scientific Thermo Scientific 7 Maintenance Maintaining the PhotoMate Light Source 5 Check that the Lamp On and Drive On LEDs illuminate Look through the Ion Max window and verify that the VUV lamp is on Note Ifthe Drive On and Lamp On LEDs do not illuminate verify that the front door of the Ion Max ion source housing is secure
16. Removing the Old VUV Lamp e Installing the New VUV Lamp To remove the old VUV lamp 1 Place the lamp On Off switch in the Off O position 2 Turn off the flow of liquid from the LC or other sample introduction device to the APCI APPI combination probe 3 Put the mass spectrometer in Standby mode CAUTION AVOID BURNS At operating temperatures the APCI vaporizer ion sweep cone spray cone and ion transfer capillary can severely burn you The APCI vaporizer typically operates at 400 to 600 xC and the ion sweep cone spray cone and ion transfer capillary typically operate at 100 to 300 xC Allow the heated vaporizer ion sweep cone spray cone and ion transfer capillary to cool to room temperature for approximately 20 min before you touch or remove these components 4 Open the lid of the APCI APPI combination probe CAUTION Always wear clean gloves when you are handling a functional VUV lamp Fingerprints on the lamp can cause the lamp to fail when it is in use 5 While wearing clean gloves grasp the VUV lamp and pull the lamp out e Ifyou are able to remove the VUV lamp go to the next section Installing the New VUV Lamp APPI Souce User Manual 95 7 Maintenance Maintaining the PhotoMate Light Source e Ifyou are having trouble removing the lamp you need to push it out from the top 6 Remove the box top from the PhotoMate light source a Remove the light source power cord from the light source b
17. Setting Up the Inlet for Tuning Using High Flow Infusion 38 Setting Up the MS Detector for APCI APPI MS Operation 42 Optimizing the Tune of the MS Detector Automatically in APCI APPI MS Moleskine 45 Saving the Tune Method 2 use 47 Cleaning the MS Detector After Tuning in APCI Mode 49 Optimizing the LTO MS Detector with Your Analyte 51 APPI Souce User Manual ix Contents x APPI Souce User Manual Chapter 6 Chapter 7 Chapter 8 Appendix A Appendix B Setting Up the Inlet for Tuning Using High Flow Infusion 52 Setting Up the MS Detector for APCI APPI MS Operation 55 Optimizing the Tune of the MS Detector Automatically in APCHAPPUMS Mode as ats ea 58 Saving the APCI APPI MS Tune Method 61 Cleaning the MS Detector After Tuning in APCI Mode 63 Optimizing the TSQ Quantum Ultra Mass Spectrometer with Your Analyte65 Setting Up to Introduce Sample by Auto Loop Injection Pe Gs Modes ee le 67 Setting Up to Optimize in APCI APPI MS MS Mode with Your Compound een 71 Optimizing in APCI APPI MS MS Mode Automatically with Your Compound rs een 77 Saving the Tune Method e datcacetens tvetsadn tedenicectucs Suse dander iaes cae 82 Cleaning the Mass Spectrometer After Tuning APGI Moden een 84 Maintenance ana 87 Maintaining the APCI Proben une see 88 Maintaining the PhotoMate Light Source 92 Cleaning and Polishing the Window of the VUV Lamp 92 Replacing
18. Tune Method for high flow APCI operation a b Choose File gt Open to display the Open dialog box Scroll down until you see the folder C Xcalibur methods Then select the file APCTTune LCQTune Click on OK to open the file XP Plus downloads the Tune Method parameters to the MS detector 3 Verify that XP Plus opened the Tune Method as follows a e Choose Setup gt Change API Source Type to specify the APCI source Then in the Change Source Type dialog box which appears select the APCI option button Click on OK to return to the Tune Plus window On the Instrument Setup toolbar click on the API Source button to open the APCI Source dialog box Figure 23 Verify that the settings in your dialog box are similar to those shown in Figure 23 To operate in APPI mode only set the discharge current to zero To operate in APCI APPI or APCI mode only set the discharge current to 5 WA Click on OK to close the dialog box 4 If you are operating in APPI or APCI APPI mode turn the APPI lamp on Verify that the lamp is operating by observing the lamp through the front window of the Ion Max ion source housing Thermo Scientific Thermo Scientific 4 Optimizing the LCQ Deca XP MAX MS Detector with Your Analyte Setting Up the MS Detector for APCI APPI MS Operation APCI Source Ea Actual Vaporizer Temp C 450 00 449 90 Sheath Gas Flow Rate arb feo 78 91 Aux Sweep Gas Flow Rate a
19. a Connect a length of PEEK tubing with a stainless steel nut and a stainless steel ferrule to port 2 of the divert inject valve b Connect the other end of the PEEK tubing with a proper fitting and a ferrule to the outlet of the LC 8 Connect an appropriate length of PEEK tubing waste line from the divert inject valve to a waste container a Connect a length of PEEK tubing with a stainless steel nut and a stainless steel ferrule to port 1 of the divert inject valve b Insert the other end of the PEEK tubing into a suitable waste container The LC plumbing connections are now properly made for APCI APPI MS sample introduction from the syringe pump into solvent flow from an LC 54 APPI Souce User Manual Thermo Scientific Setting Up the MS Detector for APCI APPI MS Operation w iil OnStandby Thermo Scientific 5 Optimizing the LTO MS Detector with Your Analyte Setting Up the MS Detector for APCI APPI MS Operation To set up the MS detector for APCI APPI MS operation on the LTQ MS detector 1 In Tune Plus click on the On Standby button to take the MS detector out of Standby mode and turn it on The MS detector begins scanning and applies high voltage to the corona needle and shows a real time display in the Spectrum view 2 Open the APCThighflow LTQTune Tune Method the Tune Method for high flow APCI operation a b Choose File gt Open to display the Open dialog box Scroll down until you
20. and auxiliary gas pressures for approximately 30 min to drive off the chemical contamination Typical values used for reconditioning the APCI vaporizer are as follows LC flow rate 400 mL min Vaporizer temperature 600 xC Sheath gas pressure 80 psi Auxiliary gas flow rate 15 units 5 Set the values for the compound dependent devices a Ensure that Discharge Current is selected in the Device Display box b In the Optimize Compound Dependent Devices view set the APCI or APPI mode e To operate in APPI mode only set the discharge current to 0 and select the APPI Lamp On check box e To operate in APCI APPI mode or APCI mode only enter 4 0 in the Device spin box to set the discharge current to 4 0 uA c Set the temperature of the APCI vaporizer i Inthe Device Display box click APCI Vaporizer Temperature This changes the Device spin box label to APCI Vaporizer Temperature and enables you to set the APCI vaporizer temperature ii In the Device box enter 500 to set the vaporizer temperature to 500 C d Set the pressure of the sheath gas i Click Sheath Gas Pressure in the Device Display box ii Enter 30 in the Device box to set the sheath gas pressure to 30 psi e Set the flow rate of the auxiliary gas i Click Aux Valve Flow in the Device Display box ii Enter 0 in the Device box to set the auxiliary gas flow rate to 0 units Thermo Scientific 6 Optimizing the TSO Quantum Ultra Mass Spectrome
21. cipients et des proc dures homologu es pour se d barrasser des d chets d huile Haute Temperature Permettre aux composants chauff s de refroidir avant tout intervention Incendie Agir avec pr caution lors de l utilisation du syst me en pr sence de gaz inflammables Danger pour les yeux Dex projections chimiques liquides ou solides peuvent tre dangereuses pour les yeux Porter des lunettes de protection lors de toute manipulationde produit chimique ou pour toute intervention sur l instrument Danger general Indique la pr sence d un risque n appartenant pas aux cat gories cit es plus haut Ce symbole figure galement sur l instrument pour renvoyer l utilisateur aux instructions du pr sent manuel Si la s ret d un procedure est incertaine avant de continuer contacter le plus proche Service Client le pour les produits de Thermo Fisher Scientific San Jose PRECAUCION Descarga el ctrica Este instrumento utiliza altas tensiones capaces de producir lesiones personales Antes de dar servicio de mantenimiento al instrumento ste debera apagarse y desconectarse de la l nea de alimentacion el ctrica No opere el instrumento sin sus cubiertas exteriores quitadas No remueva las cubiertas protectoras de las tarjetas de circuito impreso Quimica El instrumento puede contener productos quimicos peligrosos Utilice guantes al manejar productos quimicos t xicos carcinogenos mutagenos 0 corrosivos i
22. electronic circuitry for driving the VUV lamp a photodiode for detecting light emitted by the VUV lamp and a thermocouple for monitoring the temperature The electronics PCB also powers the status LEDs The VUV lamp is an electrodeless quartz cell with a magnesium fluoride window The window is transparent to VUV light but the quartz is not The VUV lamp is filled with krypton gas The lamp emits radiation at 10 0 eV and 10 6 eV Minimize the chance of breaking the VUV lamp by doing the following e Always wear clean gloves when you handle the VUV lamp Fingerprints on the lamp can cause the lamp to fail when it is in use e Do not spray solvent on the VUV lamp while it is hot The VUV lamp can crack e Do not leave the LC or other liquid delivery device on while the mass spectrometer is in Standby The absence of sheath and auxiliary gas can cause the hot lamp to break upon contact with liquids The lamp shield protects the VUV lamp The box fan cools the electronics PCB and prevents heat from the vaporizer from damaging the electronics PCB The fan draws cool air into the light source The fan runs at all times even if the lamp is off CAUTION Never disconnect the power cord from the PhotoMate light source or disconnect the PhotoMate power supply from line power while the vaporizer is hot Without power the fan will stop running and heat from the vaporizer could damage the electronics PCB The lamp On Off switch turns
23. mL of methanol 1 acetic acid in the 100 mL volumetric flask Rinse the pipette twice with the 75 mL of methanol 1 acetic acid contained in the volumetric flask by dipping the pipette tip into the solution and rinsing it back into the flask Carefully bring up this volume with methanol 1 acetic acid until the lower part of the meniscus is level with the 100 mL marking Mix this solution thoroughly Label it as Reserpine 5 pg pL Add 20 mL of the Reserpine 5 pg L to another clean 100 mL volumetric flask and carefully bring up this volume with methanol 1 acetic acid until the lower part of the meniscus is level with the 100 mL marking Mix the solution thoroughly Label this Reserpine 1 pg pL Transfer 100 UL of the 1 pg uL solution into a clean polypropylene tube Add 700 UL of 1 acetic acid in 50 50 methanol water to the tube Mix this solution 125 fg uL thoroughly Label the tube L7Q Reserpine Sample Solution 125 fg L and store it in a refrigerator until it is needed APPI Souce User Manual 113 B Reserpine Solution Formulations TSO Quantum Ultra Reserpine Sample Solution 114 TSO Quantum Ultra Reserpine Sample Solution APPI Souce User Manual Prepare 1 mL of the 200 fg uL 0 329 fmol L reserpine compound optimization solution in 1 acetic acid in methanol l 10 11 12 Pipette 1 mL of reserpine stock solution 1 ug uL into a 10 mL volumetric flask and b
24. mass for the scan range to m z 609 2 i In the Width text box enter 2 to set the width of the scan range to m z 2 APPI Souce User Manual 43 4 Optimizing the LCO Deca XP MAX MS Detector with Your Analyte Setting Up the MS Detector for APCI APPI MS Operation j Ensure that the settings in your Define Scan dialog box are the same as those shown in Figure 24 k Click on OK to save the MS detector scan parameters and return to the Tune Plus window 6 If you are operating in APCI APPI or APPI only modes turn on the APPI source a Turn on the power to the APPI lamp by flipping the switch on the PhotoMate light source housing to the On position b Verify that the lamp is operating by looking through the front window of the Ion Max ion source housing 7 On the Control Scan Mode toolbar click on the Centroid Profile button to toggle the data type to centroid The picture on the button should be the same as that shown here 8 Click on the Positive Negative button to toggle the ion polarity mode to positive The picture on the button should be the same as that shown here You have now completed setting up your MS detector for APCI APPI MS operation Define Scan Advanced Figure 24 Define Scan dialog box showing typical settings for APCI APPI MS operation 44 APPI Souce User Manual Thermo Scientific Optimizing the Tune of the MS Detector Automatically in APCI APPI MS Mode Thermo Scien
25. not Figure 4 shows ionization potentials of typical compounds and solvents APPI Souce User Manual 7 1 Introduction Atmospheric Pressure Photoionization APPI Souce User Manual Krypton 10 0 eV 10 6 eV lonization Potentials IP Anthracene 7 4 eV Fluoranthene 7 8 eV Caffeine 8 0 eV 4 Nitrotoluene Figure 5 Solvent lonization Potentials IP Toluene 8 82 eV Acetone Methanol 10 85 eV Acetonitrile 12 19 eV Water 12 61 eV lonization potentials of typical compounds and solvents Thermo Scientific Combined APCI and Thermo Scientific APPI 1 Introduction Combined APC and APPI You can easily change between APCI APPI and combined APCI and APPI techniques by turning on the corona discharge needle the PhotoMate light source or both See Table 1 You turn the light source on and off by using the On Off switch on the light source You turn the corona discharge needle on and off by using the Xcalibur software This allows you to quickly determine which technique yields the best ion signal Table 1 Light source and corona discharge needle status for APPI APCI and combined APCI APPI modes ees PhotoMate Light Corona Discharge lonization Technique Source Needle APPI On Off APCI off On Combined APCI and On On APPI APPI Souce User Manual 9 1 Introduction What Types of Buffers Should Use What Types Should Avoid Wh at Types of Buffe FS Use volatile buffers when po
26. other end of the cable to the female connector on the front of the LTQ MS detector just to the right of where the Ion Max ion source housing mounts to the detector e For TSQ Quantum Ultra mass spectrometers Connect the female end of the communications cable to the DB 15 connector on the PhotoMate light source Connect the other end of the cable to the female connector on the front of the mass spectrometer just to the riglon Max ion sourcelon Max ion sourceht of where the Ion Max ion source housing mounts to the detector You also have the option to connect the DB 15 connector to the external power supply that is included with your APPI source instead of using the TSQ Quantum Ultra s power connector The APCI APPI source is now properly installed on the mass spectrometer Thermo Scientific APPI Souce User Manual 35 To optimize the tune of your mass spectrometer proceed to one of the following chapters e Ifyou have an LCQ Deca XP MAX MS detector refer toChapter 4 Optimizing the LCQ Deca XP MAX MS Detector with Your Analyte e Ifyou have an LTQ MS detector refer to Chapter 5 Optimizing the LTQ MS Detector with Your Analyte e Ifyou have an TSQ Quantum Ultra mass spectrometer refer to Chapter 6 Optimizing the TSQ Quantum Ultra Mass Spectrometer with Your Analyte Chapter 4 Optimizing the LCO Deca XP MAX MS Detector with Your Analyte This chapter provides information on optimizing the tune of your LCQ
27. oxygen The presence of oxygen in the ion source when the MS detector is On could be unsafe The LTQ MS detector automatically turns off when you open the API source however it is best to take this added precaution 2 Remove the syringe from the syringe pump holder as follows a Squeeze the blue buttons and pull back on the syringe pump handle to free the syringe b Remove the syringe from the holder c Disconnect the tip of the syringe needle from the Teflon tubing 3 Clean the syringe thoroughly a Clean the syringe with a solution of 5 formic acid in water b Rinse the syringe with a solution of 50 50 methanol water c Use acetone to rinse the syringe Repeat this step several times CAUTION AVOID BURNS The APCI vaporizer heater can reach temperatures of 600 xC Always allow the APCI probe to cool to ambient temperature for approximately 20 min before handling or removing the APCI probe from the APCI flange CAUTION AVOID INJURY The corona discharge needle is very sharp and can puncture your skin if you handle it without caution 4 Remove the Ion Max ion source housing as described in the topic Removing the Ion Max Ion Source Housing on page 26 APPI Souce User Manual 63 5 Optimizing the LTO MS Detector with Your Analyte Cleaning the MS Detector After Tuning in APC Mode 5 Flush the sample transfer line sample tube and APCI probe thoroughly with a solution of 5 formic acid in water or with anot
28. sample ionization occurs in a series of reactions that start with the electron initiated cation formation Typical examples of primary secondary and adduct ion formation are shown below Primary ion formation e N gt N 2e Secondary ion formation N H O gt N H O H O H O H O HO Proton transfer H O M gt M H H O In negative ion mode M HY is typically formed by the abstraction of a proton by OH APPI Souce User Manual 3 1 Introduction Atmospheric Pressure Chemical lonization APCI is typically used to analyze small molecules with molecular weights up to about 1500 u APCI is a very robust ionization technique It is not affected by minor changes in most variables such as changes in buffers or buffer strength APCI Nozzle Atmospheric Pressure Region 10V lon Sweep Pressure Cone lon Chemical emic Transfer lonization Capillary a M M H 7sS gt RS uM a NZ ISum M SSS Corona Discharge Needle 3 TO 5 kV Corona Discharge Discharge Region Plasma Figure 2 APCI process in the positive ion polarity mode 4 APPI Souce User Manual You can use APCI in positive or negative ion polarity mode For most molecules the positive ion mode produces a stronger ion current This is especially true for molecules with one or more basic nitrogen or other basic atoms An exception to the general rule is that molecules with acid
29. see the folder C Xcalibur methods Then select the file APCThighflow LTQTune Click OK to open the file The Tune Method parameters are uploaded to the MS detector 3 Verify that the LTQ MS detector opened the Tune Method a On the Instrument Setup toolbar click on the API Source button to open the APCI APPI Source dialog box Figure 29 Verify that the settings in your dialog box are similar to those shown in Figure 29 Set the APCI or APPI mode e To operate in APPI mode only set the discharge current to 0 and select the APPI Lamp On check box e To operate in APCI APPI mode set the corona discharge to your desired value and select the APPI Lamp On check box Figure 29 e To operate in APCI mode only set the corona discharge to your desired value and make sure that the APCI Lamp on check box is not selected Figure 29 Click OK to close the APCI APPI Source dialog box Verify that the lamp is operating by looking through the front window of the Ion Max housing You can see purple light if the light source is working properly APPI Souce User Manual 55 5 Optimizing the LTO MS Detector with Your Analyte Setting Up the MS Detector for APCI APPI MS Operation APCI APPI Source Vaporizer Temp C 450 00 Sheath Gas Flow Rate arb lo Aux Gas Flow Rate arb Fr Sweep Gas Flow Rate arb fo Discharge Current pA 5 0 Discharge Voltage kV Capillary Temp C 200 00 Capillary
30. the syringe thoroughly a Clean the syringe with a solution of 5 formic acid in water b Rinse the syringe with a solution of 50 50 methanol water c Use acetone to rinse the syringe Repeat this step several times CAUTION AVOID BURNS The APCI vaporizer heater can reach temperatures of 600 xC Always allow the APCI probe to cool to ambient temperature for approximately 20 min before handling or removing the APCI probe from the APCI flange CAUTION AVOID INJURY The corona discharge needle is very sharp and can puncture your skin if you handle it without caution 4 Remove the Ion Max ion source housing as described in the topic Removing the Ion Max Ion Source Housing on page 26 5 Flush the sample transfer line sample tube and APCI probe thoroughly with a solution of 5 formic acid in water or with another appropriate solvent APPI Souce User Manual 49 Note The solvent that you use to flush the sample transfer line sample tube and APCI probe assembly depends on the solvent system you use to dissolve your samples For example if you are using a buffered solution of a high concentration an acidic solution is appropriate a Filla clean 250 uL Unimetrics syringe with an appropriate solvent b While holding the plunger of the syringe in place carefully insert the needle of the syringe into the free end of the Teflon tube c Flush the sample transfer line sample tube and APCI probe with the solution b
31. the tubing is cut straight In addition make sure your LC fittings ferrules and PEEK tubing are installed properly By using these precautions you prevent void dead volumes The exclusion of void volumes is critical to microbore LC Also void volumes affect the quality of the MS detector signal 5 Connect a segment of PEEK tubing from the black LC Tee union to the APCI LC inlet Figure 28 a Usea PEEK tubing cutter to cut a 4 cm 1 5 in length of the PEEK tubing b Connect the PEEK tubing with a brown fingertight fitting and a brown ferrule to a free end of the black LC Tee union c Connect the other end of the PEEK tubing with a red fingertight fitting and a brown ferrule to the LC inlet located on the APCI probe 6 Connect an appropriate length of PEEK tubing transfer line from the divert inject valve from the divert inject valve to the LC Tee union Figure 28 Thermo Scientific APPI Souce User Manual 53 5 Optimizing the LTO MS Detector with Your Analyte Setting Up the Inlet for Tuning Using High Flow Infusion a Connect a length of PEEK tubing with a stainless steel nut and a stainless steel ferrule to port 3 of the divert inject valve b Connect the other end of the PEEK tubing with a brown fingertight fitting and a brown ferrule to the free end of the LC Tee union 7 Connect an appropriate length of PEEK tubing transfer line from the LC from the divert inject valve to the LC
32. 04 with a brown Fingertight fitting and a brown ferrule to the free end of the LC union Figure 20 b Connect the other end of the infusion line with a red Fingertight fitting and a brown ferrule to the side arm of the LC Tee union LC Union Fingertight Fitting P N 00101 18202 P N 00101 18081 a Da mis oan Ferrule Teflon Tube P N 00101 18196 P N 00301 22803 Figure 21 APCI APPI MS plumbing connections for the syringe pump Note To cut the PEEK tubing used to connect your LC to the divert inject valve and the divert inject valve to the APCI source use a PEEK tubing cutter This ensures that the tubing is cut straight In addition make sure your LC fittings ferrules and PEEK tubing are installed properly By using these precautions you prevent void dead volumes The exclusion of void volumes is critical to microbore LC Also void volumes affect the quality of the MS detector signal PEEK Tubing LC Tee Union PEEK Tubing P N 00301 22912 P N 00101 18204 P N 00301 22912 From Divert PAR a Xa Stainless Steel Ferrul F CILE Stainless Steel Nut Ferrules P N 00101 18196 Infusion Line Fused Silica Capillary P N 00106 10504 Ferrules P N 00101 18120 Fingertight Fingertight Fitting Fittings P N 00101 18195 P N 00101 18081 From LC Union Figure 22 APCI APPI MS plumbing connections for the LC Tee union Thermo Scientific APPI Souce User Manua
33. 10 Install a solvent line between the LC system and the divert inject valve a Connect an appropriate length of tubing with a proper fitting and a ferrule to the outlet of the LC system b Connect the other end of the tubing with a nut and ferrule to port 2 of the divert inject valve 11 Install a waste line on the divert inject valve and direct the outlet to a waste container a Connect an appropriate length of tubing with a nut and ferrule to port 6 of the divert inject valve port 6 is labeled with the Rheodyne logo b Insert the other end of the tubing into the waste container You have completed setting up to introduce your compound by auto loop injection Go to the next section Setting Up to Optimize in APCI APPI MS MS Mode with Your Compound 70 APPI Souce User Manual Thermo Scientific 6 Optimizing the TSO Quantum Ultra Mass Spectrometer with Your Analyte Setting Up to Optimize in APCI APPI MS MS Mode with Your Compound Setting Up to Optimize To set up the mass spectrometer to optimize automatically on your in APCI APPI MS MS compound in APCI APPI MS MS mode Mode with Your Com pound turn on the mass spectrometer 1 Click the On Standby button on the Control Scan Mode toolbar to Al 1 2 Tune Master must be placed in the APCI source mode before analyzing samples with the APCI source Choose Setup gt Change Ion Source gt On Standby APCI to place Tune Master in the APCI source mode 3 If desired open a
34. 9 divert inject valve for auto loop injection 68 Save As d b 47 82 Save As dialog box 61 syringe adapter assembly 68 Tune dialog box settings for automatic tuning 59 Tune Master views Inlet Direct Control 75 Optimize Compound Dependent Devices 71 Syringe Pump and Sample Loop 74 Tune Master workspaces Compound Optimization 77 Tune Plus window Automatic page Tune dialog box 46 59 fused silica tubing APCI installing 90 G Graph view displaying 58 freezing 49 63 84 guidelines mass spectrometer operation table 11 interlocks description 20 Ion Max ion source exposing to atmosphere CAUTION 49 63 84 ion source ESI high voltage connector 33 nitrogen gas connections 33 removing 24 ion transfer capillary avoiding burns from CAUTION 88 optimizing temperature of discussion 51 58 temperatures for APPI and APCI 11 ionization modes atmospheric pressure chemical ionization APCI 3 Thermo Scientific ionization potentials 8 L lamp cleaning and polishing 92 installation 96 location 19 removing 95 replacing 95 lamp on off switch description 20 location 18 LC flow rates 11 using buffers discussion 10 LCQ Deca XP MAX cleaning for normal operation 49 LCQ Deca XP Plus system replaceable parts 99 LEDs location 18 18 light source description 17 figure 18 internal components 19 LEDs 21 maintenance 92 safety interlocks 21 light source power cord location 18 LTQ cleaning for normal operation 63 settin
35. APERAABEN EKER ERBE ZU LAM RBRALWVRARe BLAARESS EN T Re hho tH A tk PCB AR ES ER RER TERER RR ENS ho RMA KE BRSAM ANETTE WRFFR RER BG gt aH AiG A A Se Eo Bh AAAA nR N kE ENTE o KX EA HRA T h ah RE KEG gt TB LD OEE o REGS Ei RRA SE KAD T ie RR BS o RE Bh KE RS fa OF tH A KS AR FE KREGER HAREE LLRA A PNR ER eh RE RMLRAB ORR URA PARAS HP o DOM RSI ARE ERE ZWS SOE ERAS LIRR Thermo Scientific Chapter 1 Chapter 2 Chapter 3 Chapter 4 Chapter 5 Contents PIEISEEN ne ee enter ERENT xi Safety anid Special Noten unse xi Contacting Ina xii Introduction cuceasnsunenennnnnnnenn ne 1 Atmospheric Pressure Chemical Ionization n se 3 Atmospheric Pressure Photoionization usersesnesernennenennenenennenn 6 Combined APCI and APPI ouiniec 9 What Types of Buffers Should I Use What Types Should I eoa sae E EE ETE E 10 How Should I Set Up the Mass Spectrometer for Various LC Flow Rates nee 11 Functional Description sccssesesseeseeseseesesessesssseseeeeenieeeeees 13 AP SIT 14 PhotoMate Light Source na 17 Setting Up the lon Source for Acquiring Data in APCI APPI MS MS Mode23 Removing the ESI Probe uurunues ae 24 Removing the Ion Max Ion Source Housing 26 Installing the APCI Probe u aaa 27 Installing the PhotoMate Light Souree auuuuen ehe 30 Installing the Ion Max Ion Source Housing uneeneeee 33 Optimizing the LCQ Deca XP MAX MS Detector with Your Analyte37
36. ATION CAUTION Read and understand the various precautionary notes signs and symbols contained inside this manual pertaining to the safe use and operation of this product before using the device Notice on the Proper Use of Thermo Scientific Instruments In compliance with international regulations Use of this instrument in a manner not specified by Thermo Fisher Scientific could impair any protection provided by the instrument Notice on the Susceptibility to Electromagnetic Transmissions Your instrument is designed to work in a controlled electromagnetic environment Do not use radio frequency transmitters such as mobile phones in close proximity to the instrument For manufacturing location see the label on the instrument WEEE Compliance This product is required to comply with the European Union s Waste Electrical amp Electronic Equipment WEEE Directive 2002 96 EC It is marked with the following symbol Thermo Fisher Scientific has contracted with one or more recycling or disposal companies in each European Union EU Member State and these companies should dispose of or recycle this product See www thermo com WEEEROHS for further information on Thermo Fisher Scientific s compliance with these Directives and the recyclers in your country WEEE Konformitat Dieses Produkt muss die EU Waste Electrical amp Electronic Equipment WEEE Richtlinie 2002 96 EC erf llen Das Produkt ist durch folgendes S
37. Conditions of Sale which Terms and Conditions of Sale shall govern all conflicting information between the two documents Release history Revision C in February 2009 Revision B in June 2006 Revision A in September 2003 Software version Xcalibur 2 0 For Research Use Only Not regulated for medical or veterinary diagnostic use by U S Federal Drug Administration or other competent authorities Regulatory Compliance Thermo Fisher Scientific performs complete testing and evaluation of its products to ensure full compliance with applicable domestic and international regulations For more information refer to manual for your Thermo Scientific mass spectrometer Changes that you make to your system might void compliance with one or more of these EMC and safety standards Changes to your system include replacing a part or adding components options or peripherals not specifically authorized and qualified by Thermo Fisher Scientific To ensure continued compliance with EMC and safety standards replacement parts and additional components options and peripherals must be ordered from Thermo Fisher Scientific or one of its authorized representatives FCC Compliance Statement THIS DEVICE COMPLIES WITH PART 15 OF THE FCC RULES OPERATION IS SUBJECT TO THE FOLLOWING TWO CONDITIONS 1 THIS DEVICE MAY NOT CAUSE HARMFUL INTERFERENCE AND 2 THIS DEVICE MUST ACCEPT ANY INTERFERENCE RECEIVED INCLUDING INTERFERENCE THAT MAY CAUSE UNDESIRED OPER
38. D BURNS At operating temperatures the APCI vaporizer can severely burn you The APCI vaporizer typically operates between 350 and 500 xC Always allow the heated vaporizer to cool to room temperature for approximately 20 min before you touch or remove these components See Figure 8 for the location of parts 1 Place the instrument in Standby mode Thermo Scientific 7 Maintenance Maintaining the APCI Probe 2 Hold onto the APCI probe body with one hand and grasp the head of the APCI nozzle assembly Rotate the head of the nozzle assembly until the flat sides of the head are facing towards the retention flanges See Figure 8 The nozzle assembly is now free of the probe 3 Carefully pull the nozzle assembly straight out of the APCI probe 4 Place the assembly on a clean lint free tissue Cleaning the APCI Probe To clean the APCI probe components Components 1 Remove the APCI nozzle from the probe body 2 Check the condition of the O rings on the APCI nozzle 3 Clean the interior APCI components excluding the ceramic heater with a 50 50 solution of HPLC grade methanol and distilled deionized water and a lint free swab Dry the components with nitrogen gas and place them on a lint free tissue 4 Reinstall any O rings you have removed while cleaning If you do not want to replace the APCI sample tube reinstall the APCI nozzle P N 97055 60089 as described in the topic Reassembling the APCI Probe on page 91
39. Max ion source housing 7 Configure the Syringe Pump to automatically inject the reserpine sample solution into the sample loop a Choose Setup gt Syringe Pump amp Sample Loop to display the Syringe Pump and Sample Loop view in the top right corner of the workspace Figure 39 Thermo Scientific APPI Souce User Manual 73 6 Optimizing the TSO Quantum Ultra Mass Spectrometer with Your Analyte Setting Up to Optimize in APCI APPI MS MS Mode with Your Compound Syringe Flow Control of Flow Rate uL min C Dn Syringe Type Syringe Size C Hamilton Volume pL 500 v Unimetrics Other Syringe ID mm Sample Loop Sample Loop Size uL fo Figure 39 Syringe Pump and Sample Loop view showing auto loop injection setup b Select the Off option button in the Syringe Flow Control group box to turn off the syringe pump e If you are using either a Unimetrics or Hamilton syringe go to step 7 c e If you are not using either a Unimetrics or Hamilton syringe go to step 7 e c In the Syringe Type group box select the Unimetrics or Hamilton option button to specify a Unimetrics or Hamilton syringe d In the Syringe Size group box select 500 or the size of your syringe from the Volume list box to specify that the volume of your syringe is 500 uL When you specify the syringe type and syringe volume Tune Master automatically sets the proper syringe ID value Go to step 7 f e If
40. The light source is a Syagen PhotoMate vacuum ultraviolet VUV light source The assembly is mounted on the left side of the Ion Max ion source housing using a specially designed adapter ring The PhotoMate light source includes the following components See Figure 9 through Figure 11 Power supply Electronics PCB VUV lamp Lamp shield Box fan Lamp On Off switch Safety interlocks Remote LEDs Window APPI Souce User Manual 17 2 Functional Description PhotoMate Light Source Figure 9 PhotoMate light source installed in the lon Max ion source housing side view 18 APPI Souce User Manual Thermo Scientific 2 Functional Description PhotoMate Light Source Figure 10 PhotoMate light source installed in the lon Max ion source housing front view Box Fan Electronics PCB Lamp Shield VUV Lamp Figure 11 PhotoMate light source internal components Thermo Scientific APPI Souce User Manual 19 2 Functional Description PhotoMate Light Source 20 APPI Souce User Manual The power supply provides 48 V dc power for the electronics PCB and fan The LIQ MS detector and TSQ Quantum Ultra mass spectrometer can both supply this power through a DB 15 cable connection The LTQ MS detector is also able to control the lamp status through the connection The LCQ Deca XP MAX requires that this power be supplied via an external power supply which is also connected using the DB 15 connection The electronics PCB contains
41. Voltage v a0 H Tube Lens V 100 00 es V APPI Lamp On Apply Cancel Help Figure 29 APCI APPI Source dialog box showing the proper settings for a typical high flow experiment 4 Define the scan parameters for tuning the MS detector in the APCI APPI MS mode a On the Control Scan Mode toolbar click on the Define Scan Dd button to open the Define Scan dialog box See Figure 30 If your dialog box appears different from the one shown in the figure it is probably because the advanced settings are not displayed You can turn on the advanced settings as follows In Tune Plus choose ScanMode and then click Advanced Scan Features to select the option b In the Scan Description group box in the Mass Range list box select Normal to allow for a selection of mass ranges between m z 150 to 2000 c Inthe Scan Rate list box select Normal to specify a normal scan rate d In the Scan Type list box select SIM to specify a selected ion monitoring scan e In the Scan Time group box in the Microscans spin box enter 1 to set the total number of microscans to 1 f In the Max Inject Time spin box enter 200 000 to specify a 200 ms maximum injection time 56 APPI Souce User Manual Thermo Scientific 5 Optimizing the LTO MS Detector with Your Analyte Setting Up the MS Detector for APCI APPI MS Operation Define Scan Scan History ITMS c SIM ms 608 20 610 20 JB Scan Description MSn Settings Scan Ranges No
42. a waste container a Connect a length of PEEK tubing with a stainless steel nut and a stainless steel ferrule to port 1 of the divert inject valve b Insert the other end of the PEEK tubing into a suitable waste container CAUTION Prevent solvent waste from backing up into the API ion source and MS detector Always ensure that the PVC drain hose is above the level of liquid in the waste container 8 Connect an appropriate length of l in 2 5 cm OD Tygon tubing hose to the Ion Max ion source housing drain fitting Attach the other end of 40 APPI Souce User Manual Thermo Scientific 4 Optimizing the LCQ Deca XP MAX MS Detector with Your Analyte Setting Up the Inlet for Tuning Using High Flow Infusion the hose to a suitable waste container Ideally the waste container should be vented to a fume exhaust system Thermo Scientific APPI Souce User Manual 4 4 Optimizing the LCQ Deca XP MAX MS Detector with Your Analyte Setting Up the MS Detector for APCI APPI MS Operation Setting Up the MS Detector for APCI APPI MS Operation On Standby 42 APPI Souce User Manual To set up the MS detector for APCI APPI MS operation on the XP Plus 1 In Tune Plus click on the On Standby button to take the MS detector out of Standby mode and turn it on The MS detector begins scanning and applies the high voltage to the corona needle and shows a real time display in the Spectrum view 2 Open the APCTTune LCQTune Tune Method the
43. acquire data go to the next topic Cleaning the Mass Spectrometer After Tuning in APCI Mode Thermo Scientific APPI Souce User Manual 83 6 Optimizing the TSO Quantum Ultra Mass Spectrometer with Your Analyte Cleaning the Mass Spectrometer After Tuning in APCI Mode Cleaning the Mass use the following procedure to clean the mass spectrometer after tuning on Spectrometer After Tuning in APCI Mode a OnStandby A A 84 APPI Souce User Manual your analyte of interest 1 Click on the On Standby button to put the mass spectrometer in Standby mode When the mass spectrometer is in Standby the TSQ Quantum Ultra mass spectrometer turns off the vaporizer heater corona discharge voltage and syringe pump The mass spectrometer stops scanning and freezes the displays for the Spectrum and Graph views CAUTION Always place the mass spectrometer in Standby or Off before you open the API source to atmospheric oxygen The presence of oxygen in the ion source when the mass spectrometer is On could be unsafe The TSQ Quantum Ultra mass spectrometer automatically turns off when you open the API source however it is best to take this added precaution 2 Remove the syringe from the syringe pump holder a Squeeze the blue buttons and pull back on the syringe pump handle to free the syringe b Remove the syringe from the holder c Disconnect the tip of the syringe needle from the Teflon tubing 3 Clean the syringe thoroughly
44. ainer ring with four hex head screws See Figure 56 14 Reinstall your API probe in the Ion Max ion source housing You are now ready to perform ESI or APCI experiments or to install the PhotoMate light source 104 APPI Souce User Manual Thermo Scientific A Installing the PhotoMate Light Source Adapter Ring Cover Retaining Screws Probe Alignment Screw Cover Retaining Screws Figure 52 Left side of the lon Max ion source housing showing the probe alignment screw and cover retaining screws Thermo Scientific APPI Souce User Manual 105 A Installing the PhotoMate Light Source Adapter Ring Viewport Frame crews Figure 53 lon Max ion source housing with left cover removed showing the viewport frame and screws 106 APPI Souce User Manual Thermo Scientific A Installing the PhotoMate Light Source Adapter Ring Figure 54 Aligning the APPI adapter ring Figure 55 Inserting the small viewport window into the APPI adapter ring Thermo Scientific APPI Souce User Manual 107 A Installing the PhotoMate Light Source Adapter Ring Figure 56 Completed APPI adapter ring installation 108 APPI Souce User Manual Thermo Scientific Thermo Scientific Appendix B Reserpine Solution Formulations This appendix provides instructions for preparing the tuning and calibration solution and the reserpine solution that is used to optimize the tune of the mass spectrometer The sections in this appendix are as follows
45. als Wear gloves when handling toxic carcinogenic mutagenic or corrosive or irritant chemicals Use approved containers and proper procedures to dispose waste oil Heat Before servicing the instrument allow any heated components to cool Fire Use care when operating the system in the presence of flammable gases Eye Hazard Eye damage could occur from splattered chemicals or flying particles Wear safety glasses when handling chemicals or servicing the instrument General Hazard A hazard is present that is not included in the above categories Also this symbol appears on the instrument to refer the user to instructions in this manual When the safety of a procedure is questionable contact your local Technical Support organization for Thermo Fisher Scientific San Jose Products AREE EE ICH SIBBETR L MECEEESAS TER ET ORF BER UP RRE ILL BRE MoCMORMLTR SY ERA ABA LIKE T atlas SHA LAY CF EY FY HER ROR NIZA EB THE GEE SERTHLEMARHASFIFELTVZUTEENDU ET BE FEA RARER ER MREREOHSRAERY MIM FRE SALTS EADY MEORBL PIRSRALTR SY Rh AS RO KMAILINA BODE GO CDOT ERLITTEN KR TEON RAFET SB CLAT AERE EBEN HORDES thot RECH TAER EDR CRLF IRR L CARE OT DERE Y E Fo ANRI RO HSVITHAMBORT ERR L TARR E ZALTFAL RNIT OPIS LIAO 4 TORENFETSLLERLE To Er HMBC OBMAIOTWSBEIL KAVHATVPORRES FALTFAY BEEERTZEIRD hhb FEE RPRILL BES OU ELLY FOVHVA tIAGZ bOFI A WTRK bL ya lZ EEL EREE 2S RARAR
46. amounts of samples and solvents that are introduced into the system This chapter contains the following sections e Maintaining the APCI Probe e Maintaining the PhotoMate Light Source APPI Souce User Manual 87 7 Maintenance Maintaining the APCI Probe Maintaining the APCI Probe Removing the APCI Nozzle 88 APPI Souce User Manual The APCI probe requires a minimum of maintenance The APCI sample tube 100 um ID fused silica tubing is pre loaded at the factory However if the sample tube becomes obstructed with salt precipitates or is broken you need to replace it Also you might need to remove and clean the APCI nozzle Figure 7 and Figure 8 on Figure 9 show the major components of the APCI probe Note You should flush the APCI probe at the end of each working day by flowing a 50 50 methanol water solution from the LC through the APCI source Wear clean gloves when you handle APCI probe components The following procedures are discussed in this section e Removing the APCI Nozzle e Cleaning the APCI Probe Components e Removing the APCI Sample Tube e Installing a New APCI Sample Tube e Reassembling the APCI Probe To remove the APCI nozzle from the APCI probe CAUTION Do not break the APCI sample tube In step 1 carefully pull the APCI nozzle straight back from the APCI probe to prevent the sample tube from touching the sides If the sample tube hits the sides of the vaporizer it can break CAUTION AVOI
47. andby Note If your ESI probe does not already have a sample tube fused silica capillary and safety sleeve attached you need to follow the procedure for installing a sample tube and PEEK safety sleeve that is outlined in the topic Installing a New Fused Silica Sample Tube and PEEK Safety Sleeve in the Ion Max API Source Hardware Manual 2 Disconnect the sample transfer tubing from the stainless steel ZDV fitting grounding union See Figure 12 3 Remove the 8 kV cable from the ESI needle high voltage receptacle as follows See Figure 12 4 Unlock the cable by twisting the locking ring counter clockwise 5 Unplug the 8 kV cable from the ESI needle high voltage receptacle 6 Disconnect the AUX Gas fitting green from the auxiliary gas inlet A on the probe manifold Figure 12 7 Disconnect the Sheath Gas fitting blue from the sheath gas inlet S on the probe manifold Thermo Scientific Thermo Scientific PEEK Safety Sleeve Grounding Bar Grounding Union Sheath Gas Fitting Sample Transfer Tubing 3 Setting Up the lon Source for Acquiring Data in APCI APPI MS MS Mode Removing the ESI Probe 8 Remove the stainless steel ZDV fitting Grounding Union from the grounding bar on the ion source housing ESI Interlock Socket Auxiliary Fitting u DECO As AALI TTN Figure 12 lon Max ion source housing with ESI probe installed 9 Unlock the probe locking lever by twisting the
48. ate light source Thermo Scientific APPI Souce User Manual 100 8 Replaceable Parts Vaporizer Heater Cable Socket Guide Pin Retention Flange Flat Side APCI Nozzle Assembly Retention Flange Figure 50 APCI Probe Assembly OPTON 20012 00107 04500 on 07 05600 Oz 97055 20221 a 00106 10468 7005 20220 en 00101 18120 Co 00107 04000 9 Cy 70005 20250 Figure 51 APCI probe nozzle assembly P N 97055 60089 Thermo Scientific APPI Souce User Manual 101 Thermo Scientific Appendix A Installing the PhotoMate Light Source Adapter Ring This chapter provides information on installing the Photomate light source adapter ring in the Ion Max ion source housing You only need to perform this procedure the first time you use your source If you do not want to use the APPI lamp for a particular experiment you can install the smaller viewport window that fits within the Photomate light source adapter ring There is no need to remove the ring when not in APPI mode as long as the small viewport window is installed Install the APPI adapter ring as follows 1 2 Stop the flow of sample solution from the LC Place the MS detector in standby Remove the currently installed API probe as described in the lon Max API Source Hardware Manual Unscrew and remove the probe alignment screw on the left side of the Ion Max ion source housing See Figure 52 Using the special hex head wrench prov
49. automatic tuning procedure from the Tune dialog box a Click Start A message box displays the following message b Please ensure that the 500 microliter syringe is full c Ensure the syringe pump contains at least 420 uL of the 1 ng uL reserpine tuning solution d Click OK to close the message box and return to the Tune Plus window 5 On the File Display toolbar click on the Graph View button to display the view 6 Observe the Tune Plus window and the Tune dialog box While automatic tuning is in progress LCQ Deca XP MAX displays various APPI Souce User Manual 45 4 Optimizing the LCO Deca XP MAX MS Detector with Your Analyte Optimizing the Tune of the MS Detector Automatically in APCI APPI MS Mode tests in the Spectrum and Graph views in the Tune Plus window and displays various messages in the Status group box in the Tune dialog box Your Tune Plus window should now look similar to the one shown in Figure 25 You have now successfully tuned the MS detector in APCI APPI MS mode for the compound reserpine or your analyte of interest Leave the LC pumps on with a flow rate of approximately 1 mL min leave the APClhighflow LCQTune file open in the Tune Plus window and go on to the next topic Saving the APCI APPI MS Tune Method Ei Se E Va se he zul a WH isst at RED Sf 3537 IT 15 26 ST 0 37 NL 1 02e 007 2 61e 007 9 Adjusting Tube Lens Offset 100 609 2 Tune e0920 5 610 1 LA A
50. ck Save to save the Tune Method and return to the Tune Plus window Note that the Tune Method is named APCImyTune LCQTune Before you acquire data go to the next topic Cleaning the MS Detector after Tuning in APCI Mode 48 APPI Souce User Manual Thermo Scientific Cleaning the MS Detector After Tuning in APCI Mode a OnStandby Thermo Scientific A 4 Optimizing the LCQ Deca XP MAX MS Detector with Your Analyte Cleaning the MS Detector After Tuning in APCI Mode To clean the MS detector after tuning on your analyte of interest 1 Click on the On Standby button to put the MS detector in Standby mode When the MS detector is in Standby the LCQ Deca XP MAX MS detector turns off the vaporizer heater corona discharge voltage and syringe pump The MS detector stops scanning and freezes the displays for the Spectrum and Graph views CAUTION Always place the MS detector in Standby or Off before you open the API source to atmospheric oxygen The presence of oxygen in the ion source when the MS detector is On could be unsafe The LCQ Deca XP MAX MS detector automatically turns off when you open the API source however it is best to take this added precaution 2 Remove the syringe from the syringe pump holder a Squeeze the blue buttons and pull back on the syringe pump handle to free the syringe b Remove the syringe from the holder c Disconnect the tip of the syringe needle from the Teflon tubing 3 Clean
51. d The front door of the source housing must be closed and locked to engage the interlock APPI Souce User Manual 97 Thermo Scientific Chapter8 Replaceable Parts This chapter contains part numbers for replaceable and consumable parts for the Ion Max APCI probe and Photomate light source To ensure proper results in servicing the ion source order only the parts listed or their equivalent Please refer to the figures on the subsequent pages for the location of each part listed The replaceable parts are as follows ADDI Lang itasacsuisaineasendunnalhesndte OPTON 20026 APPI circuit assembly amp fan Ion Max 00950 10010 Cable APPI Ion Mascus 00950 10011 APPLIED n een 00950 10002 APPEPOWwer Sippe 00950 10012 AP Probe nase OPTON 20012 APCI Probe Nozzle Assembly sssssssssssssessesssssssseseees 97055 60089 Ferrule 0 016 ID PEEK HPLC u 00101 18120 Tubing fused silica 150 um ID X 390 um OD 00106 10498 O ring 0 239 in ID 1 16 in Viton 00107 04000 O ring 0 312 in ID 1 16 nee 00107 04500 O ring 0 500 in ID 1 16 in Vienna 00107 05600 Fitting 10 32 male nut PEER uses 70005 20220 Fitting APCI flange une 70005 20250 Nozzle APC prebesn aeg 97055 20221 APPI Souce User Manual 99 8 Replaceable Parts APCI Probe lon Max lon Source Housing Booe2000002020200008 beeoeoeoeooeoeoeoeoooe8o Photomate Light Source Figure 49 lon Max ion source housing showing the APCI probe and PhotoM
52. d with your application e Ifyou were unable to remove all material from the window you need to remove the VUV lamp and polish the window Continue with step 7 CAUTION Always wear clean gloves when you are handling a functional VUV lamp Fingerprints on the lamp can cause the lamp to fail when it is in use 6 While wearing clean gloves grasp the VUV lamp and pull the lamp out e If you are able to remove the VUV lamp go to step 10 e Ifyou are having trouble removing the lamp you need to push it out from the top Go to step 7 7 Remove the PhotoMate light source by removing the retaining screws that hold the assembly to the adapter ring then pulling the assembly straight out until it is free from the lon Max ion source housing 8 Remove the box top from the PhotoMate light source a Remove the light source power cord from the light source b Remove the 4 Phillips screws that secure the box top to the light source c Remove the box top from the electronics PCB but keep the fan power cable connected 9 Insert an Allen key into the lamp hole in the electronics PCB See Figure 48 Gently push out the VUV lamp with the Allen key Thermo Scientific APPI Souce User Manual 93 7 Maintenance Maintaining the PhotoMate Light Source 94 APPI Souce User Manual Lamp Hole me Bo he RL gt LTP 2 C4 xy EEA in bee u aa peeeeedeenes bbidsbibbid 2 T om EPPEN gt TUU Figure 48 Light so
53. de the PEEK fitting and ferrule down the fused silica tubing and into the sample tube inlet fitting Tighten the PEEK fitting to secure the new sample tube fused silica tubing Thermo Scientific 7 Maintenance Maintaining the APCI Probe 7 Use a fused silica cutting tool to cut the exit end of the sample tube so that approximately 1 mm protrudes past the tip of the APCI nozzle See Figure 47 Figure 47 Proper position of the exit end of the APC sample tube Reassembling the APCI Probe To reassemble the APCI probe 1 With one hand holding the APCI probe body to keep the probe from turning carefully insert the APCI nozzle into the APCI probe 2 With the flat sides of the APCI nozzle head facing upwards towards the retention flanges on the probe body seat the nozzle head completely flat against the probe 3 To secure the APCI nozzle in the probe rotate the head of the nozzle 90 degrees to secure the round sides of the nozzle head in the retention flanges To reinstall the probe in the lon Max API source housing see Installing the APCI Probe on page 27 Thermo Scientific APPI Souce User Manual 91 7 Maintenance Maintaining the PhotoMate Light Source Maintaining the PhotoMate Light Source Cleaning and Polishing the Window of the VUV Lamp A A 92 APPI Souce User Manual This section includes the following topics for cleaning and replacing components of the PhotoMate light source e Clean
54. duction from the syringe pump into the solvent flow from an LC are shown in Figure 34 Note You can use the reserpine sample solution described in Appendix B Reserpine Solution Formulations or you can use your compound of interest a f I Therme I FINNIGAN 750 Quantum JITRA Ss Il Mi K Figure 34 APCI MS plumbing connections for sample introduction by auto loop injection into the solvent flow from an LC Thermo Scientific To make the plumbing connections for APCI MS sample introduction from the syringe pump into the solvent flow from an LC 1 Remove the syringe from the syringe pump holder APPI Souce User Manual 67 6 Optimizing the TSO Quantum Ultra Mass Spectrometer with Your Analyte Setting Up to Introduce Sample by Auto Loop Injection in APC Mode a Lift the handle off the syringe while depressing the black release button on the syringe pump handle b Remove the syringe c Remove the tip of the syringe needle from the end of the Teflon tube on the syringe adapter assembly Figure 35 LC Union Fingertight fitting 00101 18202 00101 18081
55. e User Manual xi Preface Contacting Us Contacting Us There are several ways to contact Thermo Fisher Scientific for the information you need To contact Technical Support Phone 800 532 4752 Fax 561 688 8736 E mail us techsupport analyze thermofisher com Knowledge base www thermokb com Find software updates and utilities to download at mssupport thermo com To contact Customer Service for ordering information Phone 800 532 4752 Fax 561 688 8731 E mail us customer support analyze thermofisher com Web site www thermo com ms To copy manuals from the Internet Go to mssupport thermo com and click Customer Manuals in the left margin of the window To suggest changes to documentation or to Help Send an e mail message to the Technical Publications Editor at techpubs lcms thermofisher com xii APPI Source User Manual Thermo Scientific Thermo Scientific Chapter 1 Introduction The Ion Max ion source is a member of the Thermo Scientific family of mass spectrometer ion sources Your Ion Max APCI APPI combination probe allows you to perform successful qualitative and quantitative analysis on a wide range of compounds including steroids peptides basic drug entities and pesticides You can use APPI and APCI to study compounds that are not readily ionized by electrospray ionization ESI See Figure 1 You can operate your APCI APPI combination probe using the following ionization techniques e Atmosp
56. e tuning your TSQ Quantum Ultra in the APCI APPI MS MS mode using your analyte as the tuning compound You optimize the sensitivity of the mass spectrometer for your analyte with an automatic tuning procedure This chapter contains the following sections e Setting Up to Introduce Sample by Auto Loop Injection in APCI Mode e Setting Up to Optimize in APCI APPI MS MS Mode with Your Compound e Optimizing in APCI APPI MS MS Mode Automatically with Your Compound e Saving the Tune Method e Cleaning the Mass Spectrometer After Tuning in APCI Mode The Tune Methods that are provided with your TSQ Quantum Ultra are useful for a wide range of applications They can often be used without further tuning of your mass spectrometer However for certain applications you might need to optimize several mass spectrometer parameters For instance the parameters that affect APCI performance and signal quality are as follows e Discharge current e APCI vaporizer temperature e Sheath gas pressure e Auxiliary gas flow rate e Capillary temperature Tube lens offset voltage APPI Souce User Manual 65 6 Optimizing the TSO Quantum Ultra Mass Spectrometer with Your Analyte The optimum settings for these parameters depend on the solvent flow rate and on the structure of your analyte In general you need to fine tune the mass spectrometer parameters whenever you change the solvent flow rate conditions of your particular application When you optimize
57. eaning for normal operation 84 Tune dialog box figure 59 showing settings for automatic tuning figure 59 Tune Method saving 47 61 82 Tune Plus window tuning 46 tuning results 59 U user interface Tune Master changing syringe pump and sample loop parameters 73 direct control of Surveyor LC system 75 75 manually changing device parameters 72 manually changing scan parameters 78 optimizing in the APCI MS mode 77 optimizing in the ESI MS mode 78 preparing for optimizing 71 76 saving the Tune Method 80 switching between ESI and APCI operation 71 Thermo Scientific Index V V vaporizer APCI probe description 14 location 15 temperature 14 temperatures for APPI and APCI 11 voltages corona discharge needle 14 VUV lamp cleaning and polishing 92 discussion 20 installation 96 location 19 removing 95 replacing 95 APPI Souce User Manual Thermo Scientific 119
58. entific APPI Souce User Manual 13 2 Functional Description APCI Source 14 APCI Source APPI Souce User Manual The APCI probe ionizes the sample by atmospheric pressure chemical ionization The APCI probe accommodates liquid flows of 100 uL min to 2 mL min without splitting See Figure 6 The APCI probe includes the APCI sample tube nozzle sheath gas and auxiliary gas plumbing and vaporizer See Figure 7 and Figure 8 Sample and solvent enter the APCI nozzle through the sample tube The sample tube is a short section of 0 10 mm ID fused silica tubing that extends from the sample inlet to 1 mm past the end of the nozzle The manifold houses the APCI nozzle and includes the sheath gas and auxiliary gas plumbing The APCI nozzle sprays the sample solution into a fine mist The sheath gas and auxiliary gas plumbing deliver dry nitrogen gas to the nozzle The droplets in the mist then enter the vaporizer The vaporizer flash vaporizes the droplets at temperatures up to 500 C lon Transfer APCI Capillary Probe Corona Needle Ion Transfer Capillary Entrance Figure 6 APCI probe showing the corona discharge needle and ion transfer capillary Typical vaporizer temperatures are 350 to 450 C for flow rates of 0 1 to 2 mL min The sample vapor is swept toward the corona discharge needle by the flow of the sheath and auxiliary gasses The corona discharge needle assembly is mounted inside of the lon Max API source housing T
59. etaining Screws 7N gt lon Source Housing Locking Lever s lon Source Housing Drain Probe Alignment Screw Cover Retaining Screws Figure 13 lon Max ion source showing details of components 26 APPI Souce User Manual Thermo Scientific 3 Setting Up the lon Source for Acquiring Data in APCI APPI MS MS Mode Installing the APC Probe Installing the APCI To install the APCI probe Probe 1 Install the corona needle A CAUTION AVOID INJURY The corona discharge needle is very sharp and can puncture your skin Handle it with care a Unlock the ion source housing door by turning the locks 90 degrees so that the knobs are horizontal b Open the ion source housing door c Using pliers grasp the needle by the gold plated contact and push the needle straight into the socket See Figure 14 Gold Plated gt Figure 14 Corona needle view from rear d Make sure that the tip of the needle is aligned with the path of travel between the APCI probe and the ion source interface on the instrument e Close and lock the ion source housing door 2 Connect the 8 kV cable to the corona needle high voltage receptacle a Plug the 8 kV cable into the corona needle high voltage receptacle on the right side of the top of the ion source housing b Lock the cable by twisting the locking ring clockwise 3 Be sure to unlock the probe locking lever widest open position before attempting to install the probe T
60. g up for APCI MS operation 55 maintenance APCI probe 88 APCI probe components cleaning 89 APCI sample tube installing 90 light source 92 overview 87 87 maintenance procedures cleaning and polishing VUV lamp 92 overview 87 replacing the VUV lamp 95 mass spectrometer ionization modes 1 operational guidelines table 11 methods Tune APPI Souce User Manual Index L opening predefined 42 MS detector maintenance overview 87 setting up for APCI MS operation 42 Notes avoiding contamination of syringe 69 cutting PEEK tubing 39 53 optimizing on compound of interest 67 reconditioning the APCI 72 removing contamination from APCI 72 saving Tune Method 80 selecting appropriate inlet type 78 solvents 50 64 85 nozzle APCI reinstalling 89 APCI removing 89 0 operating parameters APPI and APC 11 P PEEK tubing cutting note 39 PEEK tubing cutting note 53 PhotoMate 17 PhotoMate light source 18 description 17 figure 18 internal components 19 LEDs 21 maintenance 92 safety interlocks 21 plumbing for divert inject valve 69 auto loop injection 68 syringe pump Tee to LC APCI 38 power supply discussion 20 procedures cleaning LCQ Deca XP MAX after tuning and calibrating 49 LTQ after tuning and calibrating 63 TSQ Quantum Ultra after tuning and calibrating 84 compound optimization APCI MS mode 77 installing ESI source 23 optimizing Thermo Scientific 117 Index R LCQ Deca XP MAX APCI Tune 45 TSQ
61. he tip of the corona discharge needle is positioned near the vaporizer A high potential typically 3 to 5 kV is applied to the Thermo Scientific 2 Functional Description APCI Source corona discharge needle to produce a corona discharge current of up to 100 uA A typical value of the corona discharge current is 5 uA The corona discharge from the needle produces reagent ion plasma primarily from the solvent vapor The sample vapor is ionized by ion molecule reactions with the reagent ions in the plasma APCI requires a constant source of electrons for the ionization process Thus the corona discharge current is set to a specific value and regulated The potential applied to the corona discharge needle varies as needed to provide the required current Vaporizer Heater Cable Socket APCI Nozzle 0 312 ID O ring Ceramic Heater Tube N 77 Tun IA O Ring u UCRDG EZ GG Ws ty A _ re O EOEOFORUHHLAe 70 0 0 0 gt 5 gt 02 92 2227 7Z In Sample WY LLLE Sample Tube Figure 7 Cross sectional viewof the APC probe Thermo Scientific APPI Souce User Manual 15 2 Functional Description APCI Source Vaporizer Heater Cable Socket Retention Flange Flat Side APCI Nozzle Assembly Retention Flange Figure 8 APCI probe exterior 16 APPI Souce User Manual Thermo Scientific PhotoMate Light Thermo Scientific Source 2 Functional Description PhotoMate Light Source
62. her appropriate solvent as follows Note The solvent that you use to flush the sample transfer line sample tube and APCI probe assembly depends on the solvent system you use to dissolve your samples For example if you are using a buffered solution of a high concentration an acidic solution is appropriate a Fill a clean 250 uL Unimetrics syringe with an appropriate solvent b While holding the plunger of the syringe in place carefully insert the needle of the syringe into the free end of the Teflon tube c Flush the sample transfer line sample tube and APCI probe with the solution by slowly depressing the syringe plunger Visually check that the solution is exiting the tip of the APCI probe on the inside of the probe assembly Use a lint free tissue to gently remove the excess solution as it exits the probe d Remove the needle of the syringe from the Teflon tube 6 Repeat step 5 with a solution of 50 50 methanol water 7 Reinstall the Ion Max ion source housing as described in topic Installing the Ion Max Ion Source Housing on page 33 Your LTQ MS detector is now ready to perform experiments in APCI APPI mode Please refer to Chapter 7 Maintenance for information regarding the maintenance of the Ion Max APPI source 64 APPI Souce User Manual Thermo Scientific Thermo Scientific Chapter6 Optimizing the TSQ Quantum Ultra Mass Spectrometer with Your Analyte This chapter provides information on fin
63. heric pressure chemical ionization APCI e Atmospheric pressure photoionization APPI e Combined APCI and APPI APPI Souce User Manual 1 1 Introduction 10 000 1 000 MW 100 10 Nonpolar lonic Polarity Figure 1 Ranges of applicability of APPI APCI and ESI 2 APPI Souce User Manual Thermo Scientific Atmospheric Pressure Chemical lonization Thermo Scientific 1 Introduction Atmospheric Pressure Chemical lonization Atmospheric pressure chemical ionization APCI is a soft ionization technique but not as soft as ESI APCI is used to analyze compounds of medium polarity that have some volatility In APCI ions are produced and analyzed as follows 1 The APCI nozzle sprays the sample solution into a fine mist of droplets 2 The droplets are vaporized in a high temperature tube the vaporizer 3 A high voltage is applied to a needle located near the exit end of the tube The high voltage creates a corona discharge that forms reagent ions through a series of chemical reactions with solvent molecules and nitrogen sheath gas 4 The reagent ions react with sample molecules to form sample ions 5 The sample ions enter the mass spectrometer and are analyzed Figure 1 shows the APCI process for positive adduct ion formation APCI is a gas phase ionization technique Therefore the gas phase acidities and basicities of the analyte and solvent vapor play an important role in the APCI process In the positive ion mode
64. hermo Scientific APPI Souce User Manual 27 3 Setting Up the lon Source for Acquiring Data in APCI APPI MS MS Mode Installing the APC Probe 4 Insert the APCI probe into the port in the ion source housing Align the guide pin on the probe body at a 45 degree angle from the ESI interlock block See Figure 15 Vaporizer Heater Cable Socket Sheath Gas Inlet Guide Pin Sample Inlet Fitting Gas Inlet Figure 15 APCI probe 5 Push the probe into the port until the guide pin meets with the locking ring on the housing 6 Turn the probe 45 degrees clockwise and align the guide pin with the slot in the ESI interlock block you might need to pull the probe towards you slightly to properly align the pin with the notch 7 After you have turned the probe far enough to align the pin with the alignment notch at the rear of the port push the probe straight in until the guide pin stops at the bottom of the alignment notch 8 Seat the probe all the way down into the alignment notch 9 Lock the probe in place by twisting the probe locking lever towards the front of the housing Closing the probe locking lever towards the rear of the ion source housing may make it difficult to unlock 10 Unplug the vaporizer heater cable from the ESI interlock plug on the ion source housing 11 Connect the vaporizer heater cable to the vaporizer heater cable socket on the APCI probe 28 APPI Souce User Manual Thermo Scientific 3 Setti
65. ic sites such as carboxylic acids and acid alcohols produce more negative ions than positive ions Thermo Scientific Thermo Scientific 1 Introduction Atmospheric Pressure Chemical lonization Although in general fewer negative ions are produced than positive ions negative ion polarity is sometimes the mode of choice This is because the negative ion polarity mode sometimes generates less chemical noise than does the positive mode Thus selectivity might be better in the negative ion mode than in the positive ion mode APPI Souce User Manual 5 1 Introduction Atmospheric Pressure Photoionization Atmospheric Pressure Atmospheric pressure photoionization APPI is also a soft ionization Photoionization technique In APPI an ion is generated from a molecule when it interacts with a photon from a source of light such as the Syagen PhotoMate light source APPI generates molecular ions for molecules that have an ionization potential below the photon energy of the light being emitted by the light source In APPI ions are produced and analyzed as follows 1 The nozzle sprays the sample solution into a fine mist of droplets 2 The droplets are vaporized in a high temperature tube the vaporizer 3 The analyte molecule interacts with the light from the PhotoMate light source The analyte molecule M is ionized to a molecular ion M if the ionization potential of the analyte is less than the photon energy hv 4 M hv gt M ce 5
66. ided with your APPI source remove the four retaining screws from the left hand side lon Max ion source housing cover Pull the cover straight out and free from the Ion Max ion source housing Remove the two screws that hold the lon Max viewport frame in place Be careful not to allow the window to fall free and break See Figure 53 Align the APPI adapter ring so that the flat side fits against the rear of the Ion Max ion source housing and so that both holes in the ring align with the holes in the Ion Max ion source housing Secure the ring with the two screws that you removed from the viewport frame See Figure 54 APPI Souce User Manual 103 A Installing the PhotoMate Light Source Adapter Ring 9 Replace the source housing cover and secure the cover with all four hex head screws 10 Replace the probe alignment screw in the Ion Max ion source housing 11 Complete the installation e Ifyou are going to proceed with an APPI experiment install the APCI probe and PhotoMate light source as described in Chapter 3 Setting Up the Ion Source for Acquiring Data in APCI APPI MS MS Mode or e Ifyou will not be performing an APPI experiment at this time complete steps 12 to 14 before continuing with your experiments Do not attempt to operate any Ion Max ion source without the viewport window installed 12 Carefully install the small viewport window in the APPI adapter ring See Figure 55 13 Secure the ret
67. ing Up the Inlet for Tuning Using High Flow Infusion Setting Up the Inlet The plumbing connections for the APCI APPI MS sample introduction for Tuning Using from the syringe pump are shown in Figure 20 High Flow Infusion To make the plumbing connections for APCI APPI MS sample introduction from the syringe pump into solvent flow from an LC 1 Connect a 4 cm 1 5 in segment of Teflon tubing with a brown Fingertight fitting and a brown ferrule to the black LC union See Figure 21 Load a clean 500 uL Unimetrics syringe P N 00301 19012 with 420 uL of a 1 ng uL solution of reserpine or your analyte of interest Refer to Appendix B Reserpine Solution Formulations for a procedure for making the reserpine tuning solution 2 Insert the needle of a syringe into the segment of Teflon tubing and place the syringe in the syringe holder of the syringe pump IC Deca XP MAX From LC SN LC Tee Union To Waste Thermo ELECTRON CORPORATION Syringe Pump Figure 20 APCI APPI MS plumbing connections for sample introduction from the syringe pump into solvent flow from an LC 3 Connect a fused silica infusion line from the black LC union to the black LC Tee union 38 APPI Souce User Manual Thermo Scientific 4 Optimizing the LCQ Deca XP MAX MS Detector with Your Analyte Setting Up the Inlet for Tuning Using High Flow Infusion a Connect the infusion line P N 00106 105
68. ing and Polishing the Window of the VUV Lamp e Replacing the VUV Lamp Typically flowing a 50 50 methanol distilled water solution from the LC through the APCI APPI combination probe at the end of each working day will clean the VUV lamp In some instances the VUV lamp window might require additional cleaning or polishing A weak ion signal might indicate a build up of salts or other contaminants on the VUV lamp window To clean or polish the VUV lamp window CAUTION AVOID BURNS The APCI vaporizer heater can reach temperatures of 600 xC Always allow the APCI APPI combination probe to cool to ambient temperatures before handling or removing the APCI APPI combination probe 1 Ensure that the MS system is in Standby and the LC flow has been halted 2 Unplug the power communication cable from the PhotoMate light source 3 Open the front door of the Ion Max ion source housing CAUTION Do not apply solvent to the VUV lamp while it is hot The VUV lamp can crack AVOID INJURY The corona discharge needle is very sharp Use caution when cleaning the VUV lamp 4 Use a cotton swab that is soaked with LC solvents to wash the window end of the VUV lamp Ensure that no lint remains on the lamp Thermo Scientific 7 Maintenance Maintaining the PhotoMate Light Source 5 Inspect the window of the VUV lamp Ifno material remains on the window close and secure the front door of the Ion Max ion source housing and procee
69. l 31 3 Setting Up the lon Source for Acquiring Data in APCI APPI MS MS Mode Installing the PhotoMate Light Source Notch Tab Figure 17 Aligning the tab on the PhotoMate light source with the adapter ring 32 APPI Souce User Manual Thermo Scientific 3 Setting Up the lon Source for Acquiring Data in APCI APPI MS MS Mode Installing the lon Max lon Source Housing Installing the lon Max Toreinstall the lon Max ion source housing lon Source Housing 1 Carefully align the two guide pin holes on the rear of the ion source housing with the ion source housing guide pins on the mass spectrometer and carefully press the ion source housing onto the ion source mount See Figure 18 and Figure 19 lon Source Housing Locking Levers Guide lon Source Pin Holes Housing Drain Figure 18 Rear view of the lon Max ion source housing PhotoMate light source not shown Thermo Scientific APPI Souce User Manual 33 3 Setting Up the lon Source for Acquiring Data in APCI APPI MS MS Mode Installing the lon Max lon Source Housing Guide Pins Figure 19 lon source mount showing ion source housing guide pins 2 Rotate the ion source housing locking levers 90 degrees to lock the ion source housing onto the ion source mount assembly CAUTION Prevent solvent waste from backing up into the ion source and mass spectrometer Always ensure that liquid in the drain tube is able to drain to a waste container and
70. l 39 4 Optimizing the LCQ Deca XP MAX MS Detector with Your Analyte Setting Up the Inlet for Tuning Using High Flow Infusion 4 Connect a segment of PEEK tubing from the black LC Tee union to the APCI LC inlet Figure 22 a Use a PEEK tubing cutter to cut a 4 cm 1 5 in length of the PEEK tubing b Connect the PEEK tubing with a brown Fingertight fitting and a brown ferrule to a free end of the black LC Tee union c Connect the other end of the PEEK tubing with a red Fingertight fitting and a brown ferrule to the LC inlet located on the APCI probe 5 Connect an appropriate length of PEEK tubing transfer line from the divert inject valve from the divert inject valve to the LC Tee union Figure 22 a Connect a length of PEEK tubing with a stainless steel nut and a stainless steel ferrule to port 3 of the divert inject valve b Connect the other end of the PEEK tubing with a brown Fingertight fitting and a brown ferrule to the free end of the LC Tee union 6 Connect an appropriate length of PEEK tubing transfer line from the LC from the divert inject valve to the LC a Connect a length of PEEK tubing with a stainless steel nut and a stainless steel ferrule to port 2 of the divert inject valve b Connect the other end of the PEEK tubing with a proper fitting and a ferrule to the outlet of the LC 7 Connect an appropriate length of PEEK tubing waste line from the divert inject valve to
71. lect the Detector option button and then click Close to return to Tune Plus 5 Start the automatic tuning procedure from the Tune dialog box a Click Start A message box displays the following message b Please ensure that the 500 microliter syringe is full c Ensure the syringe pump contains at least 450 uL of the 125 fg uL reserpine tuning solution d Click OK to close the message box and return to the Tune Plus window 6 On the File Display toolbar click on the Graph View button to display the view Thermo Scientific Thermo Scientific 5 Optimizing the LTO MS Detector with Your Analyte Optimizing the Tune of the MS Detector Automatically in APCI APPI MS Mode Figure 31 Tune dialog box showing the Automatic tuning page 7 Observe the Tune Plus window and the Tune dialog box While automatic tuning is in progress the LTQ MS detector displays various tests in the Spectrum and Graph views in the Tune Plus window and displays various messages in the Status group box in the Tune dialog box Your Tune Plus window should now look similar to the one shown in Figure 32 You have now successfully tuned the MS detector in APCI APPI MS mode for the compound reserpine or your analyte of interest Leave the LC pumps on with a flow rate of approximately 400 uL min leave the APClhighflow LCQTune file open in the Tune Plus window and go on to the next topic Saving the APCI APPI MS Tune Method APPI Souce User Manual 59
72. lever open to its widest position 10 Carefully pull the probe straight back in the port in the housing until it meets with the slot in the ESI interlock block The guide pin on the probe manifold will prevent you from twisting the probe until the pin is aligned with the slot in the ESI interlock block 11 After the probe is all the way back and aligned with the slot turn the probe 45 degrees counter clockwise to free the probe from the alignment notch Be careful not to break the fused silica sample tube or PEEK safety sleeve 12 Pull the probe straight out to remove it from the ion source housing 13 Store the ESI probe in its original shipping container APPI Souce User Manual 25 3 Setting Up the lon Source for Acquiring Data in APCI APPI MS MS Mode Removing the lon Max lon Source Housing Removing the lon Max Remove the Ion Max ion source housing to access the ion sweep cone lon Source Housing Note Disconnect any external liquid lines connected to the ion source housing before removing the ion source housing To remove the ion source housing 1 Remove the drain tube from the ion source housing drain See Figure 13 2 Rotate the ion source housing locking levers 90 degrees to release the ion source housing from the ion source mount assembly 3 Remove the ion source housing by it pulling straight off the ion source mount assembly 4 Place the housing in a safe location for temporary storage EN WG Cover R
73. meter is now optimized in APCI APPI MS MS mode for the compound reserpine or for your compound APPI Souce User Manual 81 6 Optimizing the TSQ Quantum Ultra Mass Spectrometer with Your Analyte Saving the Tune Method Saving the Tune You can save the settings obtained in a tune method specific to your Method particular analyte and solvent flow rate These settings can be recalled to be used again Using the example of the last section the settings obtained using reserpine would be saved This tune method can be recalled and used as a starting point for optimizing the mass spectrometer on reserpine at a different flow rate Note Save the Tune Method while the mass spectrometer is On To save your APCI APPI MS tune method 1 Choose File gt Save As to display the Save As dialog box Figure 45 Save in Io methods ea Save as type Tune Files TSQTune v Cancel Header Information Figure 45 Save As dialog box showing files in the folder C Xcalibur methods 2 In the Save In list box select the C Xcalibur methods folder 3 Click the File Name text box and then enter APCImyTune to name the Tune Method APClmy Tune TSQTune 82 APPI Souce User Manual Thermo Scientific 6 Optimizing the TSO Quantum Ultra Mass Spectrometer with Your Analyte Saving the Tune Method 4 Click Save to save the Tune Method and return to the Tune Plus window Note that the Tune Method is named APCImy Tune TSQTune Before you
74. n existing Tune Method a On the File Display toolbar click on the Open File button to display the Open dialog box c Confirm that the path is C Xcalibur methods and then select the desired file d Click Open to open the file Tune Master downloads the Tune Method parameters to the mass spectrometer 4 Click the Optimize Compound Dependent Devices button on the Control Scan Mode toolbar to display the Optimize Compound Dependent Devices view in the top right corner of the workspace Figure 38 Device Readback Oly Discharge Current 40 40 Oly APCI Vaporizer Tempera 500 499 Oly Sheath Gas Pressure 30 30 Oly Aus Valve Flow 0 0 Oly Capillary Temperature 350 350 f Tube Lens Offset 160 159 Oly Source CID 0 0 Oly Collision Pressure 1 5 1 5 Mv Collision Energy 38 38 Mv Quad MS MS Bias 3 0 3 0 Discharge Current 40 Hy Figure 38 Optimize Compound Dependent Devices view APCI settings Thermo Scientific APPI Souce User Manual 71 6 Optimizing the TSO Quantum Ultra Mass Spectrometer with Your Analyte Setting Up to Optimize in APCI APPI MS MS Mode with Your Compound 72 APPI Souce User Manual Note You might find that the presence of chemical contamination in the APCI vaporizer creates chemical noise in the mass spectrum If this occurs recondition the APCI vaporizer To recondition the APCI vaporizer you start LC solvent flow elevate the temperature of the APCI vaporizer and increase the sheath gas
75. nation of the assembly 5 While holding the plunger of the syringe in place carefully reinsert the tip of the syringe needle into the end of the Teflon tube on the syringe adapter assembly Figure 35 6 Place the syringe into the syringe holders of the syringe pump 7 While squeezing the black release button on the syringe pump handle push the handle down until it just contacts the syringe plunger 8 Install a sample transfer line between the divert inject valve and the APCI probe a Gather the necessary fittings for installing a sample transfer line Figure 37 b Connect an appropriate length of tubing fitted with a nut and a ferrule to port 3 of the divert inject valve Figure 36 c Connect the other end of the tubing with a FingerTight fitting and a ferrule to the sample inlet fitting LC inlet Figure 34 Stainless Steel Nut Fingertight Fitting 2522 0066 00101 18195 N To Divert O mH m p gt To APCI Probe Inject Valve LC Inlet Stainless Steel Ferrule PEEK Tubing Ferrule 2522 3830 00301 22912 00101 18196 Figure 37 Sample transfer line installed between the divert inject valve and the APCI probe Thermo Scientific APPI Souce User Manual 69 6 Optimizing the TSO Quantum Ultra Mass Spectrometer with Your Analyte Setting Up to Introduce Sample by Auto Loop Injection in APC Mode 9 Install a 5 uL sample loop with nuts and ferrules between ports 1 and 4 of the divert inject valve
76. ne LTQTune BESILowFlow LTQTune BArCILowFlow LTQTune Q BESITune LTOTune BArCITune LTQTune AutoTune LTQTune PCALI LTQTune File name APPImyTune Save as type Tune Files LTQTune Cancel m Header Information No file selected Figure 33 Save As dialog box showing files in the folder C Xcalibur methods Thermo Scientific APPI Souce User Manual 61 5 Optimizing the LTO MS Detector with Your Analyte Saving the APCI APPI MS Tune Method 4 Click Save to save the Tune Method and close the Save As dialog box Note that the Tune Method is named APPImy Tune LTQTune Before you acquire data go to the next topic Cleaning the MS Detector After Tuning in APCI Mode 62 APPI Souce User Manual Thermo Scientific 5 Optimizing the LTO MS Detector with Your Analyte Cleaning the MS Detector After Tuning in APCI Mode Cleaning the MS Use the following procedure to clean the MS detector after tuning on your Detector After Tuning in APCI Mode w OnStandby Thermo Scientific A analyte of interest 1 Click on the On Standby button to put the MS detector in Standby mode When the MS detector is in Standby the LTQ MS detector turns off the vaporizer heater corona discharge voltage and syringe pump The MS detector stops scanning and freezes the displays for the Spectrum and Graph views CAUTION Always place the MS detector in Standby or Off before you open the API source to atmospheric
77. ng Up the lon Source for Acquiring Data in APCI APPI MS MS Mode Installing the APC Probe 12 Connect the Auxiliary gas line green colored fitting to the inlet on the APCI probe marked A 13 Connect the Sheath gas line blue colored fitting to the inlet on the APCI probe marked S 14 Connect the sample transfer line to the APCI probe inlet CAUTION Prevent solvent waste from backing up into the ion source and mass spectrometer Always ensure that liquid in the drain tube is able to drain to a waste container and that the outlet of the drain tube is above the level of liquid in the waste container The APCI source is now properly installed in the Ion Max ion source housing Thermo Scientific APPI Souce User Manual 29 3 Setting Up the lon Source for Acquiring Data in APCI APPI MS MS Mode Installing the PhotoMate Light Source Installing the ifthe APPI assembly is already installed PhotoMate Light Sourc e e Ifyou have an LCQ Deca XP MAX MS Detector follow the operating procedures in Chapter 4 Optimizing the LCQ Deca XP MAX MS Detector with Your Analyte e Ifyou have an LTQ MS Detector follow the operating procedures in Chapter 5 Optimizing the LTQ MS Detector with Your Analyte e Ifyou have an TSQ Quantum mass spectrometer follow the operating procedures in Chapter 6 Optimizing the TSQ Quantum Ultra Mass Spectrometer with Your Analyte If the APPI assembly is not installed 1 Remove the scre
78. ng procedures assume that you are familiar with your LTQ instrument and the Tune Plus window If you need information refer to the LTQ online Help LTQ Getting Connected and or LTQ Hardware Manual Ensure that you have completed the procedures in the sections that describe how to calibrate your instrument in ESI mode and have properly set up your APCI APPI source This chapter includes the following sections e Setting Up the Inlet for Tuning Using High Flow Infusion e Setting Up the MS Detector for APCI APPI MS Operation e Optimizing the Tune of the MS Detector Automatically in APCI APPI MS Mode e Saving the APCI APPI MS Tune Method e Cleaning the MS Detector After Tuning in APCI Mode Thermo Scientific APPI Souce User Manual 51 5 Optimizing the LTO MS Detector with Your Analyte Setting Up the Inlet for Tuning Using High Flow Infusion Setting Up the Inlet To make the plumbing connections for APCI APPI MS sample for Tuning Using introduction from the syringe pump into solvent flow from an LC High Flow Infusion 1 Connect a 4 cm 1 5 in segment of Teflon tubing with a brown FingerTight fitting and a brown ferrule to the black LC union Figure 27 LC Union Fingertight Fitting P N 00101 18202 P N 00101 18081 mg su mo H Ferrule Teflon Tube P N 00101 18196 P N 00301 22803 Figure 27 APCI APPI MS plumbing connections for the syringe pump 2 Load a clean 500 uL Unimetrics syringe with 450 uL of a 125 fg
79. nsfer capillary and vaporizer and a higher gas flow rate Table 2 provides starting guidelines for operating in the APPI APCI or combined APCI APPI mode Chapter 4 5 or 6 depending upon your instrument will help you to optimize these settings for your specific compound Table 2 Guidelines for setting operating parameters for APPI APCI and combined APCI APPI modes i Thermo Scientific LC Flow Rate Capillary Vaporizer Auxiliary Gas mL min Temperature C Temperature C Sheath Gas psi arbitrary units 0 2 to 2 0 Typical setting Typical setting Required Not required but 150 to 225 400 to 550 Typical setting usually helps to reduce 40 to 100 solvent background ions Typical setting 0 to 20 For thermally labile compounds you might need to use a lower vaporizer temperature and a lower flow rate 1 Flows below 200 uL min require more care to maintain a stable spray APPI Souce User Manual 11 Chapter2 Functional Description This chapter describes the principal components of the APCI APPI combination probe The APCI APPI combination probe forms gas phase sample ions from sample molecules that are contained in solution You can operate the APCI APPI combination probe using either atmospheric pressure chemical ionization APCI atmospheric pressure photoionization APPI or both The APCI APPI combination probe includes e APCI Source e PhotoMate Light Source Thermo Sci
80. ock solution of reserpine Then use serial dilutions of the stock solution to make the compound optimization solution 110 APPI Souce User Manual Thermo Scientific Reserpine Stock Thermo Scientific Solution B Reserpine Solution Formulations Reserpine Stock Solution Prepare 10 mL of a 1 g L Reserpine Stock Solution in 1 acetic acid 15 Carefully weigh 10 mg of Reserpine 16 Transfer the 10 mg of reserpine into a 10 mL volumetric flask 17 Add 1 acetic acid in methanol until the 10 mL mark is reached 18 Mix the solution thoroughly 19 Transfer the solution to a clean dry vial 20 Label the vial Reserpine Stock Solution 1 g L APPI Souce User Manual 111 B Reserpine Solution Formulations LCO Deca XP MAX Reserpine Sample Solution LCO Deca XP MAX Prepare 1 mL of the sample solution of 1 pg uL 8 2 fmol uL in a solution Reserpine Sample of 1 acetic acid in methanol Solution 112 APPI Souce User Manual l Pipette 1 mL of reserpine stock solution 1 ug uL into a 10 mL volumetric flask and bring the volume up to the 10mL mark using methanol 1 acetic acid Mix the resulting solution thoroughly and label it as Reserpine 100 ng pL Place 75 mL of methanol 1 acetic acid into a clean 100 mL volumetric flask Using the 10 pL syringe provided in the accessories kit or a calibrated pipette add 5 pL of the Reserpine 100 ng L solution to the 75 mL of methanol 1 acetic acid in the 100 mL volume
81. on and off the power to the circuitry that powers the VUV lamp The box fan remains on at all times and is not controlled by the lamp On Off switch The safety interlock switch prevents the light source from operating when not attached to the Ion Max ion source housing Thermo Scientific Thermo Scientific 2 Functional Description PhotoMate Light Source The remote status light emitting diode LED is located on the front of the light source The LED is illuminated green if the APPI source is connected to an instrument that has remote control of the lamp status the LTQ MS detector When the Remote LED is illuminated the switch on the light source is inactive and will not turn the lamp on and off When the lamp is not illuminated the instrument to which it is connected has no control of the lamp status and the lamp must be turned on and off with the switch on the source TSQ Quantum Ultra mass spectrometer and LCQ Deca XP MAX MS detector The front window in the Ion Max ion source housing allows you to verify that the light source is working properly You can see purple light if the light source is working properly If the light is red due to exposure to ambient nitrogen then the lamp is broken APPI Souce User Manual 21 Chapter3 Setting Up the lon Source for Acquiring Data in APCI APPI MS MS Mode This chapter provides information on setting up the ion source for acquiring data in the APCI MS MS mode This chapter contains
82. on tube c Flush the sample transfer line sample tube and APCI probe with the solution by slowly depressing the syringe plunger Visually check that the solution is exiting the tip of the APCI probe on the inside of the probe assembly Use a lint free tissue to gently remove the excess solution as it exits the probe d Remove the needle of the syringe from the Teflon tube 6 Repeat step 5 with a solution of 50 50 methanol water 7 Reinstall the Ion Max ion source housing as described in Installing the Ton Max Ion Source Housing on page 33 Your TSQ Quantum Ultra mass spectrometer is now ready to perform experiments in APCI APPI mode For information regarding the maintenance of the Ion Max APPI source please refer to Chapter 7 Maintenance Thermo Scientific APPI Souce User Manual 85 Thermo Scientific Chapter7 Maintenance This chapter describes routine APCI APPI combination probe maintenance procedures that must be performed to ensure optimum performance of the probe Most of the procedures involve cleaning It is your responsibility to maintain the APCI APPI combination probe by performing the routine maintenance procedures on a regular basis as they are described in this chapter The APCI APPI combination probe requires minimal maintenance Periodically you need to clean the components of the APCI APPI combination probe to remove salts or other contaminants The frequency of cleaning depends on the types and
83. ot remove protective covers from PCBs Chemical This instrument might contain hazardous chemicals Wear gloves when handling toxic carcinogenic mutagenic or corrosive or irritant chemicals Use approved containers and proper procedures to dispose waste oil Heat Before servicing the instrument allow any heated components to cool Fire Use care when operating the system in the presence of flammable gases Eye Hazard Eye damage could occur from splattered chemicals or flying particles Wear safety glasses when handling chemicals or servicing the instrument General Hazard A hazard is present that is not included in the above categories Also this symbol appears on the instrument to refer the user to instructions in this manual When the safety of a procedure is questionable contact your local Technical Support organization for Thermo Fisher Scientific San Jose Products VORSICHT Elektroschock In diesem Ger t werden Hochspannungen verwendet die Verletzungen verursachen k nnen Vor Wartungsarbeiten mu das Ger t abgeschaltet und vom Netz getrennt werden Betreiben Sie Wartungsarbeiten nicht mit abgenommenem Deckel Nehmen Sie die Schutzabdeckung von Leiterplatten nicht ab Chemikalien Dieses Ger t kann gef hrliche Chemikalien enthalten Tragen Sie Schutzhandschuhe beim Umgang mit toxischen karzinogenen mutagenen oder tzenden reizenden Chemikalien Entsorgen Sie verbrauchtes l entsprechend den Vo
84. peration Thermo Scientific APPI Souce User Manual 57 5 Optimizing the LTO MS Detector with Your Analyte Optimizing the Tune of the MS Detector Automatically in APCI APPI MS Mode Optimizing the Tune of the MS Detector Automatically in APCI APPI MS Mode 58 APPI Souce User Manual You can optimize the tune of the MS detector automatically for APCI operation The most important parameters that affect the signal quality during APCI APPI MS operation are the vaporizer temperature ion transfer tube temperature API gas flows and solution flow rate If any one of these parameters is changed you need to re optimize MS detector parameters You can use the Semi Automatic tune procedure to tune the MS detector on individual parameters Use the following procedure to optimize the MS detector automatically on the reserpine peak at m z 609 2 at your particular flow rate for example 400 uL min Refer to Table 2 for guidelines about flow rates and temperatures 1 On the Control Scan Mode toolbar click on the Tune button to display the Automatic tuning page See Figure 31 2 In the What to Optimize On group box select the Mass option button to make active the Mass spin box 3 In the Mass spin box enter 609 2 to specify that you want to tune on the peak at m z 609 2 4 Ensure that the Divert Inject valve is in the Detector position a Click on the Divert Inject Valve button to open the Divert Inject Valve dialog box b Se
85. ragment oscillates contains multiple peaks or is excessively noisy go to step 5 Single Sample AutoQuan Optimization Modes MS Only MS MS MS Optimization Options Standard Custom o Parent Product Mass Mass a 1 503 281 195 066 ad 200 000 100 000 08 11 30 17 Improvement 08 11 41 Optimizing collision energy at 1 0 mTorr 08 11 41 Waiting for the collision gas to stabilize 08 11 41 Constructing the breakdown curve of ion 609 281 08 15 17 Collision Energy Optimization Results Inlet Types 08 15 17 Product lons m z Coll Energy C Manual Loop Injection 08 15 17 _ 195 07 38 08 15 17 Finish compound optimization C Syringe Pump Infusion Auto Loop Injection Accept Undo Print Figure 43 Compound Optimization workspace showing the successful completion of compound optimization Thermo Scientific APPI Souce User Manual 79 6 Optimizing the TSO Quantum Ultra Mass Spectrometer with Your Analyte Optimizing in APCI APPI MS MS Mode Automatically with Your Compound Breakdown Curve of lon 609 3 m z Intensity 0 00e 00 Product lons Coll Energy 60 Pressure 1 5 mTorr 195 1 miz 38 v 0 c Q Q gt 8 Q K T T T 30 40 Collision Energy V Figure 44 Breakdown curve of reserpine showing the relative intensity of the product ion at m z 195 066 as a function of collision energy 5 If errors occurred during the compound optimization procedure re
86. rb 20 18 96 Discharge Current pA 5 00 322 Discharge Yoltage kV 4 53 Capillary Temp C 200 00 200 20 Capillary Voltage V 30 H 8 56 Tube Lens Offset v 20 00 i OK Cancel Help Figure 23 APCI Source dialog box showing the proper settings for a typical high flow experiment 5 Define the scan parameters for tuning the MS detector in the APCI APPI MS mode a On the Control Scan Mode toolbar click on the Define Scan button to open the dialog box Figure 24 b In the Scan Description group box select the Mass Range Normal option button to specify a mass range of m z 50 to 2000 c Select the Scan Mode MS option button to select the MS scan mode Note that XP Plus sets the MS power to 1 d Click on the Scan Type SIM option button to select the SIM data type Note that XP Plus sets the Total Scan Ranges to 1 e In the Scan Time group box in the Total Microscans spin box enter 1 to set the total number of microscans to 1 f In the Input Method group box select the Center Width option button to make available the Center Mass and Width text boxes in the Scan Ranges group box Refer to steps 4h and 4i below g Inthe Ion Source Fragmentation group box confirm that the Turn On check box is not selected to specify that the ion source fragmentation option is turned off h In the Scan Ranges group box in the Center Mass text box enter 609 2 to set the center
87. ring the volume up to the 10mL mark using methanol 1 acetic acid Mix the resulting solution thoroughly and label it as Reserpine 100 ng pL Place 75 mL of methanol 1 acetic acid into a clean 100 mL volumetric flask Using the 10 pL syringe provided in the accessories kit or a calibrated pipette add 5 pL of the Reserpine 100 ng L solution to the 75 mL of methanol 1 acetic acid in the 100 mL volumetric flask Rinse the pipette twice with the 75 mL of methanol 1 acetic acid contained in the volumetric flask by dipping the pipette tip into the solution and rinsing it back into the flask Carefully bring up this volume with methanol 1 acetic acid until the lower part of the meniscus is level with the 100 mL marking Mix this solution thoroughly Label it as Reserpine 5 pg pL Add 20 mL of the Reserpine 5 pg uL to another clean 100 mL volumetric flask and carefully bring up this volume with methanol 1 acetic acid until the lower part of the meniscus is level with the 100 mL marking Mix the solution thoroughly Label this Reserpine 1 pg pL Transfer 200 uL of the 1 pg uL solution into a clean polypropylene tube Add 800 UL of 1 acetic acid in methanol to the tube Label the vial 7SQ Quantum Ultra Reserpine Sample Solution 200 fe uL and store it in a refrigerator until it is needed Thermo Scientific Index A APCI APCI process 4 discussed 3 operating parameters 11
88. rmalized Mass Range Normal T Collision Center Energy Mass m z Scan Rate Normal T Scan Type SiM r Scan Time Microscans 1 Max Inject Time ms 1200 000 Zl Source Fragmentation E Input Center width v Apply ox Cancel Help Figure 30 Define Scan dialog box showing typical settings for APCI APPI MS operation g In the Source Fragmentation group box confirm that the On check box is not selected to specify that the ion source fragmentation option is turned off h In the Scan Ranges group box in the Input list box select Center Width to make available the Center Mass and Width text boxes in the Scan Ranges table i In the Scan Ranges table in the Center Mass text box enter 609 20 to set the center mass for the scan range to m z 609 20 j In the Width text box enter 2 00 to set the width of the scan range to m z 2 00 k Ensure that the settings in your Define Scan dialog box are the same as those shown in Figure 30 l Click OK to apply the MS detector scan parameters and to close the Define Scan dialog box 5 On the Control Scan Mode toolbar click Centroid Profile to toggle the data type to centroid The picture on the button should be the same as that shown here 6 Click Positive Negative to toggle the ion polarity mode to positive The picture on the button should be the same as that shown here You have now completed setting up your MS detector for APCI APPI MS o
89. rodotti chimici tossici cancerogeni mutageni o corrosivi irritanti Utilizzare contenitori aprovo e seguire la procedura indicata per lo smaltimento dei residui di olio Calore Attendere che i componenti riscaldati si raffreddino prima di effetturare l intervento di manutenzione Incendio Adottare le dovute precauzioni quando si usa il sistema in presenza di gas infiammabili Pericolo per la vista Gli schizzi di prodotti chimici o delle particelle presenti nell aria potrebbero causare danni alla vista Indossare occhiali protettivi quando si maneggiano prodotti chimici o si effettuano interventi di manutenzione sull apparecchio Pericolo generico Pericolo non compreso tra le precedenti categorie Questo simbolo utilizzato inoltre ull apparecchio per segnalare all utente di consultare le istruzioni descritte nel presente manuale 2 Quando e in dubbio la misura di sicurezza per una procedura prima di continuare si prega di mettersi in contatto con il Servizio di Assistenza Tecnica locale per i prodotti di Thermo Fisher Scientific San Jose CAUTION Symbol gt Pe ef CAUTION Electric Shock This instrument uses high voltages that can cause personal injury Before servicing shut down the instrument and disconnect the instrument from line power Keep the top cover on while operating the instrument Do not remove protective covers from PCBs Chemical This instrument might contain hazardous chemic
90. rritantes Utilice recipientes y procedimientos aprobados para deshacerse del aceite usado Altas temperaturas Permita que lop componentes se enfrien ante de efectuar servicio de mantenimiento Fuego Tenga cuidado al operar el sistema en presencia de gases inflamables Peligro par los ojos Las salicaduras de productos qu micos o particulas que salten bruscamente pueden causar lesiones en los ojos Utilice anteojos protectores al mnipular productos qu micos o al darle servicio de mantenimiento al instrumento Peligro general Significa que existe un peligro no incluido en las categorias anteriores Este simbolo tambi n se utiliza en el instrumento par referir al usuario a las instrucciones contenidas en este manual Cuando la certidumbre acerca de un procedimiento sea dudosa antes de proseguir pongase en contacto con la Oficina de Asistencia Tecnica local para los productos de Thermo Fisher Scientific San Jose AVVERTENZA Shock da folgorazione L apparecchio alimentato da corrente ad alta tensione che puo provocare lesioni fisiche Prima di effettuare qualsiasi intervento di manutenzione occorre spegnere ed isolare l apparecchio dalla linea elettrica Non attivare lo strumento senza lo schermo superiore Non togliere i coperchi a protezione dalle schede di circuito stampato PCB Prodotti chimici Possibile presenza di sostanze chimiche pericolose nell apparecchio Indossare dei guanti per maneggiare p
91. rschriften in den vorgeschriebenen Beh ltern Hitze Warten Sie erhitzte Komponenten erst nachdem diese sich abgek hlt haben Feuer Beachten Sie die einschl gigen VorsichtsmaBnahmen wenn Sie das System in Gegenwart von entz ndbaren Gasen betreiben Verletzungsgefahr der Augen Verspritzte Chemikalien oder kleine Partikel k nnen Augenverletzungen verursachen Tragen Sie beim Umgang mit Chemikalien oder bei der Wartung des Ger tes eine Schutzbrille Allgemeine Gefahr Es besteht eine weitere Gefahr die nicht in den vorstehenden Kategorien beschrieben ist Dieses Symbol wird im Handbuch auBerdem dazu verwendet um den Benutzer auf Anweisungen hinzuweisen Wenn Sie sich ber die Sicherheit eines Verfahrens im unklaren sind setzen Sie sich bevor Sie fortfahren mit Ihrer lokalen technischen Unterst tzungsorganisation f r Thermo Fisher Scientific San Jose Produkte in Verbindung ATTENTION Choc lectrique L instrument utilise des tensions capables d infliger des blessures corprelles L instrument doit tre arr t et d branch de la source de courant avant tout intervention Ne pas utiliser l instrument sans son couvercle Ne pas elensver les tuis protecteurs des cartes de circuits imprim s Chimique Des produits chemiques dangereux peuven se trouver dans l instrument Proted dos gants pour manipuler tous produits chemiques toxiques canc amp rigenes mutagenes ou corrosifs irritants Utiliser des r
92. ssible to obtain the highest performance for Should Use What your assays Many volatile buffer solutions are available that can be used Typ es Sh oul d Avoi d instead of nonvolatile ones Volatile buffer solutions can include the following e Acetic acid e Ammonium acetate e Ammonium formate e Ammonium hydroxide e Triethylamine TEA Many LC applications use nonvolatile buffers such as phosphate and borate buffers However it s best to avoid the use of these nonvolatile buffers with the mass spectrometer Nonvolatile buffers can block the capillary in the probe and can cause salt buildup in the nozzle compromising the integrity of the spray 10 APPI Souce User Manual Thermo Scientific 1 Introduction How Should Set Up the Mass Spectrometer for Various LC Flow Rates How Should I Set Up The APCI APPI combination probe can generate ions from liquid flows of the Mass 50 L min to 2 0 mL min This flow range allows you to use microbore Spectrometer for LC analytical LC and semipreparative LC Various LC Flow As you change the rate of flow of solvents entering the mass spectrometer Rates you need to adjust several parameters For APCI and APPI you need to adjust the ion transfer capillary temperature the vaporizer temperature and the gas flow rates for the sheath gas and auxiliary gas In general an increase in the rate of liquid flowing into the mass spectrometer requires a higher temperature of the ion tra
93. ste backing into API2 source housing 40 solvent waste backing into ion source housing 29 34 venting ESI source 35 VUV lamp breaking 20 chemicals reserpine sample solution preparing 114 cleaning procedures APCI probe components 88 89 APPI Souce User Manual 115 Index D VUV lamp 92 cleaning LCQ Deca XP MAX 49 cleaning LTQ 63 cleaning TSQ Quantum Ultra 84 combined APCI and APPI corona needle status table 9 discussed 9 light source status table 9 compound optimization LC APCI MS mode 65 setting up mass spectrometer for 71 setting up syringe pump for 67 solutions preparing 110 computer terms directories 47 82 files 47 82 contamination of APCI source cleaning note 72 syringe note 69 corona discharge needle description 15 discharge current 15 figure 14 corona discharge needle avoiding injury from 27 Define Scan dialog box 44 displaying 56 dialog boxes APCI Source 43 56 Define Scan 44 Save As 47 47 61 61 82 82 Tune 46 59 59 divert inject valve plumbing for auto loop injection 68 procedure 67 E electromagnet compatibility iii electronics PCB discussion 20 location 19 F FCC compliance iii Figures APCI plumbing for Tee 39 53 116 APPI Souce User Manual APCI process 4 APCI sample tube connection 90 APCI Source dialog box 43 56 Define Scan dialog box APCI settings 44 Ion Max ion source housing 33 plumbing Tee union APCI 38 plumbing for divert inject valve to APCI probe 6
94. store the previous mass spectrometer compound sensitive device settings by completing the following steps a Click Undo to restore the prior device settings b Click Accept to reload the prior device settings to the mass spectrometer c Troubleshoot and correct the situation that caused the optimization to fail d Go to step 4 of this procedure and restart the compound optimization procedure 6 Click Accept to accept the results of the compound optimization Note Save the Tune Method while the mass spectrometer is On if any of the ion source parameters have been changed from their initial settings 7 Save the Tune Method file by doing the following a Click Save Tune As to open the Save As dialog box 80 APPI Souce User Manual Thermo Scientific Thermo Scientific 6 Optimizing the TSO Quantum Ultra Mass Spectrometer with Your Analyte Optimizing in APCI APPI MS MS Mode Automatically with Your Compound b Enter a file name such as APCI_reserpine or the name of your compound for your Tune Method file in the File Name text box c Click Save to save the Tune Method file If the file name that you entered in step 7 b is already in use a message box appears and asks whether you want to replace the existing file e Ifyou do want to overwrite the existing file click Yes e Ifyou do not want to overwrite the existing file click No Then change the name in the File Name text box and click Save The mass spectro
95. ter with Your Analyte Setting Up to Optimize in APCI APPI MS MS Mode with Your Compound f Set the temperature of the ion transfer capillary i Click Capillary Temperature in the Device Display box ii Enter 350 in the Device spin box to set the capillary temperature to 350 C g Set the ion source fragmentation CID collision energy i Click Source CID in the Device Display box ii Enter 0 in the Device box to set the collision energy to 0 V h Set the collision pressure i Click Collision Pressure in the Device Display box ii Enter 1 5 in the Device spin box to set the collision pressure to 1 5 mTorr i Set the collision energy i Click Collision Energy in the Device Display box ii Enter 38 in the Device spin box to set the collision energy to 38 eV j Set the Quad MS MS bias voltage i Click Quad MS MS Bias in the Device Display box ii Enter 3 0 in the Device box to set the bias voltage to 3 0 V Ensure that the readbacks in the Device Display box are approximately equal to the set values You might need to wait for a few minutes for the capillary and vaporizer temperatures to stabilize at their set values 6 If you are operating in APCI APPI or APPI only modes turn on the APPI source as follows a Turn on the power to the APPI lamp by flipping the switch on the PhotoMate light source housing to the On position b Verify that the lamp is operating by looking through the front window of the Ion
96. that the outlet of the drain tube is above the level of liquid in the waste container 34 APPI Souce User Manual Thermo Scientific 3 Setting Up the lon Source for Acquiring Data in APCI APPI MS MS Mode Installing the lon Max lon Source Housing CAUTION Do not vent the API source drain tube or any vent tubing connected to the waste container to the same fume exhaust system to which you have connected the forepumps The analyzer optics can become contaminated if the API source drain tube and the blue forepump exhaust tubing are connected to the same fume exhaust system Your laboratory must be equipped with at least two fume exhaust systems Route the blue forepump exhaust tubing to a dedicated fume exhaust system Route the drain tube from the API source to a waste container Vent the waste container to a dedicated fume exhaust system 3 Reinstall the ion source drain tube as follows a Connect the l in ID Tygon tubing P N 00301 22922 to the ion source housing drain fitting b Attach the free end of the hose to a waste container Ideally the waste container should be vented to a fume exhaust system 4 Complete the installation e For LCQ Deca XP MAX MS detectors Connect the external power supply of the PhotoMate light source to the DB 15 connector on the PhotoMate light source e For LTQ MS detectors Connect the female end of the communications cable to the DB 15 connector on the PhotoMate light source Connect the
97. the VUV Lamp elle 95 Replaceable Parts nsansnnseennneennnsnnnesnnnsnanennnnennnnnnnnnnnnnnnnne 99 Installing the PhotoMate Light Source Adapter Ring 103 Reserpine Solution Formulations sssssssssssssssesseesseeees 109 Reserpine Stock Solution 2 na sl le eae 111 LCQ Deca XP MAX Reserpine Sample Solution 112 LTQ Reserpine Sample Solution 113 TSQ Quantum Ultra Reserpine Sample Solution 114 DMO un 115 Thermo Scientific Preface This guide describes how to set up and install the PhotoMate light source on the Ion Max ion source housing with an APCI probe It also describes how to optimize the tune of your instrument after you have installed the Ion Max APPI source Safety and Special Notices Make sure you follow the precautionary statements presented in this guide The safety and other special notices appear in boxes Safety and special notices include the following CAUTION Highlights hazards to humans property or the environment Each CAUTION notice is accompanied by an appropriate CAUTION symbol IMPORTANT Highlights information necessary to prevent damage to software loss of data or invalid test results or might contain information that is critical for optimal performance of the system Note Highlights information of general interest Tip Highlights helpful information that can make a task easier Thermo Scientific APPI Sourc
98. the following sections e Removing the ESI Probe e Removing the Ion Max Ion Source Housing e Installing the APCI Probe e Installing the PhotoMate Light Source e Installing the Ion Max Ion Source Housing Thermo Scientific APPI Souce User Manual 23 3 Setting Up the lon Source for Acquiring Data in APCI APPI MS MS Mode Removing the ESI Probe 24 Removing the ESI Probe A On Standby APPI Souce User Manual To remove the ESI source 1 Place the LC MS system in Standby a Stop the flow of solvent to the ESI source Note The following procedures are intended for use with all systems If you have questions regarding the operation of your MS system please refer to the appropriate system specific manuals This might include the Getting Started and Hardware manuals for your system For information on installation and maintenance of other Ion Max probes please refer to the Ion Max API Source Hardware Manual Note The following procedures are intended for use with all systems If you have questions regarding the operation of your MS system please refer to the appropriate system specific manuals This might include the Getting Started and Hardware manuals for your system For information on installation and maintenance of other Ion Max probes please refer to the Ion Max API Source Hardware Manual b Turn off the ESI spray voltage c Click on the On Standby button on the toolbar to place the mass spectrometer in St
99. the mass spectrometer parameters using the automatic tuning procedure the procedure adjusts all the parameters listed above and the voltages applied to the ion optics until the ion transmission of your analyte is maximized Note Ensure that you have performed the TSQ Quantum Ultra tuning and calibration procedure within the previous three months before you optimize the tune for your compound If you need to tune and calibrate the system refer to your TSQ Quantum Ultra Getting Started manual and the procedure in Chapter 3 Tuning and Calibrating the Mass Spectrometer in ESI MS MS Mode To optimize the mass spectrometer for your compound in the APCI APPI MS MS mode do the folowing e Set up the syringe pump and divert injection valve for auto loop injection e Set up the mass spectrometer for your specific compound from the Tune Master e Run the automatic compound optimization procedure to fine tune the mass spectrometer parameters that are compound dependent e Save the new Tune Method 66 APPI Souce User Manual Thermo Scientific Setting Up to Introduce Sample by Auto Loop Injection in APCI Mode From LC To Waste gt Sample Inlet Fitting 6 Optimizing the TSO Quantum Ultra Mass Spectrometer with Your Analyte Setting Up to Introduce Sample by Auto Loop Injection in APCI Mode The following procedure describes how to introduce your compound by auto loop injection The plumbing connections for APCI MS sample intro
100. tific y 4 Optimizing the LCQ Deca XP MAX MS Detector with Your Analyte Optimizing the Tune of the MS Detector Automatically in APCI APPI MS Mode You can optimize the tune of the MS detector automatically for APCI operation The most important parameters that affect the signal quality during APCI APPI MS operation are the vaporizer temperature ion transfer capillary temperature capillary voltage tube lens offset voltage gases and solution flow rate If any one of these parameters is changed you need to re optimize the MS detector parameters You can use the Semi Automatic tune procedure to tune the MS detector on individual parameters Use the following procedure to optimize the MS detector automatically on the reserpine peak at m z 609 2 at your particular flow rate for example 1 mL min Refer to able 2 on page 1 11 for guidelines about flow rates and temperatures To optimize the MS detector automatically on the reserpine peak at m z 609 2 at your particular flow rate 1 On the Control Scan Mode toolbar click on the Tune button to display the Automatic tuning page in the Tune dialog box 2 In the Mass spin box enter 609 2 to specify that you want to tune on the peak at m z 609 2 3 Ensure that the Divert Inject valve is in the Detector position a Click on the Divert Inject Valve button to open the dialog box b Select the Detector option button and then click Close to return to Tune Plus 4 Start the
101. tric flask Rinse the pipette twice with the 75 mL of methanol 1 acetic acid contained in the volumetric flask by dipping the pipette tip into the solution and rinsing it back into the flask Carefully bring up this volume with methanol 1 acetic acid until the lower part of the meniscus is level with the 100 mL marking Mix this solution thoroughly Label it as Reserpine 5 pg uL Add 20 mL of the Reserpine 5 pg L to another clean 100 mL volumetric flask and carefully bring up this volume with methanol 1 acetic acid until the lower part of the meniscus is level with the 100 mL marking Mix the solution thoroughly This is the LCQ Deca XP MAX Reserpine Sample Solution 1 pg pL Thermo Scientific Sample Solution Thermo Scientific B Reserpine Solution Formulations LTQ Reserpine Sample Solution LTO Reserpine Prepare 1 mL of the sample solution of 125 fg uL 205 amol L in 1 10 11 12 13 1 acetic acid in 50 50 methanol water Pipette 1 mL of reserpine stock solution 1 pg L into a 10 mL volumetric flask and bring the volume up to the 10 mL mark using methanol 1 acetic acid Mix the resulting solution thoroughly and label it as Reserpine 100 ng pL Place 75 mL of methanol 1 acetic acid into a clean 100 mL volumetric flask Using the 10 pL syringe provided in the accessories kit or a calibrated pipette add 5 pL of the Reserpine 100 ng uL solution to the 75
102. uL solution of reserpine or your analyte of interest Refer to Appendix B Reserpine Solution Formulations for a procedure for making the reserpine tuning solution 3 Insert the needle of a syringe into the segment of Teflon tubing and place the syringe in the syringe holder of the syringe pump 4 Connect a fused silica infusion line from the black LC union to the black LC Tee union a Connect the infusion line with a brown fingertight fitting and a brown ferrule to the free end of the LC union See Figure 28 b Connect the other end of the infusion line with a red fingertight fitting and a brown ferrule to the side arm of the LC Tee union 52 APPI Souce User Manual Thermo Scientific 5 Optimizing the LTO MS Detector with Your Analyte Setting Up the Inlet for Tuning Using High Flow Infusion PEEK Tubing LC Tee Union PEEK Tubing P N 00301 22912 P N 00101 18204 P N 00301 22912 From Divert Inject Valve Stainless Steel 7 emule Stainless Steel Nut Ferrules P N 00101 18196 Infusion Line Ferrules Fused Silica Capillary P N 00101 18120 P N 00106 10504 Fingertight Fingertight Fitting Fittings P N 00101 18195 P N 00101 18081 From LC Union Figure 28 APCI APPI MS plumbing connections for the LC Tee union Note To cut the PEEK tubing used to connect your LC to the divert inject valve and the divert inject valve to the APCI source use a PEEK tubing cutter This ensures that
103. up Note The following procedure assumes that isopropyl alcohol and HPLC grade water are in the solvent bottles labeled A and B respectively b Set up the Surveyor MS Pump to deliver a solution of 50 50 isopropyl alcohol water at 1000 uL min i In the Inlet Direct Control view in the Solvents Proportions and Flow Rate group box enter 50 in the text box labeled A to specify a delivery proportion of 50 solvent A ii Enter 50 in the box labeled B to specify a delivery proportion of 50 solvent B Thermo Scientific APPI Souce User Manual 75 6 Optimizing the TSO Quantum Ultra Mass Spectrometer with Your Analyte Setting Up to Optimize in APCI APPI MS MS Mode with Your Compound 76 APPI Souce User Manual gt iii In the Flow Rate box enter 1000 to set a flow rate of 1000 uL min c Inthe Direct Control Panel group box click the Start button to start the Surveyor MS pump The system is now set up to automatically deliver reserpine to the ion source for optimizing the mass spectrometer with your compound Next you will optimize the compound dependent devices for your compound in APCI APPI MS MS mode as discussed in the next section Optimizing in APCI APPI MS MS Mode Automatically with Your Compound Thermo Scientific Thermo Scientific Optimizing in APCI APPI MS MS Mode Automatically with Your Compound 6 Optimizing the TSQ Quantum Ultra Mass Spectrometer with Your Analyte Optimizing in APCI APPI MS
104. urce with box top removed showing the lamp hole 10 Dip a cotton swab in isopropyl alcohol then dip the wet swab in aluminum oxide polishing compound 5 micron powder 11 Polish the lamp window with the swab and polishing compound until the material is removed 12 Use another cotton swab soaked in isopropyl alcohol to remove the polishing compound from the lamp window 13 While wearing clean gloves install the VUV lamp by pushing it all the way to the stopping position in the light source assembly 14 If necessary reinstall the box top a Tip the box top forward and make sure the lamp On Off switch passes through the hole in the box top Then push the box top down over the fan connector b Reinstall the four screws to secure the box top c Reconnect the light source power cord to the light source 15 If necessary reinstall the PhotoMate light source in the Ion Max ion source housing Thermo Scientific Replacing the VUV Lamp Removing the Old VUV Lamp Thermo Scientific A A 7 Maintenance Maintaining the PhotoMate Light Source You can minimize the chance of breaking the VUV lamp by doing the following e Always wear clean gloves when you are handling the VUV lamp Fingerprints on the lamp can cause the lamp to fail when it is in use e Do not spray solvent on the VUV lamp while it is hot The VUV lamp can crack If the VUV lamp beaks or fails use the following procedures to replace it e
105. ws holding the window retainer ring CAUTION If you have operated your APCI probe recently be sure to allow it to cool completely before installing the PhotoMate light source The APCI probe and corona needle may be hot The corona needle is sharp If you are installing the APPI assembly with the APCI probe installed be careful not to poke yourself with the needle 2 Carefully remove the retainer ring while keeping your free hand under the side of the Ion Max ion source housing to be sure that the window does not fall out and break If the window does not come out with the retainer ring you might need to push gently on the window from inside the Ion Max ion source housing Figure 16 30 APPI Souce User Manual Thermo Scientific 3 Setting Up the lon Source for Acquiring Data in APCI APPI MS MS Mode Installing the PhotoMate Light Source Figure 16 Removing the small viewport window 3 Place the window retainer ring and screws in a secure place Note While inserting the PhotoMate light source into the Ion Max ion source housing be sure to watch that the APPI lamp does not contact the corona discharge needle or the ceramic heater tube on the APCI probe 4 Carefully align the PhotoMate light source so that the locking tab on the bottom of the APPI assembly aligns with the notch in the APPI adapter ring Figure 17 5 Secure the PhotoMate light source with two of the hex head screws Thermo Scientific APPI Souce User Manua
106. y slowly depressing the syringe plunger Visually check that the solution is exiting the tip of the APCI probe on the inside of the probe assembly Use a lint free tissue to gently remove the excess solution as it exits the probe d Remove the needle of the syringe from the Teflon tube 6 Repeat step 5 with a solution of 50 50 methanol water 7 Reinstall the Ion Max ion source housing as described in topic Installing the Ion Max Ion Source Housing on page 33 Your LCQ Deca XP MAX MS detector is now ready to perform experiments in APCI APPI mode For information regarding the maintenance of the Ion Max APPI source refer to Chapter 7 Maintenance Chapter5 Optimizing the LTQ MS Detector with Your Analyte This chapter provides information on optimizing the tune of your LTQ MS detector in the APCI APPI MS high flow mode It is not necessary to recalibrate the MS detector when you switch to APCI APPI MS operation You can use the calibration settings you obtained from the successful automatic calibration procedure you performed in the ESI MS mode For APCI APPI MS operation you simply open a default Tune Method located in your C Xcalibur methods folder in this case APClhighflow LTQTune From this starting point you optimize automatically the tube lens voltage for your particular analyte The capillary voltage and ion transfer capillary temperature can then be optimized manually to enhance ion transmission Note The followi
107. ymbol gekennzeichnet Thermo Fisher Scientific hat Vereinbarungen mit Verwertungs Entsorgungsfirmen in allen EU Mitgliedsstaaten getroffen damit dieses Produkt durch diese Firmen wiederverwertet oder entsorgt werden kann Mehr Information ber die Einhaltung dieser Anweisungen durch Thermo Fisher Scientific ber die Verwerter und weitere Hinweise die n tzlich sind um die Produkte zu identifizieren die unter diese ROHS Anweisung fallen finden sie unter www thermo com WEEEROHS Conformite DEEE Ce produit doit tre conforme a la directive europ enne 2002 96 EC des D chets d Equipements Electriques et Electroniques DEEE Il est marqu par le symbole suivant Thermo Fisher Scientific s est associ avec une ou plusieurs compagnies de recyclage dans chaque tat membre de l union europ enne et ce produit devrait tre collect ou recycl par celles ci Davantage d informations sur la conformit de Thermo Fisher Scientific a ces directives les recycleurs dans votre pays et les informations sur les produits Thermo Fisher Scientific qui peuvent aider la d tection des substances sujettes a la directive RoHS sont disponibles sur www thermo com WEEEROHS CAUTION Symbol gt OPP f CAUTION Electric Shock This instrument uses high voltages that can cause personal injury Before servicing shut down the instrument and disconnect the instrument from line power Keep the top cover on while operating the instrument Do n
108. you are using a make of syringe other than Unimetrics or Hamilton you need to manually specify the syringe ID by doing the following i Select the Other option button in the Syringe Type group box This specifies that you are using a syringe other than Unimetrics or Hamilton syringe and enables the Syringe ID spin box ii In the Syringe Size group box select the volume of your syringe from the Volume list box 74 APPI Souce User Manual Thermo Scientific 6 Optimizing the TSO Quantum Ultra Mass Spectrometer with Your Analyte Setting Up to Optimize in APCI APPI MS MS Mode with Your Compound iii Enter the inner diameter of your syringe in the Syringe ID spin box f In the Sample Loop box enter 5 in the Sample Loop Size box to specify a loop size of 5 uL g Click Apply to apply these settings The syringe pump is now configured to fill the sample loop with the appropriate amount of sample 8 Start the flow of solvent a On the Control Scan Mode toolbar click on the AS LC Direct Control button to display the Inlet Direct Control view in the top right corner of the workspace Figure 40 Sa Surveyor AS Surveyor MS Pump Direct Control Panel a ig 7 Solvents Proportions and Flow Rate Ay 50 50 o 0 B 50 50 D Oo 0 Flow Rate l min 1000 1000 Pressure Status Pressure bar 155 0 SD 0 1 Run Time Status RunTime min 0 1 Figure 40 Inlet Direct Control view showing high flow set

Ion Max APPI Source User Manual Version C

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