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MSQ Plus Mass Detector Hardware Manual

1. O o gt K i Bounded ions successfully OC transmitted by the mass analyzer reaching ion detector Unbounded neutralized ions being pumped away by the vacuum system Forepump Split flow turbomolecular pump Thermo Scientific MSQ Plus Mass Detector Hardware Manual 27 2 Functional Description Mass Detector Then at a later time as the mass analyzer scans to a higher mass both RF and de voltages change and ions of the next mass to charge ratio for example m z 181 are allowed to pass while all other ions including m z 180 become unstable and undergo unbounded oscillations As the mass analyzer scans over the designated mass range this process continues with ions of one mass to charge ratio after another being transmitted as the RF and de voltages change in value At the end of the scan the RF and dc voltages are discharged to zero and the process is repeated The MSQ Plus Mass Detector can scan the RF and dc voltages over the full mass range of the system for example m z 17 to 2000 in as short a time as 0 2 seconds However under the conditions usually employed in mass analysis such a scan should normally be done in about 2 or more seconds to fall within the upper limit of the calibrated scan rate of 1000 Da s lon Detection System The MSQ Plus Mass Detector is equipped with a high sensitivity off axis ion detection system that produces a high signal to noise ratio and allows for voltage pol
2. Note When you create an instrument method to control your LC MS instrument during a sequence run you import the tune file that contains the empirically determined optimal needle voltage or corona current for your analyte You then manually enter all of the other MS parameters and the chromatography conditions for your analyte You create instrument methods in the Instrument Setup window in the Xcalibur data system Figure 30 shows the features of the Tune window Figure 30 Features of the Tune window Title bar a Menu bar Toolbar Peak Display Scan Events table Status bar Title Bar Menu Bar 42 MSQ Plus Mass Detector Hardware Manual Comms Indicator Per Method Parameters table C Xcalibur methods default tune MSInst atl File View Help l l c i MSO Pus foe edo Description Readback Setpoint Width 1 2H 0 000 Zoom 1 Tune Control BPI 0 00e 000 BPM 0 00 Probe Temperature C 0 550 1 30e 008 Needle kV 0 0 3 0 Acquisition Control 17206006 Retention Time mins 0 00 n a 1 10e 008 General Control pal Operate n a Off 1 00e 008 4 Nitrogen Gas n a Off 3 00e 007 fay onization Mode n a ESI H 8 00e 007 3 7 00e 007 6 00e 007 a 5 00e 007 3 4 00e 007 S 3 00e 007 2 00e 007 1 00e 007 0 00e 000 T T wa T T T i T 1 498 0 498 5 499 0 499 5 500 0 500 5 501 0 501 5 502 0 HLECTRON CORPORATION Name H Mass H Span
3. e Select All in the Device Type box to display all the available devices controlled by the Xcalibur data system e Select LC in the Device Type box to display only LC pumps e Select AS in the Device Type box to display only autosamplers and devices that include an autosampler e Select Detector in the Device Type box to display only detectors e Select MS in the Device Type box to display only mass detectors 14 MSQ Plus Mass Detector Hardware Manual Thermo Scientific 2 Functional Description Reference Inlet System Figure 9 Thermo Foundation Instrument Configuration window 2 Thermo Foundation Instrument Configuration Device Types Configured Devices Liquid Chromatograph Mass Spectrometer MSO Plus MSQ Plus For more information on configuring the software for LC devices see the chapter in the MSQ Plus Mass Detector Getting Connected Guide that pertains to LC devices or to the Help available from the Xcalibur Instrument Configuration window For information on controlling your LC devices from the Xcalibur data system refer to the Help available from the Xcalibur Instrument Setup window Front panel keypad operation of the LC devices and maintenance procedures for the LC devices are described in the documentation provided with the LC Reference Inlet System Use the reference inlet system to introduce calibrant solution into the MSQ Plus Mass Detector to perform a full system autotune
4. ESI ceramic sleeve ESI probe mount M3 x 8 cap head screws Installing the ESI Capillary The ESI capillary is presized for the probe but its installation requires careful alignment To install the ESI capillary CAUTION Take care when handling the ESI capillary It bends easily 1 Using tweezers insert the ESI capillary into the PEEK tube insert and graphite ferrule Adjust the graphite ferrule so that 2 mm of the PEEK tube insert is visible on the back end of the assembly See Figure 43 Thermo Scientific MSQ Plus Mass Detector Hardware Manual 63 5 Routine and Preventive Maintenance Maintaining the ESI Probe Figure 43 Capillary PEEK tube and graphite ferrule assembly 2mm Graphite ferrule Capillary PEEK insert 9 mm 2 While holding the ESI probe in the vertical position use tweezers to insert the capillary PEEK tube insert and graphite ferrule assembly into the ESI probe See Figure 44 Figure 44 View of ESI probe mount showing the insertion of the capillary PEEK sleeve insert Do Graphite ferrule ESI capillary Internal bottom of probe mount 3 Adjust the position of the ESI capillary a Holding the ESI probe in the vertical position carefully shake the PEEK tube insert into the probe until it meets resistance Tap the body of the ESI probe until it falls past the obstruction at the end of the steel sleeve b Using tweezers push the capillary
5. gt Narrow double headed arrows represent electrical connections Broad single headed arrows represent the flow of sample molecules through the instrument Thermo Scientific A sample transfer line connects the Accela LC to the MSQ Plus Mass Detector The Accela LC system is usually installed to the left of the MSQ Plus Mass Detector to minimize the length of tubing required to connect the outlet from the LC to the inlet of the mass spectrometer You can also integrate liquid chromatography systems supplied by other manufacturers with the MSQ Plus Mass Detector An autosampler injects samples into the mobile phase stream provided by the LC pump As the stream passes through the LC column the sample mixture divides between a solid stationary phase of large surface area and the liquid mobile phase The molecular structure of each component of the mixture determines when each component elutes from the column The outlet of the LC column can be directly connected to a UV detector the mass detector or both with a split flow tee For instructions on connecting a split flow tee see Optimizing the LC Conditions on page 127 When preformed sample ions enter the API source of the mass detector they are desolvated by electrospray ESI or sample molecules are desolvated and ionized by atmospheric pressure chemical ionization APCI The vacuum system draws the vaporized molecules and ions into the ion optics The ion optics focus and acceler
6. Exposure can cause eye damage Wear UV eye protection Sharp object Avoid physical contact with the object Pinch point Keep hands away from this area Heavy objects Never lift or move the instrument by yourself you can suffer personal injury or damage the equipment For specific lifting instructions refer to the instrument manual Trip obstacle Be aware of cords hoses or other objects located on the floor When the safety of a procedure is questionable contact Technical Support for Thermo Scientific San Jose products VORSICHT Gefahr durch Laserstrahlen Der in diesem Ger t verwendete Laser kann zu Verletzungen f hren Dieses Symbol wird auch auf dem Ger t angebracht Einzelheiten zu dieser Gefahr finden Sie in den Ger tehandb chern Gefahr durch UV Licht Richten Sie Ihren Blick nicht direkt auf ultraviolettes Licht UV Licht oder in die UV Quelle Dies kann zu Augensch den f hren Tragen Sie eine UV Schutzbrille Scharfes Objekt Vermeiden Sie den physischen Kontakt mit dem Objekt Quetschgefahr Halten Sie Ihre H nde von diesem Bereich fern Schweres Objekt Bewegen und heben Sie das Ger t niemals allein an dies kann zu Verletzungen oder zur Besch digung des Ger ts f hren Spezifische Anweisungen zum Anheben finden Sie im Ger tehandbuch Stolpergefahr Achten Sie auf Kabel Schl uche und andere Objekte auf dem Fu boden Wenn Sie sich ber die Sicherheit eines Verfahrens im unklaren
7. Figure 47 ESI probe tip with the capillary protruding by 0 7 mm Hole in middle o 4 of spacer e lt 0 64mm 0 01 mm depth of ESI spacer bel lt 0 7mm Installing the ESI Probe Follow this procedure to install the ESI probe To install the ESI probe into the mass detector CAUTION Take care when inserting the ESI probe into the probe heater The capillary protruding from the end of the ceramic sleeve and the ceramic sleeve itself are easily damaged In addition you can contaminate the capillary if you let it touch the inner surface of the probe heater as you insert the probe into the probe heater 1 If you have not already done so turn the probe heater off 2 Turn the locking plate of the probe clockwise to the open position and then carefully slide the ESI probe into the probe heater 3 Turn the locking plate counterclockwise to the closed position to lock the probe in place See Figure 35 on page 58 4 Connect the PEEK fingertight fitting to the ESI probe See Figure 35 Maintaining the APCI Probe Flushing the probe on a regular basis helps to prevent contamination and blockage of the capillary But even with the best preventive maintenance occasionally the capillary can become blocked Thermo Scientific MSQ Plus Mass Detector Hardware Manual 67 5 Routine and Preventive Maintenance Maintaining the APCI Probe A significant increase
8. Hardware Manual 60111 97046 Revision A September 2013 DOCUMENTATION 2013 Thermo Fisher Scientific Inc All rights reserved Thermo Scientific Accela and Xcalibur are registered trademarks and MSQ and MSQ Plus are trademarks of Thermo Fisher Scientific in the United States The following are registered trademarks in the United States and other countries Agilent is a registered trademark of Agilent Technologies Inc Intel and Pentium are registered trademarks of Intel Corporation Microsoft and Windows are registered trademarks of Microsoft Corporation The following are registered trademarks in the United States and possibly other countries Swagelok is a registered trademark of Crawford Fitting Company Teflon Vespel and Viton are registered trademarks of E I du Pont de Nemours amp Co Pfeiffer Vacuum is a registered trademark of Pfeiffer Vacuum GmbH Limited Pozidriv is a registered trademark of the American Screw Company Nitronic is a registered trademark of AK Steel Corporation Rheodyne and Upchurch Scientific are registered trademarks of IDEX Health amp Science LLC PEEK is a trademark of Victrex plc Edwards is a trademark of Edwards Limited All other trademarks are the property of Thermo Fisher Scientific Inc and its subsidiaries Thermo Fisher Scientific Inc provides this document to its customers with a product purchase to use in the product operation This document is copyright protected and any reproducti
9. Note When it is not in use ensure that the cone wash nozzle faces away from the entrance cone See Figure 62 on page 82 You do not need to disassemble the source block assembly to clean the entrance cone and the cone wash nozzle To clean the RF dc prefilter the extraction cone or the source block itself you must remove the source block assembly from the mass detector and disassemble it MSQ Plus Mass Detector Hardware Manual 79 5 Routine and Preventive Maintenance Maintaining the Source Block Assembly To clean any or all of the components of the source block assembly follow these procedures Preparing the LC MS System for Maintenance Clearing Access to the Source Block Assembly Removing the Entrance Cone and the Cone Wash Nozzle Cleaning the Entrance Cone and the Cone Wash Nozzle Removing the Source Block Assembly Cleaning the RF dc Prefilter Cleaning the Extraction Cone and the Source Block Repairing the Entrance Cone Assembling the Source Block Assembly Installing the Source Block Assembly CAUTION Wait for the source block and probe heater assembly to cool before carrying out any maintenance Preparing the LC MS System for Maintenance The first step in maintaining the source block assembly is to prepare the LC MS system for maintenance To prepare your LC MS system for maintenance Turn off the flow from the LC pump If the cone wash is in use turn it off Turn off the nitrogen gas the ion optic
10. 9 Close the nitrogen gas cylinder at the main regulator Restarting the System Following a Complete Shutdown Following a long term shutdown carry out the visual checks listed in the Pre switch On checklist shown in Table 5 and then follow the system start up procedure After you complete these procedures the system is ready for a full system autotune Refer to the MSQ Plus Mass Detector Getting Started Guide for details Checking the System Connections Before you switch on the system after an extended shutdown period a major overhaul or instrument relocation perform the visual checks on the system listed in Table 5 Table 5 Pre switch On checklist Sheet 1 of 2 Items Check Power Connections The MSQ Plus Mass Detector and your LC devices are connected to line power The Edwards forepump is connected to the Pump Out receptacle on the back panel of the MSQ Plus Mass Detector Thermo Scientific MSQ Plus Mass Detector Hardware Manual 105 6 System Shutdown Restarting the System Following a Complete Shutdown Table 5 Pre switch On checklist Sheet 2 of 2 Items Check Communication Connections MSQ Plus Mass Detector is connected to the data system computer with a USB cable The communication cables for the LC devices are appropriately connected to the data system computer Gas Connections The GAS IN port on the back panel of the MSQ Plus Mass Detector is connected to a nitrogen supply and th
11. COMRORMIS OUTIL WEO 7IL EBRLT CEE REDERI HEM UV HE EE UV HRA BALOT HESEL R EE YES UV REHE LET SOLA 7 HOTA WII RREA BEIT T CSL EVFRS Yb COMAITILFERENBWEDISCLTC ESL Bey A CHECHELITLVUBRHLEYCCKESL SABES SU RESBETSATHAHVET SAMGHELITAR LOL MBOVIAYIVDESRLTCESLY ERROREM RTD RF BWAR TOREDA EELT EEL FEDRE CAAA BASH SIGAIEL Thermo Scientific San Jose Si DO FIADIVGR bFECHHMYAHE CK ESL ches Bote AMEMARESRA SHS WAS wae Mas E W AAMC Sint Rote TRAWKI UV RAIS BAMA ESSER BAE MERRIE IRE SEF Ss ERRER Ra DIFFERE BY oI BRER TREES A HA E RRM ARRERA SENER Gi A o HFa Peale SIE QRS te ARE RES Thermo Scientific San Jose F mbra Fait Contents Thermo Scientific Chapter 1 Chapter 2 AER eeler XV Related Documentation dek EE E dest Sak gei gh E Ek xv Safety and Special Notices sie e sky vie hee eee EE xvii Safety Preca tionS e345 cis EE Rees eae bbe OT Co Ee xvii Solvent and Gas Purity Requirements ve AN ZANKERT isa up ene tes xix Contacting Us eebe EE cdo eae Ghee deen ae dech xix et EE 1 EE H Ion Polarity Modes erco a AEN Eeer ACEN ee Ee H Ionization Techniques gedet ee ee See EA 3 Electrospray ESD EE 3 Atmospheric Pressure Chemical Ionization APCD 0 0000 5 Sean Types viva SR gr ne Ek Re ER de a Eege SE EE A 7 a EE EE 7 Selected Ion Monitoring SIM 2 2 64 Ee EERLEETEESN EEN EE EE EEN H Data KEE 8 Profile Hartert tee Sek deck e boar cis h
12. Inserting the capillary PEEK sleeve and graphite ferrule into the APC probe PEEK sleeve insert D Graphite Vespel ferrule Bottom of the probe mount aa Figure 52 APCI capillary PEEK sleeve and graphite ferrule inserted into probe PEEK sleeve Graphite Vespel ferrule Capillary 3 Adjust the position of the APCI capillary a Holding the APCI probe in the vertical position carefully shake the PEEK tube insert into the probe until it meets resistance Tap the probe assembly b Using tweezers push the capillary into the probe until it is flush with the PEEK sleeve Thermo Scientific MSQ Plus Mass Detector Hardware Manual 71 5 Routine and Preventive Maintenance Maintaining the APCI Probe c Visually verify that the capillary is protruding from the tip of the probe 4 Depending on whether the capillary protrudes from the tip of the probe do one of the following e Ifthe capillary protrudes from the probe tip go to step 5 e Ifthe capillary does not protrude from the tip of the probe turn the probe upside down and gently shake the capillary assembly out of the probe Adjust the position of the graphite ferrule so that it is closer to the end of the PEEK insert and repeat step 2 and step 3 of this procedure Continue to adjust the position of the graphite ferrule until the capillary protrudes from the tip of the probe when you
13. The black knobs are connected to locking cams When the black knobs are facing away from each other the cams are in the unlocked position and you can pull the probe heater out of the probe mount 3 Pull the probe heater out of the probe mount and then disconnect the green connector and the white connector from the mass detector Be careful not to lose the O rings See Figure 57 Figure 57 Power connector and thermocouple connector Green thermocouple connector White power connector The green connector connects the probe heater to the temperature sensor The white connector connects the probe heater to its power source 4 Store the probe heater in the holder to the left of the source compartment until you are ready to clean it See Figure 58 The probe heater is attached to the mass detector by the grounding strap but it is not necessary to remove the grounding strap during the cleaning procedure See Figure 58 Figure 58 Probe heater with the operator detaching the grounding strap 76 MSQ Plus Mass Detector Hardware Manual Thermo Scientific 5 Routine and Preventive Maintenance Maintaining the Probe Heater Note The 18 gauge wires in the probe heater may darken with time Cleaning the Probe Heater Be sure to clean the probe heater periodically To clean the probe heater Clean the inside of the heater tube with a cotton swab soaked in 50 50 methanol water See Figure 61 on page 79 Replacing the Dete
14. the menu or e Open the Per Method Parameters table in the Tune window Take the system out of Operate mode by clicking the Operate On Off toggle button and then turn off the nitrogen gas by clicking the Nitrogen Gas On Off toggle button 3 Allow the probe heater to cool 4 Unscrew and remove the PEEK fingertight fitting from the APCI probe 5 Turn the corona pin knob 90 degrees to its vertical position Thermo Scientific MSQ Plus Mass Detector Hardware Manual 53 4 Switching Probes Switching from APCI to ESI 6 Turn the locking plate of the APCI probe clockwise to the open position and remove the APCI probe from the mass detector 7 Remove the ESI probe from the holder located in the door of the MSQ Plus Mass Detector and replace it with the APCI probe CAUTION Take care not to damage the capillary of the probe as you insert the ESI probe into the probe heater 8 Turn the locking plate on the ESI probe clockwise to the open position Insert the ESI probe into the probe heater as shown in Figure 34 Then turn the locking plate counterclockwise to the closed position Figure 34 MSQ Plus Mass Detector setup for ESI mode ESI probe Probe heater Probe mount Corona pin knob Source housing 9 Insert the PEEK fingertight fitting into the ESI probe and screw in See Figure 34 which shows the MSQ Plus Mass Detector setup for the ESI mode 10 Adjust the nitrogen gas pressure to 520 kPa 75 psi
15. 10 uM If the cone has been damaged and is no longer circular you can use the corona pin needle part number 70005 98033 by gently inserting the needle from the back of the cone until it makes contact Slowly roll the needle back and forth applying light pressure Re examine the cone under magnification The steel pin should be able to recircularize the titanium cone but it might leave a ragged and somewhat larger opening You can polish the ragged edge of the cone to a sharp circular rim by using 12 uM grit sandpaper or similar abrasive MSQ Plus Mass Detector Hardware Manual 91 5 Routine and Preventive Maintenance Maintaining the Source Block Assembly 4 Clean the repaired entrance cone and attach it to the MSQ Plus Mass Detector system The cone inner diameter is likely to be somewhat larger than the specification 5 Test the cone for sensitivity using erythromycin or another test compound with known performance specifications Assembling the Source Block Assembly After you clean and dry the components of the source block assembly reassemble it Ze 1 To reassemble the source block assembly Install the three O rings see Figure 71 on page 90 e Top left O ring 9 12 mm ID x 3 53 mm THK Viton black part number 00107 01 00047 e Bottom left O ring BS207 Viton black part number FM101417 e Right O ring BS225 Viton black part number FM103048 Install the extraction cone insulator part number FM10
16. 5 Using the supplied locking cap removal tool shown in Figure 76 unscrew the locking cap by turning the tool and cap counterclockwise Figure 76 Removing the locking cap A gt LE 6 Remove the cap including the O ring and wipe with a clean lint free cloth Place in a secure location 7 Using a small flat blade screwdriver or tweezers gently pry out the lubricant reservoir including the O ring as shown in Figure 77 2 Image of the turbomolecular pump from the Compact Turbo TurboDrag Pump TMH TMU 261 Manual PM 0470 BE O 0709 by Pfeiffer Vacuum Thermo Scientific MSQ Plus Mass Detector Hardware Manual 97 5 Routine and Preventive Maintenance Maintaining the Turbomolecular Pump Figure 77 Removing the lubricant reservoir 8 Lift the reservoir and dispose of it safely 9 Using a clean lint free cloth remove any dirt from the opening Replacing the Turbomolecular Pump Lubricant Reservoir This procedure explains how to replace the lubricant reservoir of the turbomolecular pump To replace the turbomolecular pump lubricant reservoir 1 Insert the new reservoir part number 00950 0116 into the opening 2 Replace the O ring and cap Use a new O ring if necessary 3 Tighten the cap using the supplied locking cap removal tool turning it clockwise Do not over tighten the cap 4 Replace the access plate a Insert the left hand side lug first b Ensure that the PEEK tubing is located in the
17. Danger li aux rayons ultraviolets ne jamais regarder directement la lumi re ultraviolette UV ou la source d UV Une exposition peut entra ner des l sions oculaires Porter des protections oculaires anti UV Objet tranchant viter tout contact physique avec l objet Risque de pincement loigner les mains de cette zone Objet lourd ne jamais soulever ou d placer l instrument seul sous peine de blessure corporelle ou d endommagement de l instrument Pour obtenir des instructions de levage sp cifiques se reporter au manuel de l instrument Risque de tr buchement faire attention aux c bles tuyaux et autres objets situ s sur le sol Si la s ret d une proc dure est incertaine contacter l assistance technique pour les produits Thermo Scientific San Jose CAUTION Symbol gt PPP gt gt CAUTION Risk electric shock This instrument uses voltages that can cause electric shock and or personal injury Before servicing shut down the instrument and disconnect it from line power While operating the instrument keep covers on Do not remove the protective covers from the printed circuit board assemblies PCBAs Chemical hazard Wear gloves and other protective equipment as appropriate when handling toxic carcinogenic mutagenic corrosive or irritant chemicals Use approved containers and proper procedures to dispose of waste oil and when handling wetted parts of the instrument Hot surface Be
18. Detector Hardware Manual 103 6 System Shutdown Shutting the System Down for Non Routine Maintenance 5 Turn off the power to the ion optics by clicking the Operate On Off toggle button The On Off button turns from green to gray and the text to the left of the button changes from On to Off 6 Turn off the nitrogen gas by clicking the Nitrogen Gas On Off toggle button in the General Control group of the Per Method Parameters table The On Off button turns from green to gray and the text to the left of the button changes from On to Off Within a few seconds you hear the nitrogen supply to the API source shut off In the Nitrogen Gas Off mode the system maintains a bleed of nitrogen gas to the probe to prevent a rise in humidity within the source compartment 7 When you plan to leave the MSQ Plus Mass Detector in the Off mode for a significant period of time turn off the nitrogen supply to the system at the main regulator Shutting the System Down for Non Routine Maintenance You might need to shut down the MSQ Plus Mass Detector for a non routine maintenance procedure or to relocate the instrument lt To shut down the MSO Plus Mass Detector 1 If you are using the optional cone wash pump turn it off by turning its power switch to the Off position 2 Open the Xcalibur data system by choosing Start gt Programs gt Thermo Xcalibur gt Xcalibur from the Windows desktop 3 If the Information view is not displayed choose
19. Time Range Peak Format ScanTime Polarity Cone H Rdbk H Zoom On OfF Fol 500 00 4 00 0 00 Profile 1 00 ve 100 0 1 Sen Ready 000000 bytes sec NUM The title bar is the horizontal band at the very top of the window It contains the file name of the currently active tune file For example default tune is the name of the MSQ Plus Mass Detector default tuning file The Tune window menu bar contains the File View and Help menus Thermo Scientific Toolbar Comms Indicator Scan Events Table 2 Functional Description Data System You can use the toolbar buttons to start and stop acquiring data and to print a tune report The Tune Comms Indicator positioned to the right of the Tune toolbar indicates whether there is proper communication between the Tune software and the MSQ Plus Mass Detector The Comms Indicator is represented by an icon depending on whether you are in Tune mode or Acquisition mode The icon can be either stationary or spinning depending on whether working communication is occurring The Tune icon Al appears when you are in Tune mode that is when you are in the Tune window and not acquiring data to a file The icon spins continuously to show that communication between the MSQ Plus Mass Detector and the computer is established For example whenever the Tune software uploads or downloads a command the icon spins to indicate that communication is working correctly The Acquisition icon s appears whe
20. Vent Valve 30 MSQ Plus Mass Detector Hardware Manual Thermo Scientific Vacuum Manifold Turbomolecular Pump Thermo Scientific 2 Functional Description Mass Detector A functional block diagram of the vacuum system is shown in Figure 21 Figure 21 Functional block diagram of the vacuum system Air filter ee a Atmospheric M Path RF dc Analyzer l LC l pressure region prefilter region Pirani l orother 1 region region gauge l Sample tube sample input r device 10 3 Torr 1 g Torr 1 Torr ee Split flow turbomolecular pump Forepump Foreline The vacuum manifold encloses the ion optics mass analyzer and ion detection system assemblies The vacuum manifold is a thick walled aluminum chamber with a removable top cover plate machined flanges on the front sides and bottom and various electrical feedthroughs and gas inlets The vacuum manifold is divided into three chambers by two baffles The region inside the first chamber called the M path region is evacuated to 1 torr by the forepump The region inside the second chamber called the transfer lens region is evacuated to 107 gt torr by the interstage port of the split flow turbomolecular vacuum pump The region inside the third chamber called the mass analyzer region is evacuated to 10 torr by the high vacuum port of the split flow turbomolecular pump A Balzers Pfe
21. View gt Info View to display it 4 Turn off the flow from the LC pump as follows a If your LC pump is controlled from the Xcalibur data system turn it off from its respective Direct Control dialog box or place it in the Standby mode from the Info View Status page b Ifyour LC pump is not controlled from the Xcalibur data system turn it off from its keypad control panel 5 Right click the MSQ Plus listing on the Status page and choose Turn Device Off from the shortcut menu 104 MSO Plus Mass Detector Hardware Manual Thermo Scientific 6 System Shutdown Restarting the System Following a Complete Shutdown 6 Right click the Server icon in the system tray of the Windows taskbar and choose Vent from the shortcut menu to vent the system Venting the system turns off the turbomolecular pump The Server is displayed as an icon in the Windows Taskbar just to the left of the time display as shown in Figure 81 Figure 81 View of taskbar showing the Server icon and the shortcut menu Manual Tune Instrument Tune and Calibration Exit 7 Exit the Xcalibur data system and close the server 8 Wait for approximately two minutes and turn off the MSQ Plus Mass Detector by setting the MAINS IN switch to the Off position Turning off the power to the MSQ Plus Mass Detector also turns off the power to the Edwards forepump which gets its line power from the Pump Out receptacle on the back panel of the mass detector
22. When you activate the server by running either the Xcalibur data system or Tune the Server LED icon is displayed in the system tray of the Windows taskbar just to the left of the time display Figure 28 View of taskbar showing the Server icon start e aaa X Roadmap Home Pl C Xcalibur metho Ee Z O 5 09pm The Server icon provides you with information about the status of the MSQ Plus Mass Detector and mimics a tristate LED display red green yellow showing e Steady red when the mains are on and the instrument is vented or an error has occurred within the system e Flashing yellow when the instrument is pumping down 40 MSQ Plus Mass Detector Hardware Manual Thermo Scientific Tune Window Thermo Scientific 2 Functional Description Data System e Steady yellow when the instrument is pumped down but is not in Operate mode e Steady green when the instrument is pumped down and is in Operate mode Right clicking the Server icon opens the shortcut menu shown in Figure 29 Figure 29 Server shortcut menu Manual Tune Instrument Tune and Calibration Vent Exit Use the menu commands as follows e Choose Manual Tune to open the Tune window where you can optimize the performance of your MSQ Plus Mass Detector for a specific application e Choose Instrument Tune and Calibration to display the Instrument Tuning and Calibration wizard e Choose Vent to turn off the turbomolecular pu
23. and O ring MSQ Plus 60111 62018 Oil reservoir 190 240 260 for turbomolecular pump 00950 01116 Turbomolecular pump oil change tool FM104442 Tube insert for API probe PEEK 3 each FM102591 Heater Repair Kit 60111 62010 Detent screw insulator FM102585 Screw sleeve FM102582 Spring screw FM102583 Spring cup FM102584 MSQ Plus Hardware and O ring Kit 60111 62018 Sealing plug 2 each FM102277 Ferrule SGE 1 16 graphite Vespel 10 each 6070119 Spring E type clip stainless steel MSQ only 3 FM102574 each Not available as a separate item Spring compression 4 6 mm OD 0 45 N mm 00111 01 00013 30 mm length O ring 13 87 mm ID x 3 53 mm THK BS207 FM101417 BLK Viton 1 each O ring 3 68 mm ID x 1 78 mm THK BS007 FM101464 BLK Viton 2 each O ring 3 0 mm ID x 1 0 mm THK BLK Viton 5711933 2 each O ring 9 25 mm ID x 1 78 mm THK BS012 FM100231 Viton for entrance cone 2 each O ring 12 42 mm ID x 1 78 mm THK BS014 FM101522 BLK Viton 1 each MSQ Plus Mass Detector Hardware Manual Thermo Scientific Thermo Scientific 7 Replaceable Parts Consumables Table 6 Parts in the MSQ Plus Annual Maintenance Kit Sheet 3 of 3 Item O ring 9 0 mm ID x 3 0 mm THK BLK Viton 1 each Part number 00107 01 00026 O ring 3 30 mm ID x 2 4 mm THK BLK Viton FM103016 2 each O ring 47 22 mm ID x 3 53 mm THK BS225 FM103048 B
24. appropriate grooves c Insert the bottom lug d Insert the right hand side lug 3 Image of the turbomolecular pump from the Compact Turbo TurboDrag Pump TMH TMU 261 Manual PM 0470 BE O 0709 by Pfeiffer Vacuum 98 MSQ Plus Mass Detector Hardware Manual Thermo Scientific System Shutdown When you are not performing analyses you can temporarily turn off the nitrogen gas or set the MSQ Plus Mass Detector to the Off mode Turning off the nitrogen gas between intermittent analyses conserves the nitrogen supply Placing the system in the Off mode conserves the laboratory nitrogen supply and increases the life of the ion detection system Some of the maintenance procedures contained in Chapter 5 Routine and Preventive Maintenance require that the system be completely shut down To shut down the system you must turn the vacuum system off Restarting the system after a complete shutdown requires building up the vacuum to a working level If you are restarting the system after moving it to a new location Thermo Fisher Scientific recommends that you perform a full system autotune Contents e Shutting Down the System in an Emergency e Turning Off the Nitrogen Gas e Placing the System in the Off Mode e Shutting the System Down for Non Routine Maintenance e Restarting the System Following a Complete Shutdown e Resetting the MSQ Plus Mass Detector Shutting Down the System in an Emergency Thermo Scientific If you
25. before you turn the corona pin knob to its vertical position See Figure 73 Figure 73 Cone wash nozzle turned to the right in the source block Corona pin knob Cone wash nozzle Thermo Scientific MSQ Plus Mass Detector Hardware Manual 93 5 Routine and Preventive Maintenance Maintaining the Source Block Assembly To install the source block assembly into the mass detector 1 Insert the source block assembly part number 60111 60051 into the source block enclosure and tighten the thumbscrews on the source block The source block is self aligning when the thumbscrews are fully secure Finger tighten only See Figure 67 on page 86 CAUTION The tip of the cone wash nozzle is very fragile 2 Handling the cone wash nozzle by its base because the tip is fragile insert the cone wash nozzle part number FM102521 into the source block and carefully rotate the nozzle tip to the right Lubricating the O ring with a little methanol helps the insertion process See Figure 73 3 Remove the lint free cloth from the bottom of the source enclosure 4 Insert the entrance cone into the source block and turn it counterclockwise Note The entrance cone assembly is reverse threaded Therefore to remove it turn it clockwise To install it turn it counterclockwise 5 Install the probe heater a Remove the probe heater from its holder and rotate the black knobs of the probe heater so that they face away from each other S
26. in LC pump backpressure that is up to 300 psi at a flow rate of 1 mL min added to the total LC system backpressure or instability in the signal can be symptomatic of a blocked or partially blocked capillary Replace the capillary if it has become blocked or partially blocked during operation The APCI capillary part number FM102594 is pre sized for the probe but its installation requires careful alignment CAUTION Wait for the source block and probe heater assembly to cool before changing ionization modes Follow these maintenance procedures to replace a capillary or clean the APCI probe e Removing the APCI Probe e Removing the APCI Capillary e Installing the APCI Capillary e Installing the APCI Probe Removing the APCI Probe Follow these steps to remove the APCI probe from the probe heater To remove the APCI probe from the probe heater 1 Ensure that the flow from the LC pump is turned off 2 Turn off the nitrogen gas the probe heater and the ion optics by doing one of the following e In the Status page in the Information view of the Xcalibur data system right click the MSQ Plus listing and choose Turn Device Off from the shortcut menu or e Open the Per Method Parameters table in the Tune window Take the system out of Operate mode by clicking the Operate toggle button and turn off the nitrogen gas by clicking the Nitrogen Gas toggle button See Figure 30 on page 42 3 Wait for the source block and th
27. insert the capillary assembly into the probe 5 Screw the capillary retaining nut adapter into the probe until fingertight and recheck that the capillary protrudes from the tip of the probe See Figure 53 Figure 53 APCI probe with the capillary retaining nut screwed in finger tight CENL Capillary retaining nut AYA 6 Using the probe clamp tighten the capillary retaining nut by one half turn Do not overtighten the screw 7 Finish reassembling the probe a Place the locking plate and probe clamp in position b Insert the M3 x 10 cap head stainless steel screw part number FM103046 and tighten with the 2 5 mm Allen key Typically a visual confirmation that the capillary protrudes from the probe tip is sufficient but you can also use the APCI spacer plate provided in the MSQ Plus Mass Detector tool kit to check the capillary protrusion depth 8 Optional Align the hole in the center of the APCI spacer plate over the tip of the probe and check that you can feel the capillary protruding through the spacer 72 MSQ Plus Mass Detector Hardware Manual Thermo Scientific 5 Routine and Preventive Maintenance Maintaining the APCI Probe The APCI spacer is 0 41 mm thick If you can feel the capillary protruding through the hole in the center of the space plate the capillary protrudes from the APCI probe tip by more than 0 41 mm See Figure 54 Figur
28. location of 95 maintaining 96 operating speed 19 purpose 31 removing lubricant reservoir 96 replacing lubricant reservoir 98 turning off 41 81 Thermo Scientific Index T U unsuitable additives 131 USB cable 22 USB port 20 22 USER I O contact closure connector 20 22 UV detector 13 V vacuum manifold 30 31 vacuum spare parts 124 vacuum system 30 95 vent valve 32 W waste reservoir nitrogen pressurization line 16 waste solvent 49 water 128 WEEE compliance v X Xcalibur data system configuring for LC devices 14 controlling modules of LC MS system 37 Instrument Configuration application 14 Instrument Setup view 42 Roadmap view 37 39 software features 38 Xcalibur icon 101 MSQ Plus Mass Detector Hardware Manual 143
29. mode the system is left under vacuum but the nitrogen flow is reduced to a bleed through the API probe The electron multiplier and conversion dynode are turned off the power to the ion optics is turned off and the probe heater is turned off Therefore placing the instrument in the Off mode allows you to conserve your laboratory nitrogen supply and increase the lifespan of the electron multiplier In addition you can restart and operate a MSQ Plus Mass Detector that has been left in the Off mode without waiting for the vacuum system to pump down to a working level Note 1 Leave the MSQ Plus Mass Detector under vacuum when you are switching the API probes Do not vent the instrument unless you are performing a maintenance procedure that requires you to break the integrity of the vacuum 2 Before you place the MSQ Plus Mass Detector in the Off mode turn off the flow from the LC pump and the flow from the optional cone wash pump Turn the mass detector off from the Status view in the Xcalibur data system or from the Tune window Turning Off the Mass Detector from the Xcalibur Data System One way to turn off the MSQ Plus Mass Detector is to use the Status page of the Information view of the Xcalibur data system To turn off the MSQ Plus Mass Detector from the Xcalibur Status page 1 If you are using the optional cone wash pump turn it off by turning its power switch to the Off position 2 If the Xcalibur data system i
30. or a mass scale calibration which is a subset of the full system autotune procedure During an automated full system autotune the MSQ Plus Mass Detector and instrument control software perform these steps e The mass detector infuses the calibrant solution and the software electronically adjusts the resolution of the peaks at low mid and high mass The resolution of the peaks is adjusted to unity Dalton at their baselines e Performs a mass scale calibration During a mass scale calibration the software performs these steps Thermo Scientific MSQ Plus Mass Detector Hardware Manual 15 2 Functional Description Reference Inlet System Compares the empirically determined masses of the factory supplied calibrant solution to a reference file of the same compound that contains the correct mass for each peak Adjusts the empirically determined masses in the acquired data file to match those in the reference file The software applies these adjustments to all subsequent acquisitions until you perform a new full system autotune or mass scale calibration After installing the MSQ Plus Mass Detector a Thermo Fisher Scientific service engineer performs a full system autotune You must repeat the procedure if you move the MSQ Plus Mass Detector to a new location install or update the Xcalibur data system or change the laboratory environment If you notice a drift in the mass accuracy of your analyses you should perform a mass sca
31. protein analysis High levels greater than 0 1 v v can cause suppression of sensitivity in positive ion mode TFA might completely suppress ionization in negative ion mode Triethylamine TEA can suppress the ionization of less basic compounds in positive ion mode because it is also readily ionized to give a M H ion at m z 102 TEA enhances ionization of other compounds in negative ion mode because it is basic It is a particularly useful additive for the analysis of nucleic acids In ESI using THF can reduce sensitivity You can counteract this effect by the post column addition of ammonium acetate It has no effect in APCI CAUTION Do not use a concentration of THF greater than 5 with PEEK tubing THF causes swelling in the PEEK tubing and consequently presents a risk of the LC tubing bursting Inorganic acids for example sulfuric acid or phosphoric acid can be used Check the suitability of the LC column to low pHs CAUTION After using phosphoric acid thoroughly clean the source source enclosure and hexapole RF lens to minimize the physical damage 130 MSQ Plus Mass Detector Hardware Manual Thermo Scientific Unsuitable Additives A Optimizing the LC Conditions Cone Wash System Unsuitable additives include surface active agents and detergents Surface active agents and detergents can suppress the ionization of other compounds Detergents by their very nature are concentrated at the surface of a liquid They can cause pr
32. regulator Checking the Disk Space Periodically verify that your hard disk drive has enough free space for data acquisition The amount of available disk space is shown in the Disk Space dialog box To determine the amount of available disk space 1 From the Roadmap view which is available by choosing Start gt Thermo Xcalibur gt Xcalibur from the Windows taskbar choose Actions gt Check Disk Space Thermo Scientific MSQ Plus Mass Detector Hardware Manual 45 3 Daily Operation Before Operating the Mass Detector The Disk Space dialog box opens It lists the following e Current drive and directory for example C Xcalibur system programs e Number of megabytes that are available free on the current drive e Percentage of the current drive that is available e Total capacity of the current drive 2 To select another disk drive so that you can determine its disk space click the Directory button 3 When you have completed this procedure click OK to close the dialog box If necessary free space on the hard disk by deleting obsolete files and by moving files from the hard disk drive to a backup medium First copy files to the backup medium and then delete them from the hard disk Checking the Oil Level in the Oil Mist Filter Once the oil level in the oil mist filter that is attached to the Edwards forepump rises above the maximum oil level mark as shown in Figure 31 the oil mist filter becomes ineffective in trapping
33. remove the capillary as described in Removing the ESI Capillary on page 59 3 Use the 2 5 mm Allen key to unscrew the two M3 x 8 cap head stainless steel screws from the ESI probe mount See Figure 42 4 Pull the ESI probe mount out of the ESI ceramic sleeve and ceramic mount assembly 5 Remove the ESI ceramic sleeve from the ESI ceramic mount by pulling the sleeve forward through the top of the mount As Figure 41 shows the ESI ceramic sleeve is slightly flared at one end This flare holds the ESI ceramic sleeve in place when you insert it into the ESI ceramic mount Figure 41 ESI ceramic mount and ceramic sleeve ESI ceramic mount o O 8 3 90 mm OD 6 Insert a new ESI ceramic sleeve part number FM103394 into the ESI ceramic mount See Figure 42 ESI ceramic sleeve 3 80 mm OD 7 Place the O rings in position in the ESI ceramic mount and then insert the ESI probe mount into the ESI ceramic mount and ceramic sleeve assembly 62 MSQ Plus Mass Detector Hardware Manual Thermo Scientific 5 Routine and Preventive Maintenance Maintaining the ESI Probe 8 Insert the two M3 x 8 cap head stainless steel screws into the ESI probe mount and tighten with the 2 5 mm Allen key 9 Reinstall the ESI capillary and reassemble the probe as described in Installing the ESI Capillary on page 63 Figure 42 Pulling the ESI probe mount out of the ESI ceramic mount ESI ceramic mount call
34. required pH Addition of acids can suppress ionization in negative ion analysis and weakly acidic compounds might not form M H ions in acidic conditions Ammonium hydroxide ammonia solution is suitable for increasing the pH of the mobile phase which can enhance LC separations When you analyze weakly acidic compounds in negative ion mode it is unlikely that there will be any suppression of ionization Thermo Scientific MSQ Plus Mass Detector Hardware Manual 129 D Optimizing the LC Conditions LC Solvents and Mobile Phase Additives Volatile salts such as ammonium acetate or ammonium formate are often used to buffer mobile phases Use as little ammonium acetate or ammonium formate as possible keeping the concentration below 100 mM Ensure that the cone wash is running when using high concentrations When using non volatile salts ensure that the cone wash is running because they can crystallize in the source block the entrance cone and prevent the mass spectrometer from functioning The most common non volatile salts used are phosphates Ensure that the cone wash is running when using ion pairing agents for example sodium octanesulfonic acid Many ion pairing agents suppress electrospray Less Commonly Used Additives The following additives are less commonly used e Trifluoroacetic acid TFA Triethylamine TEA Tetrahydrofuran THF e Inorganic acids Trifluoroacetic acid TFA is frequently used for peptide and
35. sind setzen Sie sich bevor Sie fortfahren mit Ihrer lokalen technischen Unterst tzungsorganisation f r Thermo Scientific San Jose Produkte in Verbindung PRECAUCI N Peligro por l ser Este instrumento utiliza un l ser que puede producir lesiones personales Este s mbolo tambi n aparece en el instrumento Si desea obtener m s informaci n sobre el peligro consulte el manual del instrumento Peligro por luz ultravioleta No mire directamente a una luz ultravioleta UV ni a una fuente UV La exposici n puede causar da os oculares Lleve protecci n ocular para UV Objeto puntiagudo Evite el contacto f sico con el objeto Puntos de pinzamiento Mantenga las manos apartadas de esta rea Objeto pesado Nunca levante ni mueva el instrumento por su cuenta podr a sufrir lesiones personales o da ar el equipo Para obtener instrucciones espec ficas sobre levantamiento consulte el manual del instrumento Tropiezo con obst culos Tenga en cuenta los cables mangueras u otros objetos colocados en el suelo En caso de duda sobre la seguridad de un procedimiento p ngase en contacto con el personal de servicio t cnico de los productos Thermo Scientific San Jose MISE EN GARDE Danger li au laser l instrument utilise un laser susceptible de provoquer des blessures corporelles Ce symbole figure galement sur l instrument Pour plus de d tails sur ce danger potentiel se reporter au manuel de l instrument
36. system turn it off from its respective Direct Control dialog box or place it in the Standby mode from the Status page of the Information view of the Xcalibur data system b Ifyour LC pump is not controlled from the Xcalibur data system turn it off from its keypad control panel 3 If the Tune window is not open open it a Double click the Tune icon fe on the Windows desktop The Server icon now appears in the System tray to the left of the clock of the Windows taskbar b Double click the Server icon to open the Tune window 100 MSQ Plus Mass Detector Hardware Manual Thermo Scientific 6 System Shutdown Placing the System in the Off Mode 4 If the Per Method Parameters table is not open open it by clicking the Expand icon on the right side of the Tune window 5 Turn off the nitrogen gas by clicking the Nitrogen Gas On Off toggle button in the General Control group of the Per Method Parameters table The On Off button turns from green to gray and the text to the left of the button changes from On to Off Within a few seconds you hear the nitrogen supply to the API source shut off In the Nitrogen Gas Off mode the system maintains a bleed of nitrogen gas to the probe to prevent gases from back streaming from the waste solvent bottle Placing the System in the Off Mode Place the MSQ Plus Mass Detector in the Off mode if you are not going to use it for a short period of time such as overnight or over weekends In the Off
37. that contained in the MSQ Plus Mass Detector Hardware Manual To avoid personal injury or damage to the instrument do not perform any servicing other than that contained in the MSQ Plus Mass Detector Hardware Manual or related manuals unless you are qualified to do so CAUTION Shut down the mass detector and disconnect it from line power before you service it High voltages capable of causing personal injury are used in the instrument Some maintenance procedures require that the mass detector be shut down and disconnected from line power before service is performed Do not operate the mass detector with the top or side covers off Do not remove protective covers from PCBs CAUTION Do not interfere with the safety interlock Interfering with the safety interlock will expose you to potentially lethal electrical hazards Thermo Scientific MSO Plus Mass Detector Hardware Manual xvii Preface Safety Precautions CAUTION Respect heated zones Treat heated zones with respect The ion transfer capillary and the APCI vaporizer might be very hot and might cause severe burns if touched Allow heated components to cool before you service them CAUTION Place the mass detector in Standby or Off mode before you open the atmospheric pressure ionization API source The presence of atmospheric oxygen in the API source when the mass detector is on could be unsafe The mass detector automatically goes into standby mode when you open the API source however t
38. the MSQ Plus Mass Detector is available from the Information view of the Xcalibur data system and from the Server LED icon MSQ Plus Mass Detector Hardware Manual 37 2 Functional Description Data System The data system for the MSQ Plus Mass Detector includes the following components Computer Hardware Computer Hardware Xcalibur Software MSQ Plus Mass Detector Server Tune Window Printer The data system computer satisfies the following minimum system requirements Intel Pentium 4 at 2 4 GHz processor 256 MB of random access memory RAM 40 GB HDD CD ROM drive USB adapter data system to mass detector Ethernet adapter data system to local area network 1 44 MB 3 5 in disk drive Video Graphics card and monitor capable of 1024 x 768 resolution and 65536 colors 16 bit color quality For more information about the computer refer to the manuals that come with it Xcalibur Software Xcalibur software controls the MSQ Plus Mass Detector and a variety of liquid chromatography devices The Xcalibur software package for the MSQ Plus Mass Detector includes the application programs listed in Table 2 Xcalibur Home Page version 2 2 SPlor later is required for the MSQ 2 0 version of the MSQ Plus Mass Detector software The firmware versions of the LC devices controlled by the Xcalibur data system are listed in the MSQ Plus Mass Detector Getting Connected Guide 38 MSQ Plus Mass Detector Hardware Manual Thermo Scientifi
39. 129 130 ammonium formate 129 ammonium hydroxide 129 APCI capillary installing 71 removing 69 replacing 68 APCI probe installing 73 installing the APCI capillary 71 maintaining 67 removing 68 removing APCI capillary 69 APCI probe assembly 121 APCI See atmospheric pressure chemical ionization API probe 32 47 48 94 atmospheric pressure chemical ionization adduct ion formation 6 API source 22 24 capillary 5 definition of 5 description 2 flow rates 128 ion generation 5 ion polarity modes 7 Thermo Scientific molecular weights suited for 7 molecule desolvation 13 negative ion mode 6 nitrogen consumed 36 positive ion mode 6 primary ion formation 6 regulation of nitrogen gas 33 secondary ion formation 6 spectral characteristics 7 switching to electrospray 53 tuning parameters to set 41 atmospheric pressure ionization API source 22 autosamplers Accela 12 contact closure 14 purpose 2 13 back panel of the MSQ Plus Mass Detector 20 backing manifold 20 22 backpressure 56 68 basic compounds 4 5 C calibrant 35 calibrant spare parts 125 carboxylic acids 3 7 centroid data type 8 chemicals 117 compliance WEEE v cone voltage 41 cone wash nozzle as part of cone wash system 37 cleaning 83 handling 84 optimizing position of 132 removing from source block assembly 82 cone wash pump 132 133 MSQ Plus Mass Detector Hardware Manual 139 Index D cone wash system components of 3
40. 2264 Verify proper orientation by checking for the indent on the facing surface Install the extraction cone part number FM102263 with the cone facing the source block Install the hexapole screw insulator part number FM102248 Be certain that this part is free from contamination particularly from metal filings that might result from the action of the hexapole screws on the source block See Figure 71 on page 90 Ensure that the semicircular cutouts in these three components line up as shown in ey ar Figure 72 92 MSQ Plus Mass Detector Hardware Manual Thermo Scientific 5 Routine and Preventive Maintenance Maintaining the Source Block Assembly Figure 72 Source block with the proper alignment of the extraction cone insulator extraction cone and hexapole insulator Properly aligned components 7 Align the three spring screws at the base of the RF dc prefilter to the three holes on the back of the source block Support the quadrupole as you alternately screw the three spring screws at the base of the RF dc prefilter into the source block It might help to remove the thumbscrews from the source block allowing the block to sit upright on a flat surface See Figure 68 on page 87 Installing the Source Block Assembly You must reinstall the source block assembly before you prepare the system for operation CAUTION The corona pin is very sharp Do vot attempt to install the entrance cone or the cone wash nozzle
41. 3 2 Functional Description Data System Printer Thermo Fisher Scientific does not ship a printer with the MSQ Plus Mass Detector If you want to connect a printer that communicates through a USB cable connect the cable to one of the USB ports on the front of the data system computer Set up the printer from the Print Setup dialog box To open the Print Setup dialog box choose File gt Print Setup in any window 44 MSQ Plus Mass Detector Hardware Manual Thermo Scientific Daily Operation To optimize the performance of your MSQ Plus Mass Detector you must perform various routine operations both before and after you operate the system Contents e Before Operating the Mass Detector e After Operating the Mass Detector Before Operating the Mass Detector This section describes procedures that you might want to perform on a daily basis before you begin your analyses e Checking the Nitrogen Supply e Checking the Disk Space e Checking the Oil Level in the Oil Mist Filter Checking the Nitrogen Supply Check the nitrogen supply on the regulator of the nitrogen gas tank or liquid nitrogen boil off tank Make sure that you have sufficient gas for your analysis Typical nitrogen consumption is 15800 liters per day based on a 24 hr day If necessary replace the tank Verify that the pressure of nitrogen reaching the mass spectrometer is between 520 35 kPa 75 5 psi If necessary adjust the pressure with the tank pressure
42. 54 MSQ Plus Mass Detector Hardware Manual Thermo Scientific Routine and Preventive Maintenance This chapter contains a maintenance schedule and instructions for the maintenance tasks that you must perform to keep the MSQ Plus Mass Detector in optimal working condition The MSQ Plus Mass Detector is a low maintenance instrument Apart from fairly light y 1g periodic preventive maintenance it requires only simple source cleaning and inspection on a loss of performance basis Contents e Maintenance Schedule e Maintaining the ESI Probe e Maintaining the APCI Probe e Maintaining the Probe Heater e Maintaining the Source Block Assembly e Maintaining the Forepump e Maintaining the Turbomolecular Pump Maintenance Schedule Table 3 contains a list of routine maintenance procedures that you must perform at the intervals specified The maintenance schedule provides only a rough guide to the maintenance tasks that you are responsible for The appropriate frequency for these tasks depends on instrument usage and the level of system induced contamination from samples and mobile phase solvents Thermo Scientific MSQ Plus Mass Detector Hardware Manual 55 5 Routine and Preventive Maintenance Maintaining the ESI Probe Table 3 Maintenance schedule Frequency As needed Action Clean the source if you see a drop in sensitivity during analyses Flush the capillaries after running an analysis that required buffered sol
43. 7 cone wash pump pinouts 132 optimizing 127 purpose 36 connection kits 126 consumable parts 111 contact closure 14 contact closure connector 22 contacting us xix conversion dynode 29 30 corona current 41 42 corona needle 82 corona pin 24 52 data system computer connecting to MSQ Plus Mass Detector 22 requirements 38 dc voltage 26 28 default tune file 25 deprotonated molecules 4 7 detent screw insulator 77 dichloromethane 128 dimethyl sulfoxide DMSO 128 disassembling the RF dc prefilter 89 disk space 45 Disk Space dialog box 46 documentation survey xx drug metabolism studies 3 E Edwards forepump 32 EEK tube insert 71 electron multiplier 30 electronic spare parts 126 electrospray acidic compounds 4 5 API source 22 23 basic compounds 4 5 definition of 3 description 2 flow rates 128 fragmentation in 4 ion desolvation in 3 13 molecular weights suited for 5 nitrogen consumption 36 polar compounds 5 polarity modes available in 5 recommended guidelines 5 140 MSQ Plus Mass Detector Hardware Manual regulation of nitrogen gas 33 solvents used in 5 spectral characteristics 4 spectrum produced 4 switching to atmospheric pressure chemical ionization 51 tuning parameters to set 41 entrance cone cleaning 83 removing from source block assembly 82 repairing 91 ESI capillary cleaning or replacing 61 installing 63 removing 59 ESI probe installing 67 installing capillary 63 maintaining 56 removing 57 removing c
44. 8 ESI mount subassembly Locking plate M3 x 10 cap head screw P N FM103046 ec a Graphite Vespel ferrule P N 6070119 cap head screws Capillary retaining nut FM102590 APCI Probe Assembly Table 13 lists the parts in the APCI probe assembly Table 13 APCI probe assembly parts Sheet 1 of 2 7 Replaceable Parts P N FM103394 O ring BS012 P N FM100231 ESI ceramic sleeve Spares Item Part number Assembly APCI probe FM102587 APCI capillary tube 6 each FM102594 Ferrule GVF 16 graphite Vespel 6070119 O ring 9 25 mm ID x 1 78 mm THK BS012 FM100231 BLK Viton Thermo Scientific MSQ Plus Mass Detector Hardware Manual 121 7 Replaceable Parts Spares Table 13 APC probe assembly parts Sheet 2 of 2 Item Part number O ring 5 28 mm ID x 1 78 mm THK BS009 5711020 BLK Viton PEEK tube insert 12 each FM102591 Screw M3 x 8 cap head stainless steel N A Screw M3 x 10 cap head stainless steel FM103046 Figure 87 shows an exploded view of the APCI probe assembly Figure 87 Exploded view of APC probe assembly APCI probe subassembly O ring BS009 P N 5711020 APCI probe mount Locking plate subassembly APCI capillary P N FM102594 PEEK sleeve insert O ring BS012 M3 x 10 P N FM100231 cap head screw P N FM103046 cap head screws Probe clamp Capillary Graphite Vespel ferrule retai
45. 8LA Nitrogen Generator for Mass Spectrometers Dionex N118LOA N418LA Unpacking amp Installation Dionex N 18KLA Nitrogen Generator User Manual Dionex MSQ Getting Started Safety and Regulatory Guide You also receive a printed copy of the Safety and Regulatory Guide with your MSQ Plus Mass Detector This guide contains important safety information about Thermo Scientific LC and MS systems Make sure that all lab personnel have read and have access to this document The software also provides Help xvi MSQ Plus Mass Detector Hardware Manual Thermo Scientific Preface Safety and Special Notices 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 Safety Precautions Observe the following safety precautions when you operate or perform service on the MSQ Plus Mass Detector CAUTION Do not perform any servicing other than
46. AUSE HARMFUL INTERFERENCE AND 2 THIS DEVICE MUST ACCEPT ANY INTERFERENCE RECEIVED INCLUDING INTERFERENCE THAT MAY CAUSE UNDESIRED OPERATION CAUTION Read and understand the various precautionary notes signs and symbols contained inside this manual pertaining to the safe use and operation of this product before using the device Notice on Lifting and Handling of Thermo Fisher Scientific Instruments For your safety and in compliance with international regulations the physical handling of this Thermo Fisher Scientific instrument requires a team effort to lift and or move the instrument This instrument is too heavy and or bulky for one person alone to handle safely Notice on the Proper Use of Thermo Fisher 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 Scien
47. CK ESL tees Web AMP ABE RSM RAS AS ETHERS BY SORA ae IRA ANAT Re ERR RIER SNE TRE EN NEN MIR eImgann PCBA BIRIP temic SUBS Sek Mt Bina RAS mijt RFE hp IE SUBS A SS SREL S A SAAT MAMA BMA R ARE Heimat EE DAHER EBDARMDRO ARERR Bb iis Ee ARPS ARABS AA AIR Caton SA PAR St Salon REMADE ALEMMARE Dat pure MLR RTEZ ZS Enns Hib EIDA RHIbZS Spe UFSHAAMBEHM GZ Iebpot ne e SHEESH alt pe SS EES ja BS Thermo Scientific San Jose e AVIRA SIF HID CAUTION Symbol gt PPE Pe CAUTION Laser hazard This instrument uses a laser that is capable of causing personal injury This symbol also appears on the instrument For details about the hazard refer to the instrument manual Ultra violet light hazard Do not look directly at the ultra violet UV light or into the UV source Exposure can cause eye damage Wear UV eye protection Sharp object Avoid physical contact with the object Pinch point Keep hands away from this area Heavy objects Never lift or move the instrument by yourself you can suffer personal injury or damage the equipment For specific lifting instructions refer to the instrument manual Trip obstacle Be aware of cords hoses or other objects located on the floor When the safety of a procedure is questionable contact Technical Support for Thermo Scientific San Jose products S L HERORRH Oe Cs SAGES d Zi s COMES LI tA e THES
48. Detector is a PEEK union This union is located behind the front door of the mass detector to the left of the source block cover Figure 14 shows this connection Figure 14 Connection between LC and mass detector 0 005 in ID red PEEK tubing to port 2 of Rheodyne 0 005 in ID red micro injection valve Flow PEEK tubing from LC CH ime Ge r Flow The atmospheric pressure ionization API source forms gas phase sample ions from sample molecules that are contained in solution The API source also serves as the sample interface between the LC and the mass detector A catch on the left side of the source enclosure door shuts off the high voltage supply if the door is opened You can operate the API source using electrospray ESI or atmospheric pressure chemical ionization APCI 22 MSQ Plus Mass Detector Hardware Manual Thermo Scientific Electrospray ESI Thermo Scientific 2 Functional Description Mass Detector The sample consisting of preformed ions in solution enters the source through a stainless steel insert capillary held at a voltage of 1 to 5 kV The insert capillary is surrounded by a tube that directs a concentric flow of nitrogen nebulizing gas past the droplets of liquid forming at the tip of the probe The action of the nebulizing gas and the high voltage produces an aerosol of liquid droplets containing sample ions and solvent ions A second concentric flow of nitrogen gas referred to as sheath gas assi
49. For unknown mixtures select the positive negative switching mode Droplet size surface charge liquid surface tension solvent volatility and ion solvation strength affect the ESI process Large droplets with high surface tension low volatility strong ion solvation low surface charge and high conductivity prevent good electrospray The buffer type and buffer strength have a noticeable effect on sensitivity making it important to choose these variables correctly Organic solvents such as methanol acetonitrile and isopropyl alcohol are superior to water for ESI Volatile acids and bases can be used but salt concentrations above 10 mM and strong acids and bases are extremely detrimental to the mass spectrometer The rules for a good electrospray are as follows e Keep salts out of the solvent system e Use organic or aqueous solvent systems and volatile acids and bases e Optimize the pH of the solvent system Atmospheric Pressure Chemical lonization APCI Atmospheric pressure chemical ionization APCI is a soft ionization technique that is used to analyze compounds of medium polarity that have some volatility lon Generation Mechanism The following sequence of events produces ions in APCI 1 The APCI capillary sprays the sample solution into a fine mist of droplets 2 A high temperature tube the heated nebulizer vaporizes the droplets Thermo Scientific MSQ Plus Mass Detector Hardware Manual 5 1 Introduction lonization
50. IN e USB port e User I O panel e Reset button e Source line e Backing line e Exhaust line e GAS IN 20 MSQ Plus Mass Detector Hardware Manual Thermo Scientific 2 Functional Description Mass Detector Figure 13 Back panel of the MSQ Plus Mass Detector uss irr USB connection to e ell l data system computer USER UO aiae kt Connector for o aks contact closure RESET Gr Reset button for downloading firmware Connected to SOURCE forepump 8 8 Connected to BACKING forepump D gt ee MAINS ON OFF i QO ell Power switch e Connected to EXHAUST el Lk solvent trap aio ty 6BARSMAX 0 MAINS IN ei 7 lel Connection to line power Power supply for forepump 8 Connected to user supplied nitrogen source The main power circuit breaker switch labeled MAINS ON OFF the power source for the forepump labeled PUMP OUT and the connection to line power labeled MAINS IN are located in the lower right corner of the back panel of the mass detector In the Off O position the circuit breaker removes all power to the mass detector including the forepump rotary vacuum pump In the On I position power is supplied to the mass detector and the forepump rotary vacuum pump In the standard operational mode the circuit breaker is kept in the On J position Th
51. LK Viton 1 each O ring 6 07 mm ID x 1 78 mm THK BS010 5711000 BLK Viton 2 each O ring 18 77 mm ID x 1 78 mm THK BS018 5711035 BLK Viton 2 each O ring 2 90 mm ID x 1 78 mm THK BS5006 TORN003 BLK Viton 2 each O ring 5 28 mm ID x 1 78 mm THK BS009 5711020 BLK Viton 2 each a British Standard Table 7 shows where the O rings are used and lists them in order by size Figure 84 on page 115 shows the location of the O rings Table 7 O ring locations Sheet 1 of 2 Part number Size Where used ID mm THK mm Iso O ring size TORNO03 2 9 1 78 BS006 Probe heater assembly 5711933 3 0 1 0 Source block assembly small sealing plug FM103016 3 3 2 40 Probe mount assembly FM101464 3 68 1 78 BS007 Cone wash nozzle 5711020 5 28 1 78 BS009 API probe 5711000 6 07 1 78 BS010 Entrance cone 00107 01 00026 9 12 3 53 Source block assembly FM100231 9 25 1 78 BS012 API probe FM101522 12 42 1 78 BS014 Source block assembly large sealing plug FM101417 13 87 3 53 BS207 Source block assembly MSQ Plus Mass Detector Hardware Manual 113 7 Replaceable Parts Consumables Table 7 O ring locations Sheet 2 of 2 Part number Size Where used ID mm THK mm ISO O ring size 5711035 18 77 18 77 BS018 Probe heater assembly FM103048 47 22 3 53 BS225 Source block assembly 114 MSQ Plus Mass Detector Hardware Manual Thermo Scientific Figure 84 Location of O rings Probe heater P N 5711035 P N
52. M101433 Source board sub assembly standard with bracket 60111 61030 Thumbnuts source block Nitronic 60 alloy FM101528 Hexapole screws Nitronic 60 alloy 60111 20055 Tubing 6 mm OD PTFE for nitrogen line order by 00109 99 00004 the foot length Kits Table 9 lists the kits available Table 9 Kits Sheet 1 of 2 Item Part number MSQ engineer tool kit 60111 62100 MSQ Plus installation kit 60111 62006 116 MSQ Plus Mass Detector Hardware Manual Thermo Scientific 7 Replaceable Parts Spares Table 9 Kits Sheet 2 of 2 Item Part number Qualification kit OPTON 09015 Software DVD kit MSQ Plus 60111 62005 Chemicals Table 10 lists the chemicals that are available Table 10 Chemicals Item Part number 4 nitrophenol FM101945 Erythromycin FM101946 Source Block Assembly Table 11 lists the parts in the source block assembly Table 11 Source block assembly parts Sheet 1 of 2 Item Part number Assembly source block and transfer lens 60111 60051 Assembly titanium entrance cone with O ring 60111 60049 and bayonet pins Assembly cone wash nozzle includes O ring FM102521 CAP kit 60111 62012 CAP repair kit 60111 62017 Circlip 2 5 mm E type not available as a separate FM102574 item Exit cone extraction skimmer FM102263 Exit cone insulator extraction cone insulator FM102264 Hexapole screw insulator FM102248 O ring 6 07 mm ID x 1 78 mm THK BS010 5711000 BLK Viton
53. Plus Mass Detector Hardware Manual 89 5 Routine and Preventive Maintenance Maintaining the Source Block Assembly To clean the extraction cone and the source block 1 Disassemble the remaining components of the source block assembly a Remove the hexapole screw insulator extraction cone and extraction cone insulator See Figure 71 Note Check the source block screws to ensure that they are tight but do not remove them Figure 71 Exploded view of the source block and its components O ring 9 mm ID x3 mm THK Extraction cone insulator part number FM102264 Extraction cone 6 with the cone facing the source block OA A Indent should be 7 visible on the facing surface of FM102264 Q O ring O ring BS207 BS225 Hexapole screw insulator CAUTION When the extraction cone is not installed in the source block store it with its cone side facing upwards b Remove the three O rings e Top left O ring 9 12 mm ID x 3 53 mm THK Viton black part number 00107 01 00047 This O ring seals the exit cone wash e Bottom left O ring BS207 Viton black part number FM101417 e Right O ring BS225 Viton black part number FM103048 CAUTION Because solvent and acid can damage the O rings do not sonicate them 90 MSQ Plus Mass Detector Hardware Manual Thermo Scientific 5 Routine and Preventive Maintenance Maintaining the Source Block Assembly 2 To clean the source block sequentially sonicate
54. TORNOO3 7 Replaceable Parts Consumables Entrance cone Ze Q 6 07 mm ID P N FM5711000 Cone wash nozzle CE a 3 68 mm ID P N FM101464 ESI probe assembly 5 28 mm ID P N 5711020 P N FM100231 Source block assembly 30mm ID P N FM5711933 3 0 mm ID P N FM5711933 g SON 47 22 mm ID P N FM103048 12 42 mm ID P N FM101522 9 12 mm ID P N 00107 01 00026 13 87 mm ID P N FM101417 Probe mount assembly 3 3 mm ID P N FM103016 Thermo Scientific MSQ Plus Mass Detector Hardware Manual 115 7 Replaceable Parts Spares Spares Order the spare parts listed in Table 8 and the kits listed in Table 9 as required Table 8 General spare parts Item Part number Assembly probe heater 60111 60023 Cable USB A to B 2 m 00302 99 00008 Conversion dynode FM102888 Electron multiplier 96000 60036S Digital board 60111 61050S Exchange board EXFM102818 Door main assembly MSQ Plus 60111 60009 Door main assembly MSQ Classic 60111 62019 Entrance cone titanium with O ring and bayonet 60111 60049 pins Fitting Swagelok tube fitting stainless steel female 00101 02 00006 ISO tapered thread connector for 1 4 in OD tubing Fitting pipe 6 mm x 1 4 in NPT 00103 02 00001 Hexapole screw insulator FM102248 Needle corona MSQ Plus for APCI mode 70005 98033 Needle corona MSQ Classic F
55. Techniques 3 A high voltage applied to a needle located near the exit end of the tube creates a corona discharge Energized electrons produced by the corona discharge ionize the nitrogen nebulizing gas The nitrogen ions react with the solvent molecules to form solvent ions 4 The solvent ions react with sample molecules to form sample ions Figure 3 shows these four steps in APCI Figure 3 Positive ion APC mechanism Step 1 Step 2 Step 3 Step 4 Ny cf O O e ees o Oo S ER Liquid KE O H gt be SL Os O CP Q Solvent molecules lonized sample Heated nebulizer Corona pin produces molecules Sample molecules a corona discharge APCI is a gas phase ionization technique in which the gas phase acidities and basicities of the analyte and solvent vapor play an important role In the positive ion mode sample ionization occurs in a series of reactions that start with the electron initiated cation formation Following are typical examples of primary secondary and adduct ion formation Primary ion formation e Na gt N 267 Secondary ion formation N HO gt N H O H O e H O gt HOT HOe Proton transfer H30 M gt M H H O In negative ion mode M HY is typically formed by the abstraction of a proton by OH 6 MSQ Plus Mass Detector Hardware Manual Thermo Scientific 1 Introduction Scan Types Because the APCI process produces only singly cha
56. added to the total LC system backpressure can be symptomatic of a blocked capillary Instability in the MS signal can be symptomatic of a partially blocked capillary Replace the capillary if it becomes blocked or partially blocked The inner diameter of the ESI probe is 127 30 uM and the expected backpressure at 1 ml mn is about 150 psi CAUTION Wait for the source block and the probe heater assembly to cool before you remove the ESI probe 56 MSQ Plus Mass Detector Hardware Manual Thermo Scientific 5 Routine and Preventive Maintenance Maintaining the ESI Probe Follow these procedures to perform maintenance on the ESI probe Removing the ESI Probe Removing the ESI Capillary Cleaning or Replacing the ESI Capillary Replacing the Ceramic Sleeve of the ESI Probe Installing the ESI Capillary Installing the ESI Probe Removing the ESI Probe Follow these steps to remove the ESI probe from the probe heater Thermo Scientific To remove the ESI probe from probe heater Ensure that the solvent flow from LC pump is turned off If you are using the optional cone wash pump ensure that it is turned off Turn off the nitrogen gas the probe heater and the ion optics by doing one of the following e From the Status page of the Information view in the Xcalibur data system right click the MSQ Plus listing and choose Turn Device Off from the shortcut menu or e Open the Per Method Parameters table in the Tune windo
57. age 21 The inlet gas hardware then controls the flow of nitrogen gas to the API probes and the reference inlet reservoir As Figure 22 shows the inlet gas hardware consists of two regulators three solenoid valves and two restrictors Figure 22 Functional block diagram of the inlet gases hardware Sheath Vent to 2 gas atmosphere el DS a API probe Nebulizing gas i i Restrictor On Off solenoid valve CG Regulator The first regulator which is located on the front of the mass detector below the source compartment as shown in Figure 23 limits the flow of nitrogen gas to the API probe You nominally set this regulator to 5 2 bar 75 psi for ESI mode or 3 1 bar 45 psi for APCI mode N GAS IN Reference inlet reservoir Thermo Scientific MSQ Plus Mass Detector Hardware Manual 33 2 Functional Description Mass Detector Figure 23 User controlled auxiliary nitrogen regulator Pressure gauge W424 __ Nitrogen gas line Control dial Reference inlet reservoir containing calibrant The second regulator limits the flow of nitrogen gas to the reference inlet reservoir This regulator which is inside the mass detector is preset at the factory Note Call a Thermo Fisher Scientific service representative if you suspect that the nitrogen regulator inside the mass detector is malfunctioning The first solenoid valve is the On Off control
58. ake aan ee 108 Chapter Replaceable Parts 111 EE 111 SPARES tty eee thee aha he oe EN SUR aaNet es 116 tg sgh co Past Sesh de A E BS dek 116 EE 117 Source Block Assembly ee eg eee hue EE EE A e 117 ESI Probe Assembly EE 120 e EE 121 Prove Heater Assembly tee enee vee ue auger eee ees 123 KEE 124 Gas Flow Spares and Nitrogen Generator 125 Solvent Path and Calibrant Spatesic icc tices dels NENNEN E 125 Electronic EE 126 Connection Kits s o7e4 gat EE and ee 126 Manuals eegene phone Greet hain anak Egbert 126 Thermo Scientific MSQ Plus Mass Detector Hardware Manual xiii Contents Appendix A Optimizing the LC Conditions 0c cece eee eee ees 127 Fow Rares seses s eebe ke ea dat ge Kent dae Raw dated ahd nada daa 127 LC Solvents and Mobile Phase Additives ve SEN s0c00e s00e0evcanees 128 LG Solvents lt 4 5 023 ebe ste ce dee ee ea eae ewes 128 Mobile Phase Additives 2 Ak e EEN EE Eee kes 128 Cone Wash System 3 44 4 544525 thaw bere dE EE ER es 131 Controlling the Cone Wash Pump Through Timed Events 133 Flow Splitting e eeh eh eed Ee Chad 134 PEEK Tubing Segoe decke E etcheg tars EENEN EN REEE REEE CE 134 Chemical Kit gue ENEE pace ae EEN ES 135 OT EE 139 xiv MSQ Plus Mass Detector Hardware Manual Thermo Scientific e Preface This MSQ Plus Mass Detector Hardware Manual describes the operational modes and principal hardware components of the Thermo Scientific MSQ Plus M
59. ake this added precaution for safety reasons CAUTION Take care when handling the corona pin The corona pin is sharp and can cause personal injury Take care when removing or installing the corona pin CAUTION Make sure you have sufficient nitrogen for your API source Before you begin normal operation each day make sure that you have sufficient nitrogen for your API source The presence of atmospheric oxygen in the API source when the mass detector is on could be unsafe CAUTION Contain waste streams Because the API source can accommodate high solvent flow rates you must make provisions to collect the waste solvent CAUTION Provide adequate fume exhaust systems for the API source solvent waste container and the forepump Your laboratory must be equipped with at least two fume gt e PPR EE exhaust systems one to vent the waste container connected to the exhaust port API solvent drain on the back of the mass detector and the other to vent the forepump exhaust As described in the MSQ Plus Mass Detector Getting Connected Guide route the blue forepump exhaust hose to a dedicated fume exhaust system Because the exhaust hose acts as a trap for exhaust fumes that would otherwise recondense in the forepump oil the hose should travel at floor level for a minimum of two meters 78 5 in before it reaches the external exhaust system Route tubing from the waste container connected to the exhaust port on the back of the mass detector to a
60. ant that you drain the oil back into the forepump and purge the oil on a routine basis CAUTION Do not operate the forepump with the oil level in the oil mist filter above the maximum level mark Operating the Edwards forepump with the gas ballast valve open allows the oil in the oil mist filter to drain back into the forepump by way of the oil return tubing Operating the forepump with the gas ballast valve open also allows the removal of water and other volatile contaminants from the forepump oil A good time to drain the oil from the oil mist filter and to remove volatile contaminants from the oil in the forepump is at the end of the working day or after the LC MS system completes a sequence run 48 MSQ Plus Mass Detector Hardware Manual Thermo Scientific 3 Daily Operation After Operating the Mass Detector To drain the oil mist filter and purge volatile contaminants from the oil in the forepump 1 Turn off the LC pump flow 2 Turn the nitrogen gas ion optics and probe heater off by doing one of the following e From the Status page of the Information view in the Xcalibur data system right click the MSQ Plus listing and choose Turn Device Off from the shortcut menu or e Open the Per Method Parameters table in the Tune window Take the system out of Operate mode by clicking the Operate On Off toggle button and then turn off the nitrogen gas by clicking the Nitrogen Gas On Off toggle button 3 Open the gas ballast
61. apillary from 59 replacing ceramic sleeve 61 ESI probe assembly 120 ESI See electrospray ethanol 128 exhaust manifold 20 22 extraction cone 89 F flow splitting 134 forepump checking oil level in oil mist filter 46 connection to turbomolecular pump 32 draining oil mist filter 48 49 Edwards 32 maintaining 95 power source for 20 21 turning off 41 81 vacuum produced by 2 4 formic acid 84 129 131 front panel of MSQ Plus Mass Detector 18 front panel status indicator of the MSQ Plus Mass Detector 18 full scan 7 full system autotune 15 Functionality Test Standard 136 G gas ballast valve 48 gas flow spare parts 125 GAS IN 20 22 32 Thermo Scientific graphite ferrule 60 63 70 71 grounding union 16 H hexane 128 Information view 37 Inject From Ref Inlet button 35 inorganic acids 130 Instrument Configuration application 14 Instrument Configuration icon 14 Instrument Setup view 42 ion detection system 28 ion optics 13 31 ion polarity modes 2 ion pairing agents 129 isopropanol 128 isopropyl alcohol 5 K kits 116 L LC column 13 LC column flow rates 127 LC devices 15 LC pump 14 56 68 100 104 LC solvents 128 LC system Accela 1 chemical test kit 136 connecting to MSQ Plus Mass Detector 111 optimizing 127 waste solvents 49 LC MS analysis 2 light emitting diode LED 18 line power 21 lubricant reservoir 96 98 MAINS IN connection to line power 20 21 MAINS ON OFF circuit breaker sw
62. are Manual Thermo Scientific 5 Routine and Preventive Maintenance Maintaining the Source Block Assembly 3 Decant the methanol and fill the graduated cylinder with 100 acetone Sonicate for 15 minutes 4 Carefully remove the RF dc prefilter from the cylinder Rinse the RF dc prefilter with methanol 5 Dry the prefilter with a gentle stream of nitrogen gas 6 If the differential aperture plate is contaminated with ion burn clean it a Unscrew the three screws that connect the differential aperture plate to the quadrupole See Figure 70 Figure 70 View of differential aperture plate Differential aperture plate b Wipe the inside of the differential aperture plate with a cotton swab soaked in 50 50 methanol water c Reconnect the differential aperture plate to the quadrupole d Examine the screws of the differential aperture plate to ensure that they are burr free and flush or below the plane of the aperture plate If you do not need to clean the remaining components of the source block assembly proceed to Assembling the Source Block Assembly on page 92 Cleaning the Extraction Cone and the Source Block If you use buffered mobile phases or inject samples with complex matrices or both you might need to clean the source block and the extraction cone on a weekly basis CAUTION Wait for the source block and probe heater assembly to cool before carrying out any maintenance Thermo Scientific MSQ
63. arity switching between positive ion and negative ion modes of operation The ion detection system includes a 10 kV conversion dynode and a channel electron multiplier The ion detection system is located at the back of the vacuum manifold behind the mass analyzer Figure 20 shows a cross sectional view of the ion detection system 28 MSQ Plus Mass Detector Hardware Manual Thermo Scientific Thermo Scientific 2 Functional Description Mass Detector Figure 20 Cross sectional view of the ion detection system showing the electron multiplier and the conversion diode Vacuum manifold top cover plate High voltage tube High voltage ring Cathode Electron multiplier Secondary particles Lo Conversion dynode feedthrough electrode Mass Conversion Conversion dynode analyzer dynode shield tube The conversion dynode is a concave metal surface that is located at a right angle to the ion beam A potential of 10 kV for negative ion detection or 10 kV for positive ion detection is applied to the conversion dynode When an ion strikes the surface of the conversion dynode one or more secondary particles are produced These secondary particles can include positive ions negative ions electrons and neutrals When positive ions strike a negatively charged conversion dynode the secondary particles of interest are negative ions and electrons When negative ions strike a positively charged conversion dynode the se
64. as summed profile with only one intensity accumulated scan being written to disk for a given experiment As the Xcalibur data system acquires each scan it adds the intensity data to the accumulated summed data of previous scans Thermo Scientific MSQ Plus Mass Detector Hardware Manual 9 1 Introduction Data Types Figure 6 Spectrum of horse heart myoglobin shown as MCA in full scan 100 848 m z 700 800 900 1000 1100 1200 1300 An advantage of MCA is that although noise accumulates at the same rate as sample related data summing random noise over a number of scans reduces its effect increasing the signal to noise ratio A further advantage of MCA is that the Xcalibur data system writes data to disk only at the end of an experiment significantly reducing disk space requirements Because an MCA raw file contains only one scan you cannot use the MCA for time resolved data such as LC MS analyses Generally you use MCA to acquire data when you perform infusion or loop injection experiments on samples of fairly weak concentration to enhance the signal You can view the real time spectrum and stop the data acquisition when you obtain the required results MCA is particularly useful for the acquisition of raw data from the infusion of proteins and peptides 10 MSQ Plus Mass Detector Hardware Manual Thermo Scientific Functional Description Thermo Scie
65. as are 10 to 10 V In the default tune file default tune the RF lens bias is set to 1 0 V The default RF lens bias for the autotune procedure is 0 5 V MSQ Plus Mass Detector Hardware Manual 25 2 Functional Description Mass Detector Figure 17 RF dc prefilter square array of square profile rods Mass Analyzer The mass analyzer separates ions according to their mass to charge ratio and then passes them to the ion detection system In the MSQ Plus Mass Detector the mass analyzer is a single quadrupole rod assembly RF and DC Fields Applied to the Quadrupoles In a quadrupole rod assembly rods diagonally opposite each other in the array are connected electrically so the four rods can be considered to be two pairs of two rods each Ac and dc voltages are applied to the rods and these voltages are ramped during the scan Voltages of the same magnitude and sign are applied within the rods of each pair Voltages equal in magnitude but opposite in sign dc and phase RF are applied to the different rod pairs See Figure 18 Figure 18 Polarity of the RF and dc voltages applied to the rods of the mass analyzer RF voltage dc voltage RF voltage dc voltage The ac voltage applied to the quadrupole rods is of constant frequency Because the frequency of this ac voltage is in the radio frequency range
66. as salpicaduras de sustancias qu micas las part culas flotantes en el aire y los objetos afilados pueden causar lesiones oculares Entre los objetos afilados que los clientes pueden instalar en el instrumento se encuentran tubos de s lice fundida agujas del muestreador autom tico etc Para manipular sustancias qu micas o realizar tareas de mantenimiento utilice gafas de seguridad Peligro general Existen peligros que no se incluyen en las otras categor as Este s mbolo tambi n aparece en el instrumento Si desea obtener m s informaci n sobre estos peligros consulte el manual del instrumento En caso de duda sobre la seguridad de un procedimiento p ngase en contacto con el personal de servicio t cnico de los productos Thermo Scientific San Jose MISE EN GARDE Risque de choc lectrique l instrument utilise des tensions susceptibles de provoquer une lectrocution et ou des blessures corporelles Il doit tre arr t et d branch de la source de courant avant toute intervention Ne pas utiliser l instrument sans ses couvercles Ne pas enlever les capots de protection des cartes circuit imprim PCBA Danger li aux produits chimiques porter des gants et d autres quipements de protection appropri s pour manipuler les produits chimiques toxiques canc rig nes mutag nes corrosifs ou irritants Utiliser des r cipients homologu s et des proc dures ad quates pour la mise au rebut des huiles usag e
67. ass Detector It also provides step by step instructions for cleaning and maintaining the mass detector This manual documents features of the MSQ Plus Mass Detector controlled by the Thermo MSQ 2 0 software To view the instrument software version of the mass detector once you have configured it choose Help gt About Home Page from the Xcalibur Roadmap view Contents e Related Documentation e Safety and Special Notices e Safety Precautions e Solvent and Gas Purity Requirements Contacting Us To suggest changes to documentation or to Help Complete a brief survey about this document by clicking the button below Thank you in advance for your help SURVEY Related Documentation In addition to this guide Thermo Fisher Scientific provides the following documents for the MSQ Plus Mass Detector as PDF files e MSQ Plus Mass Detector Getting Started Guide e MSQ Plus Mass Detector Getting Connected Guide e MSQ Plus Mass Detector Preinstallation Guide Thermo Scientific MSO Plus Mass Detector Hardware Manual xv Preface Related Documentation MSQ Plus Mass Detector Calmix Kit Preparation Guide Dionex AXP AXP MS Metering Pump Operators Manual Dionex Chromelon MSQ Plus Operators Guide Dionex MSQ Plus Facilities Preinstallation Requirements Guide Dionex MSQ Hardware Manual Dionex Installation and Commissioning Guide Dionex MSQ Preventive Maintenance Dionex MSQIOLA Nitrogen Generator for Mass Spectrometers Dionex MSQI
68. ate the resulting sample ions into the mass analyzer where they are analyzed according to their mass to charge ratios As the mass analyzer ejects sample ions an ion detection system detects them producing an ion current signal The system electronics receive the ion current signal which is proportional to the number of ions in solution and amplify it Then they pass it on to the data system for further processing storage and display MSQ Plus Mass Detector Hardware Manual 13 2 Functional Description Liquid Chromatograph Liquid Chromatograph The LC pump pumps the mobile phase through the LC column and into the API source The autosampler introduces the sample into the mobile phase stream Contact closure provides autosampler start and stop signals to the MSQ Plus Mass Detector Refer to the MSQ Plus Mass Detector Getting Connected Guide for information on connecting an autosampler to the MSQ Plus Mass Detector by contact closure Configure the Xcalibur data system for your LC devices with the Xcalibur Instrument Configuration application To open the Instrument Configuration application e Double click the Instrument Configuration icon al on the Windows desktop or e Choose Start gt Programs gt Thermo Foundation x x gt Instrument Configuration The Thermo Foundation Instrument Configuration window opens as shown in Figure 9 To minimize the number of devices displayed in the Devices box Do one of the following
69. bing Because the MSQ Plus Mass Detector can handle flow rates up to 2 mL min flow splitting of the LC eluent is not usually required However if hyphenated detection using both a UV detector and a mass detector is required you can split the flow by using a zero dead volume tee fitting Eliminating the flowcell of the UV detector from the solvent path to the mass detector minimizes the peak broadening for the chromatograms produced by the mass detector The split ratio between the flow going to the UV detector and the flow going to the mass detector is determined by the relative backpressure in the two lines If the backpressure exerted by the connection to the API source probe is greater than the backpressure exerted by the connection to the UV detector the flow to the API source probe is lower than the flow to the UV detector PEEK Poly Ether Ether Ketone tubing is a widely used alternative to stainless steel tubing in the high pressure parts of the system It is compatible with most LC solvents except THF tetrahydrofuran methylene chloride and concentrated nitric acid It works well to a reasonably high pressure is easy to cut and route and is less expensive than stainless steel PEEK tubing is manufactured by SGE International Pty Ltd PEEK tubing comes in eight different internal diameters that are color coded The tubing comes in solid colors or in natural with a color coded stripe on its external surface Table 23 lists the inne
70. c Thermo Scientific 2 Functional Description Data System Table 2 Xcalibur software application programs Desktop icon Program name File name K Xcalibur Homepage exe a LA Instrument Configuration Xconfig exe a fe Tune MSinst exe H Signal to Noise Calculator SigNoise exe HN Note The Signal to Noise Calculator program SigNoise exe is only installed for Xcalibur 2 0 data systems It is not installed for Xcalibur 2 0 x data systems When you start the Xcalibur data system from the Windows desktop by clicking its application icon the Xcalibur Roadmap view shown in Figure 27 opens to show a view of the data system The icons shown on this view provide an easy way to access all the major modules of the data system In addition the Xcalibur data system runs the MSQ Plus Mass Detector server MSQ Plus Mass Detector Hardware Manual 39 2 Functional Description Data System Figure 27 Xcalibur Roadmap view Thermo Xcalibur Roadmap File Actions View Tools GoTo Help Status Acquisition Queue Run Manager Waiting For Devices Sequence Sample Name Working On Position Raw File Inst Method MSQ Plus off ON LINE Processing Setup Sequence Setup D ResulfSRMeview Browser For Help press F1 2 23 2010 2 57 PM MSQ Plus Mass Detector Server The server is the software that handles all communication between the MSQ Plus Mass Detector and its controlling computer
71. cm 1 in ID reinforced PVC tubing The power cord of the forepump is plugged into the outlet labeled PUMP OUT on the back panel of the MSQ Plus Mass Detector This outlet supplies power to the forepump and is controlled by the main power circuit breaker switch The Edwards forepump has an On Off switch that must be turned to the On position to operate the forepump CAUTION Always plug the forepump power cord into the outlet labeled PUMP OUT on the back panel of the MSQ Plus Mass Detector Never plug it into a wall outlet Failure to follow these instructions could lead to instrument damage and personal injury A Pirani gauge measures the pressure in the analyzer region of the vacuum manifold The vent valve allows the vacuum manifold to be vented to air that has been filtered through a metal mesh The vent valve is a solenoid operated valve The vent valve is closed when the solenoid is energized 32 MSQ Plus Mass Detector Hardware Manual Thermo Scientific 2 Functional Description Mass Detector Inlet Gas Hardware Nitrogen gas is used as both the nebulizing gas and the sheath gas for the API probe Nitrogen gas is also used to pressurize the reference inlet reservoir that contains the calibration solution for the mass detector Dry nitrogen nominally set to 520 kPa 75 psi or 450 kPa 45 psi 99 purity enters the MSQ Plus Mass Detector through a 6 mm port labeled GAS IN located on the back panel of the mass detector See Figure 13 on p
72. condary particles of interest are positive ions These secondary particles are focused by the curved surface of the conversion dynode and are accelerated by a voltage gradient into the electron multiplier The conversion dynode shield tube and disk shield the vacuum manifold from the electric field produced by the conversion dynode MSQ Plus Mass Detector Hardware Manual 29 2 Functional Description Mass Detector Vacuum System The electron multiplier is mounted on the top cover plate of the vacuum manifold next to the mass analyzer The electron multiplier includes a cathode and an anode The cathode of the electron multiplier is a lead oxide funnel like resistor A potential of up to 2 5 kV is applied to the entrance of the cathode by the high voltage ring The exit end of the cathode at the anode is near ground potential The anode of the electron multiplier is a small cup located at the exit end of the cathode The anode collects the electrons produced by the cathode The anode screws into the anode feedthrough in the top cover plate Secondary particles from the conversion dynode strike the inner walls of the electron multiplier cathode with sufficient energy to eject electrons The ejected electrons are accelerated farther into the cathode drawn by the increasingly positive potential gradient Because of the funnel shape of the cathode the ejected electrons do not travel far before they again strike the inner surface of the catho
73. d 48 Draining the Oil Mist Filter and Purging the Pump Oil 48 Emptying the Solvent Waste Bottles oon ieee owed devs e phatase 49 Chapter4 Switching Probes c cece eee e eee eee eee eens 51 Switching from ESI to APCI 4 ever ee hen ete EE bees 51 Switching from EE 53 Chapter5 Routine and Preventive Maintenance 55 M intenance Schedule Eet ER EEN ER E a E E R e 55 Maintaining the ESI EE 56 Removing the WEE 57 Removing the ESI Capillary Kerg a e at Seet Ratha ain Ee ch 59 Cleaning or Replacing the ESI Capillary ns Et SEN at wei cantubce teint 61 Replacing the Ceramic Sleeve of the ESI Probe ee er Zen gc A en Ne 61 Installing the ESI Capillary EE 63 Installing the ESI Probes beneit e Eeer anes a p ae Eeer weed 67 Maintaining the APCI Ee Gye otto ties bes ie ea ea ea te ae 67 Removing the EE 68 Removing the APCI Capillary o o ne wasn EE 69 Installing the APCI Capillary et eege rep adente des Sean 71 Installing the APCI Krebs e stead eee See atu E 73 Maintaining the Probe Blat 22 Age EEN EE 74 Removing the Probe Heater acc Zebra ae dak arias a nunne 74 Cleaning the EE 77 Replacing the Detent Screw Insulator e e NEEN el E Aebe 77 Installing the Probe Heater gen BEE EE EELER 78 xii MSQ Plus Mass Detector Hardware Manual Thermo Scientific Contents Maintaining the Source Block Assembly 0000 000 c cee eee 79 Preparing the LC MS System for Maintenance 80 Cleari
74. d ingredients Material Safety Data Sheet which provides health safety and handling information in compliance with ISO requirements e Sensitivity Kit part number FM104824 which contains the two test chemicals used to perform the sensitivity specification tests during MSQ performance qualification e Functionality Test Standard part number HAZMAT 01 00044 which is a 20 ppm caffeine standard that is used to check performance of the LC MS system as a complete system The Sensitivity Kit part number FM104284 only tests the MS portion The LC system includes its own chemical test kit The chemical kit is shipped separately from the MSQ Plus Mass Detector Figure 94 Contents of Chemical Kit part number 60111 62023 Outer box with label Working label for customer 3 qty Box with 3 ampoules Poly bag with label 136 MSQ Plus Mass Detector Hardware Manual Thermo Scientific A Optimizing the LC Conditions Chemical Kit Figure 95 Contents of MSQ Plus Mass Detector CALMIX Kit part number 60111 62021 Material Safety Data Sheet Certificate of Analysis MSQ Plus Mass Detector Calmix Kit Preparation Guide Thermo Scientific MSQ Plus Mass Detector Hardware Manual 137 Index Numerics 2 methoxyethanol 128 A Accela Autosampler 12 133 Accela autosampler 133 Accela LC pump 12 acetic acid 129 131 acetonitrile 5 128 acid alcohols 7 acidic compounds 4 5 Acquisition icon 43 adduct ions 4 6 ammonium acetate
75. de thereby causing the emission of more electrons A cascade of electrons is therefore created that finally results in a measurable current at the end of the cathode where the electrons are collected by the anode The current collected by the anode is proportional to the number of secondary particles striking the cathode Typically the electron multiplier is set to a gain of about 3 x 10 which means that for each ion or electron that enters 3 x 10 electrons exit The current that leaves the electron multiplier by way of the anode is converted to a voltage by the electrometer circuit and recorded by the data system The ion detection system of the MSQ Plus Mass Detector increases the signal while maintaining a low noise level The high voltage applied to the conversion dynode results in a high conversion efficiency and increased signal That is for each ion striking the conversion dynode many secondary particles are produced Because of the off axis orientation of the ion detection system relative to the mass analyzer neutral molecules from the mass analyzer tend not to strike the conversion dynode or electron multiplier As a result the noise from neutral molecules is greatly reduced The vacuum system evacuates the region around the ion optics mass analyzer and ion detection system The principal components of the vacuum system include the following e Vacuum Manifold e Turbomolecular Pump e Turbomolecular Pump e Pirani Gauge e
76. e 50 View of partially disassembled APC probe with capillary removed APCI probe mount Locking plate PEEK tube insert APCI capillary tube Graphite ferrule Capillary retaining nut Probe clamp M3 x 10 cap head stainless steel screws 2 Remove the probe clamp and the locking plate 3 Using the probe clamp unscrew the capillary retaining nut 4 Carefully shake the graphite Vespel ferrule part number 6070119 PEEK tube insert part number FM102591 and APCI probe capillary part number FM102594 out of the probe CAUTION Exercise care when handling the APCI capillary because it is fragile and can be damaged easily 5 Pull the APCI capillary out of the PEEK tube insert and then do one of the following e Ifthe capillary is partially blocked or blocked dispose of it or e Ifthe capillary is reusable clean its surface with 50 50 methanol water 70 MSQ Plus Mass Detector Hardware Manual Thermo Scientific 5 Routine and Preventive Maintenance Maintaining the APCI Probe Installing the APCI Capillary This procedure describes how to install the APCI capillary in the APCI probe To install the APCI capillary in the APCI probe 1 Using tweezers insert the APCI capillary into the PEEK tube insert and graphite Vespel ferrule assembly 2 Using tweezers insert the APCI capillary PEEK tube insert and graphite ferrule assembly into the probe See Figure 51 and Figure 52 Figure 51
77. e 54 Enlarged view of the tip of the APC probe APCI 0 41 mm depth of APCI spacer 10 mm 05mm AS Installing the APCI Probe Follow these steps to insert the APCI probe into the probe heater To install the APCI probe into the probe heater CAUTION Take care when inserting the APCI probe into the probe heater The capillary protruding from the end of the probe is fragile and easily damaged In addition you can contaminate the capillary if you let it touch the inner surface of the probe heater as you insert the probe into the probe heater 1 Turn the locking plate of the probe clockwise to the open position and then carefully slide the APCI probe into the probe heater See Figure 49 on page 69 2 Turn the locking plate counterclockwise to the closed position to lock the probe in place See Figure 48 on page 69 3 Connect the PEEK fingertight fitting to the APCI probe See Figure 48 Thermo Scientific MSQ Plus Mass Detector Hardware Manual 73 5 Routine and Preventive Maintenance Maintaining the Probe Heater Maintaining the Probe Heater If you use the instrument primarily in the ESI mode you can clean the probe heater less frequently Occasionally tension or sharp edges on the probe latching plate can cause breakage of the PEEK mounting pins Use the parts supplied in the Probe Heater Repair Kit part number 60111 62010 to repair the probe Filing down the edges
78. e auxiliary regulator is set to 75 psi 5 2 bar Any gas connections required for the LC system have been made Vacuum Connections The source manifold on the back panel of the MSQ Plus Mass Detector is connected to the forepump The backing manifold on the back panel of the MSQ Plus Mass Detector is connected to the forepump Exhaust Connections The Exhaust manifold on the back panel of the MSQ Plus Mass Detector is connected to the solvent trap The solvent trap is connected to a fume hood or an industrial vent The oil mist filter is connected to the exhaust port of the Edwards forepump The blue hosing is used to connect the oil mist filter to a fume hood or an industrial vent LC Plumbing Hardwire Connections and Solvent Supply The appropriate plumbing connections have been made for the LC system The appropriate contact closure connections have been made between the modules of the LC system and between the LC system and the MSQ Plus Mass Detector For the Accela LC check the connections for the system synchronization harness The solvent reservoirs for the LC system are filled with the appropriate solvents The waste bottle for the LC system waste solvents is empty The solvent lines for the LC system are free of air Restarting the MSQ Plus Mass Detector Follow these steps to start the MSQ Plus Mass Detector To start the MSO Plus Mass Detector 1 Turn on the power for yo
79. e interaction reaction between a molecule and an ionic species to form an ion that contains all the constituent atoms of the original molecule as well as one or more additional atoms Common adducts are ammonium ions NH AT yielding an m z value of M 18 sodium ions Na yielding an m z value of M 23 and potassium ions K yielding an m z value of M 39 4 MSO Plus Mass Detector Hardware Manual Thermo Scientific 1 Introduction lonization Techniques Sample ions can carry a single charge or multiple charges The number of charges carried by the sample ions depends on the structure of the analyte of interest and the carrier solvent Because of multiple charging you can use the ESI mode to analyze ions with molecular weights greater than 100000 Da This makes ESI especially useful for the mass analysis of polar compounds including biological polymers and industrial polymers The mass spectra for these compounds typically consist of a series of peaks corresponding to a distribution of multiply charged analyte ions You can run ESI in three ion polarity modes positive negative or positive negative switching Because like charges repel each other select the ion polarity mode that matches the polarity of your analytes e For acidic compounds which form negative ions in solution select the negative ion polarity mode e For basic compounds which form positive ions in solution select the positive ion polarity mode e
80. e power supply requirements for the MSQ Plus Mass Detector are 230 Vac regulated to 5 at 50 or 60 Hz The application ships with power cords appropriate to its shipping destination Thermo Scientific MSQ Plus Mass Detector Hardware Manual 21 2 Functional Description Mass Detector A USB port an eight terminal contact closure connector labeled USER I O and a reset button are located in the upper right corner of the back panel A USB cable connects the MSQ Plus Mass Detector to the data system computer Hardwiring terminals 1 and 2 on the User I O panel to the autosampler provides contact closure Pressing the Reset button downloads the software firmware for the MSQ Plus Mass Detector from the data system and restores Communications Three manifolds are located on the left side of the back panel The lines that exit the source and backing manifolds are connected to the forepump also referred to as a backing pump rotary vacuum pump or roughing pump The line that exits the exhaust manifold is connected to a solvent trap which is connected to a user supplied fume hood or industrial vent The connection to the user supplied nitrogen source labeled GAS IN is located in the bottom middle of the back panel The MSQ Plus Mass Detector is connected to the user supplied nitrogen source with 6 mm OD PTFE tubing Connection Between LC and Mass Detector API Sources The connection between the liquid chromatograph and the MSQ Plus Mass
81. e probe heater to cool 4 Unscrew and remove the PEEK fingertight fitting from the APCI probe See Figure 48 CAUTION Because it is fragile and can be damaged easily exercise care when handling the APCI capillary 68 MSQ Plus Mass Detector Hardware Manual Thermo Scientific 5 Routine and Preventive Maintenance Maintaining the APCI Probe Figure 48 MSQ Plus Mass Detector set up for the APC mode PEEK fingertight fitting Locking plate in locked position Probe heater 5 Turn the locking plate clockwise to the open position and remove the APCI probe from the probe heater See Figure 49 Figure 49 Remove the APCI probe from the probe heater Locking plate in open position Probe heater Removing the APCI Capillary Follow these steps to remove the capillary from the APCI probe To remove the capillary from the APCI probe 1 Using a 2 5 mm Allen key unscrew the M3 x 10 cap head stainless steel screw part number FM103046 from the probe clamp See Figure 50 Thermo Scientific MSQ Plus Mass Detector Hardware Manual 69 5 Routine and Preventive Maintenance Maintaining the APCI Probe Figur
82. echniques The information obtained from a positive ion mass spectrum is different from and complementary to that obtained from a negative ion spectrum Switching between positive and negative ionization modes in a single analytical run gives you the ability to identify more compounds in a single run Rapid ion polarity switching is a technique that is applied to several important areas of MS analysis for example e Quantitation of different chemistries within the same run In drug metabolism studies certain compounds have functional groups that readily accept a proton H for example compounds containing a primary amino group R NH H gt R NH3 and respond best in the positive ion polarity mode Other compounds have functional groups that readily lose a proton for example carboxylic acids R COjH gt R CO and respond best in the negative ion polarity mode e Rapid screening of unknown analytes Some compounds with functional groups such as carboxylic acids respond only in the negative mode Some compounds with functional groups such as amines alcohols and ketones respond better or only in the positive mode If you do not know the identity of your analyte screen in both modes lonization Techniques You can operate the MSQ Plus Mass Detector in both electrospray ESI and atmospheric pressure chemical ionization APCI modes Electrospray ESI The electrospray ESI technique transfers ions in solution i
83. ee Figure 56 on page 75 b Insert the tube portion of the probe heater into the probe mount Be certain that the two small O rings are still in place on the probe mount c Rotate the black knobs of the probe heater forward to their locking position See Figure 55 on page 75 6 Install the API probe a Turn the locking plate clockwise to the open position and carefully insert the ESI probe part number FM102595 see Figure 36 on page 58 or the APCI probe part number FM102587 see Figure 49 on page 69 into the probe heater CAUTION Take care not to damage the tip of the API probe capillary If you are installing the ESI probe take care not to damage its ceramic sleeve b Turn the locking plate counterclockwise into the closed position c Screw the PEEK fingertight fitting into the ESI probe assembly part number FM102595 or APCI probe assembly part number FM102587 94 MSQ Plus Mass Detector Hardware Manual Thermo Scientific 5 Routine and Preventive Maintenance Maintaining the Forepump 7 Pump down the mass detector a Right click the Server icon Ge pg _ in the system tray portion of the Windows taskbar to open the shortcut menu The Server icon is red because the system is vented b Choose Pump from the shortcut menu c Wait for the MSQ Plus Mass Detector to reach high vacuum The server light will change from flashing amber to solid amber Reaching high vacuum takes approximately 10 minutes Mainta
84. eets all pertinent electromagnetic compatibility EMC and safety standards as described below EMC Directive 89 336 EEC as amended by 92 31 EEC and 93 68 EEC EMC compliance has been evaluated by UNDERWRITERS LABORATORY INC UL EN 55011 1998 EN 61000 4 3 2002 EN 61326 1 1998 EN 61000 4 4 2001 EN 61000 3 2 1995 EN 61000 4 5 2001 EN 61000 3 3 1995 EN 61000 4 6 2001 EN 61000 4 2 2001 EN 61000 4 11 2001 CFR 47 Part 15 Subpart B 2004 Code of Federal Regulations Part 15 Subpart B Radio Frequency Devices Unintentional Radiators Class A Low Voltage Safety Compliance This device complies with the EU directive 73 23 EEC equivalent to IEC 1010 1 1990 plus Amendment 1 1991 and Amendment 2 1995 by meeting the following standard EN 61010 1 2001 with Corrigendum No 1 and 2 Changes that you make to your system may void compliance with one or more of these EMC and safety standards Changes to your system include replacing a part or adding components options or peripherals not specifically authorized and qualified by Thermo Fisher Scientific To ensure continued compliance with EMC and safety standards replacement parts and additional components options and peripherals must be ordered from Thermo Fisher Scientific or one of its authorized representatives 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 C
85. eim 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 auch auf dem Ger t angebracht Einzelheiten zu dieser Gefahr finden Sie in den Ger tehandb chern Wenn Sie sich ber die Sicherheit eines Verfahrens im Unklaren sind setzen Sie sich bevor Sie fortfahren mit dem technischen Support f r Thermo Scientific San Jose Produkte in Verbindung PRECAUCI N Riesgo de descargas el ctricas Este instrumento utiliza voltajes que pueden causar descargas el ctricas y o lesiones personales Antes de revisar o reparar el instrumento ap guelo y descon ctelo de la red el ctrica Mantenga colocadas las cubiertas mientras se utiliza el instrumento No retire las cubiertas protectoras del circuito impreso completo PCBA Peligro por sustancias qu micas Cuando manipule sustancias qu micas t xicas carcinog nicas mut genas corrosivas 0 irritantes utilice guantes y otro equipo de protecci n Utilice siempre recipientes homologados y siga los procedimientos adecuados cuando deseche aceite residual o manipule partes mojadas del instrumento Superficies calientes Antes de tocar los componentes calientes espere a que se enfrien Peligro por sustancias inflamables Tenga mucho cuidado cuando utilice el sistema cerca de sustancias inflamables Riesgo de lesiones oculares L
86. elected ion monitoring SIM A full scan provides a mass spectrum over a defined mass range Because the mass detector has to monitor multiple m z values during a chromatographic run a full scan does not provide the sensitivity that SIM provides The faster the chromatographic peaks elute the lower the sensitivity Selected lon Monitoring SIM Thermo Scientific In selected ion monitoring SIM you specify the monitoring of a particular ion or set of ions Because only a few ions are monitored during a chromatographic run SIM can provide lower detection limits than a full scan analysis Use SIM if you need to detect small quantities of a target compound and you know the mass spectrum of your target compounds and the mass spectrum of the sample matrix MSQ Plus Mass Detector Hardware Manual 7 1 Introduction Data Types SIM can improve the detection limit for quantitative analyses but it can also reduce specificity SIM monitors only specific ions Therefore any compound that produces those ions appears to be the target compound resulting in false positives Data Types The MSQ Plus Mass Detector provides profile centroid and MCA data types From the Xcalibur data system you can acquire and display mass spectral data intensity versus mass to charge ratio in the profile or centroid data types peak formats From the Tune window you can acquire and display mass spectral data in all three data types Profile Data Type In
87. er Then dry the prefilter with a gentle stream of nitrogen gas Reassemble the source block assembly and reinstall it into the mass detector Pay careful attention to the orientation of the Teflon insulator which has an indent on one side that should face up when assembling the transfer lens Improper placement of this insulator interrupts the delivery of voltage to the entrance cone leading to charging of the source block and a decrease in sensitivity Pump down the system and determine if the RF dc prefilter is still dirty To make this determination increase the voltage on the lens to see if beam intensity improves If the prefilter is dirty the default voltages result in lower than expected sensitivity especially for ions below 200 m z Note Typically sonicating the RF dc prefilter in methanol is adequate to remove contamination However contamination from some compounds and some sample matrices can be more difficult to remove If your RF dc prefilter is still dirty after sonicating it in methanol deep clean it as described in the following procedure If the RF dc prefilter is still dirty perform a deep cleaning as described in the following procedure To perform a deep cleaning of the RF dc prefilter Immerse the RF dc prefilter in a graduated cylinder containing 100 distilled water Sonicate for 15 minutes Decant the water and fill the graduated cylinder with 100 methanol Sonicate for 15 minutes rdw
88. er Scientific 4 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 la directive RoHS sont disponibles sur www thermoscientific com rohsweee CAUTION Symbol gt PPP gt gt CAUTION Risk electric shock This instrument uses voltages that can cause electric shock and or personal injury Before servicing shut down the instrument and disconnect it from line power While operating the instrument keep covers on Do not remove the protective covers from the printed circuit board assemblies PCBAs Chemical hazard Wear gloves and other protective equipment as appropriate when handling toxic carcinogenic mutagenic corrosive or irritant chemicals Use approved containers and proper procedures to dispose of waste oil and when handling wetted parts of the instrument Hot surface Before touching allow any heated components to cool Flammable substances hazard Use care when operating the system in the presence of flammable substances Risk of eye injury Eye injury could occur from splattered chemicals airborne particles or sharp objects Sharp objects that customers might install in the instrument include fused silica tubing the autosampler needle and so on Wear safety glasses when handling chemicals or servicing the instrument General hazard A hazard is present that is not included in the other categ
89. exhaust fumes Therefore it is important that you check the oil level in the oil mist filter on a daily basis See Draining the Oil Mist Filter and Purging the Pump Oil on page 48 for instructions on draining the oil mist filter 46 MSQ Plus Mass Detector Hardware Manual Thermo Scientific 3 Daily Operation After Operating the Mass Detector Figure 31 View of an Edwards forepump with oil mist filter showing the maximum oil level mark To exhaust vent r Gas ballast knob RI Oil Mist Filter EMI JL l _ Maximum oil level mark Oil return tubing After Operating the Mass Detector This section describes procedures that you might want to perform after you complete your analyses e Flushing the API Probes e Placing the System in the Off Mode e Draining the Oil Mist Filter and Purging the Pump Oil e Emptying the Solvent Waste Bottles Flushing the API Probes After running phosphate salts ion pairing agents acids or other additives through the system flush the probe with 50 50 acetonitrile water or methanol water to prevent blockage Note To prevent blockage always flush the probes after using buffered solvents Thermo Scientific MSQ Plus Mass Detector Hardware Manual 47 3 Daily Operation After Operating the Mass Detector To flush the capillary of the API probe 1 Attach the analytical pump outlet directly to the MSQ Plus Mass Detector Because they m
90. for entrance cone O ring 3 0 mm ID x 1 0 mm THK BLK Viton 5711933 for sealing plug O ring 13 87 mm ID x 3 53 mm THK BS207 FM101417 BLK Viton Thermo Scientific MSQ Plus Mass Detector Hardware Manual 117 7 Replaceable Parts Spares Table 11 Source block assembly parts Sheet 2 of 2 O ring 12 42 mm ID x 1 78 mm THK BS014 BLK Viton Part number FM101522 O ring 9 0 mm ID x 3 0 mm THK BLK Viton 00107 01 00026 O ring 47 22 mm ID x 3 53 mm THK BS225 FM103048 BLK Viton O ring 3 68 mm ID x 1 78 mm THK BS007 FM101464 BLK Viton for cone wash nozzle Plug source block sealing FM102277 Screw M3 x 10 cap head stainless steel FM103046 Screw hexapole 60111 20055 Source block new alloy to prevent galling FM102279 Spring transfer lens special and part numbers 118 MSO Plus Mass Detector Hardware Manual 00111 01 00013 Figure 85 shows an exploded view of the source block assembly with component descriptions Thermo Scientific 7 Replaceable Parts Figure 85 Exploded view of the source block assembly Thumbscrews P N FM101528 Nitronic 60 alloy BE to prevent galling _ _ Entrance cone titanium with O ring and bayonet pins P N 60111 60049 O ring BS010 6 07 mm ID x 1 78 mm THK P N 5711000 D W Zy Bayonet pins provided with entrance cone 7 S7 O ring BS007 3 68 mm ID x 1 78 mm THK P N FM101464 Cone
91. for the entrance cone and the cone wash nozzle reinstall the O rings This O ring is difficult to remove and put back Lubricating the O ring with methanol might help It is usually not necessary to remove the O rings when you sonicate the metal parts Tip Wetting an O ring with 100 methanol makes it easier to install Depending on whether the internal components of the source block need cleaning do one of the following To determine whether these components need cleaning look for evidence of ion burn or sample deposit behind the entrance cone e Ifthe internal components of the source block assembly do not need cleaning go to step 7 or e Ifthe internal components of the source block assembly need cleaning go to the next procedure Removing the Source Block Assembly Holding the cone wash nozzle by its base insert it into the source block and then turn the nozzle to the right See Figure 62 on page 82 Insert the entrance cone into the source block and then turn the entrance cone counterclockwise until it locks in place See Figure 62 Remove the lint free cloth from the bottom of the source enclosure Take the probe heater out of its holder Ensure that the knobs of the probe heater are facing away from each other and then insert the probe heater into the probe mount See Figure 56 on page 75 MSQ Plus Mass Detector Hardware Manual 85 5 Routine and Preventive Maintenance Maintaining
92. for the flow of nitrogen gas into the MSQ Plus Mass Detector To turn this valve on or off click the Nitrogen Gas On Off toggle button in the Per Method Parameters table of the Tune window shown in Figure 24 After you turn on the nitrogen gas you can hear the jet of nitrogen gas flowing into the API probe 34 MSQ Plus Mass Detector Hardware Manual Thermo Scientific 2 Functional Description Mass Detector Figure 24 Per Method Parameters table Description Readback Setpoint Tune Control Probe Temperature C 0 550 Needle IT 0 0 3 0 RF Lens Bias 0 0 0 5 lon Energy wi n a 0 5 LM Res n a 12 7 HM Res n a 12 5 Acquisition Control Profile Resolution 32 points da 32 points da Retention Time mins 0 00 n a General Control Operate n a Off i Nitrogen Gas n a On a lonization Mode n a ESI Sequence Control Togale butions Inject from Ref Inlet n a Started The second solenoid valve is the On Off control for the flow of nitrogen gas into the reference inlet reservoir The third solenoid valve is the On Off control for venting the reference inlet reservoir to the atmosphere When the nitrogen gas flow is On selecting either a full system autotune or a mass scale calibration causes the system to alternate between pressurizing and depressurizing the reference inlet reservoir Clicking the Inject From Ref Inlet button in the Per Method Parameters table has a similar effect When you click this toggle button nit
93. fore touching allow any heated components to cool Flammable substances hazard Use care when operating the system in the presence of flammable substances Risk of eye injury Eye injury could occur from splattered chemicals airborne particles or sharp objects Sharp objects that customers might install in the instrument include fused silica tubing the autosampler needle and so on Wear safety glasses when handling chemicals or servicing the instrument General hazard A hazard is present that is not included in the other categories This symbol also appears on the instrument For details about the hazard refer to the instrument manual When the safety of a procedure is questionable contact Technical Support for Thermo Scientific San Jose products S REO RR COMB RBEKO ELFSAGECS FHC ZELLE Bie ROMS HOS MED BRIA FERUTCESL ROMS ANS rt SEI LRSL PUY RRP LY TY PCBA AY D RRE HIS ERY EROTIES CFARE SE KE RARE ARIE EHHID H5 c RmERURI Ek VRET FRG ENRER aa L ES RMEUDLEY HAORRAMeEMVIRICS BAS NEBae RAL SU ZIBI ELE mam S in MALERE REELT ESL TREENER TREDANEL TDTYR TLE E S tze ES RHEO ERIE RA LH Rm AIF EHRE Ehe ECKE ECKE ERR Y tH 54S TREED S nn kca RY kk FILA ECT CSszpuUItU Wat Em OEEk RE ARREBALET ET IL ZHENOATIAY ICH CLES HUERAHYE d COMMASILHBICERRENMTOKS TOERNE Clk BBOVIAVIVESRLTCESL FEDRE CPG RASH SIGAIEL Thermo Scientific San Jose Si DO FIADIGR bFECHHLAHDE
94. he mass detector the charged capillary acts as a charge filter The vacuum produced by the forepump draws both neutral molecules and ionized molecules through the entrance cone into the M path region of the mass detector The charge on the ionized molecules depends on the selected ion polarity mode In the M path region the low vacuum of 1 torr produced by the forepump draws the neutral molecules out of the mass detector enriching the ion stream By the time the ion stream reaches the exit cone the solvent flow has decreased by three orders of magnitude The charge on the exit cone focuses and propels the ionized molecules into the intermediate vacuum region of the mass detector As the ionized molecules pass through the exit cone the transfer lens focuses them into a fine particle stream and transmits them to the mass analyzer The mass analyzer transmits ions of a selected mass to charge ratio to the ion detection system where they produce a signal The system electronics amplify the signal which is then transmitted through a USB connection to the MSQ Plus Mass Detector data system lon Polarity Modes You can operate the MSQ Plus Mass Detector in the following ion polarity modes positive negative or positive negative switching The application controls the ion polarity by placing either a positive or negative charge on the capillary of the API probe 2 MSQ Plus Mass Detector Hardware Manual Thermo Scientific 1 Introduction lonization T
95. heir use tends to be application specific DMSO is commonly used by synthetic chemists for primary dilutions Mobile Phase Additives Additives can be divided into three categories e Commonly Used Compatible Additives e Less Commonly Used Additives e Unsuitable Additives Table 20 lists suitable additives 128 MSO Plus Mass Detector Hardware Manual Thermo Scientific Optimizing the LC Conditions LC Solvents and Mobile Phase Additives Table 20 Summary of suitable additives lon Polarity Mode Additive Positive ion e Acetic acid e Formic acid e Ammonium acetate lt 0 1M Negative ion e Triethylamine TEA e Ammonium hydroxide ammonia solution e Ammonium acetate lt 0 1M Table 21 lists additives to avoid Table 21 Summary of additives to avoid lon Polarity Mode Additive Positive ion e Surfactants e Trifluoroacetic acid TFA gt 0 1 v v Negative ion e Surfactants e Organic acids such as acetic acid formic acid trifluoroacetic acid TFA Commonly Used Compatible Additives The following additives are the most compatible with the MSQ Plus Mass Detector e Acetic acid or formic acid e Ammonium hydroxide e Ammonium acetate or ammonium formate e Non volatile salts e lon pairing agents You can enhance LC separations by reducing the pH of the mobile phase Suitable additives for this are acetic acid or formic acid Formic acid is stronger than acetic acid and therefore less needs to be added to reach a
96. iffer TMH 260 250 split flow turbomolecular pump provides the vacuum for the transfer lens and mass analyzer regions of the vacuum manifold The turbomolecular pump mounts onto the underside of the vacuum manifold with two 4 mm socket screws The interstage port of the turbomolecular pump which evacuates the transfer lens region is rated MSQ Plus Mass Detector Hardware Manual 31 2 Functional Description Mass Detector Forepump Pirani Gauge Vent Valve at 125 L s The high vacuum port of the turbomolecular pump which evacuates the mass analyzer region is rated at 200 L s Under normal operating conditions the pump provides a vacuum of approximately 107 torr in the transfer lens region and 10 torr in the mass analyzer region The main power circuit breaker switch turns the power to the turbomolecular pump on or off The turbomolecular pump controller regulates the power provided to the turbomolecular pump A fan that draws air in from the underside of the instrument cools the turbomolecular pump An Edwards forepump also known as a roughing pump backing pump or rotary pump establishes the vacuum necessary for the proper operation of the turbomolecular pump The forepump also evacuates the M path region of the vacuum manifold The pump has a maximum displacement of 30 m h and maintains a minimum pressure of approximately 100 Pa 0 75 torr The forepump is connected to the turbomolecular pump by a section of 2 54
97. ific Use the Timed Events page shown in Figure 91 to set timed events for the time function terminals TF1 to TF4 located on the back panel of the Accela Autosampler See Figure 92 You can use the TF terminals to control the cone wash pump Figure 91 Timed Events page on the Accela AS Instrument Setup view Accela AS Method Sample Preparation Reservoir Content Timed Events fm m e m lm Figure 92 Time function event terminals on the back panel of the Accela Autosampler TF Terminals 123468678 910111213141516 Ve g idddge RT The timed event output signals are issued after the inject out signal in the signal sequence To display the Timed Events page click the Timed Events tab in the Accela AS Instrument Setup view Program timed events by adding entries to the Timed Events table The Timed Events table contains time boxes and event TF1 TF2 TF3 and TF4 lists In the Time box you can specify the time in minutes when the Accela Autosampler TF terminal TF1 to TF4 signals an event Time 0 0 is defined as the time when the Accela Autosampler issues an inject out signal The range of values is 0 0 to 9999 9 minutes With the event TF1 TF2 TF3 and TF4 lists you can select whether the TF1 TF2 TF3 and TF4 output terminal is On or Off at the time specified in the Time box MSQ Plus Mass Detector Hardware Manual 133 D Optimizing the LC Conditions Flow Splitting Flow Splitting PEEK Tu
98. ight contain contaminants bypass the injection valve of the autosampler and the LC column 2 Pump a non buffered solvent that is miscible with the buffered mobile phase through the probe at a flow rate of 2 mL min for a few minutes 3 Pump 50 50 acetonitrile water or 50 50 methanol water through the probe at a flow rate of 2 mL min for 30 minutes Placing the System in the Off Mode Place the MSQ Plus Mass Detector in the Off mode if you are not going to use it for a short period of time such as overnight or over weekends In the Off mode the system is left under vacuum but the nitrogen flow is reduced to a bleed through the API probe The electron multiplier and conversion dynode are turned off the power to the ion optics is turned off and the power to the probe heater is turned off For instructions on turning the system to the Off mode see Placing the System in the Off Mode on page 101 Draining the Oil Mist Filter and Purging the Pump Oil During normal operation the oil in the forepump becomes contaminated with dissolved chemicals and water vapor In addition the oil mist filter fills with condensed oil Over time the rising water content of the oil can cause corrosion and decrease the lifetime of the forepump And once the oil level in the oil mist filter rises above the maximum oil level mark as shown in Figure 31 on page 47 the oil mist filter becomes ineffective in trapping exhaust fumes Therefore it is import
99. ing FM101633 Tee KF25 FM100203 Vent valve with 1 m cable assembly FM104308 Hose blue exhaust 1 in ID order by the foot length 00301 08301 10 10 ft 124 MSQ Plus Mass Detector Hardware Manual Thermo Scientific 7 Replaceable Parts Spares Gas Flow Spares and Nitrogen Generator Table 16 lists the gas flow spare parts and the nitrogen generator parts Table 16 Gas flow spare parts and nitrogen generator parts Item Part number Flow controller 00110 01 00008 The flow controller is only available as part of a replacement nitrogen manifold assembly part number 60111 60019S This assembly comes with the flow controller preadjusted for the fixed sheath and nebulizer flows of the MSQ Plus Mass Detector and has a tamper proof feature Tubing 6 mm OD PTFE for nitrogen line order by 00109 99 00004 the foot length Nitrogen valve assembly Order as an S part The new 60111 60019S style diverters are set in Manufacturing PEAK nitrogen generator OPTON 97104 Solvent Path and Calibrant Spares Table 17 lists the spare parts for the solvent path and the calibrant Table 17 Solvent path and calibrant spare parts Item Part number Assembly waste bottle FM102770 Assembly reference bottle FM102771 MSQ calibration solution kit for MSQ software 60111 62021 version 1 4 and later Nut PEEK 1 piece FM100513 Thermo Scientific MSQ Plus Mass Detector Hardware Manual 125 7 Replaceable Part
100. ining the Forepump Thermo Scientific The vacuum system consists of two types of vacuum pumps a turbomolecular pump and a forepump The turbomolecular pump is housed within the MSQ Plus Mass Detector and requires a trained service engineer for servicing The forepump also referred to as a backing pump a rotary pump or a roughing pump is external to the MSQ Plus Mass Detector and requires routine maintenance for optimal performance Note You can find more information on operating and maintaining the rotary pump in the manual that is shipped with the pump Check both the level and the color of the oil in the forepump at least once a month Check the oil by looking through the oil sight level window of the forepump See Figure 74 The oil level should be between the upper and lower marks positioned next to the window The oil color should be a clear straw color Figure 74 View of Edwards forepump that shows the oil sight level window MT EDWARDS Oil sight level Sg window e If the oil level is near or below the lower mark add more oil as described in the manual that comes with the Edwards forepump MSQ Plus Mass Detector Hardware Manual 95 5 Routine and Preventive Maintenance Maintaining the Turbomolecular Pump e If the oil has turned red in color or if the pump has been in operation for more than 3000 hours since the oil was replaced replace the oil as described in the manual that comes with the Edwa
101. intenance on page 80 and clear the access to the source block as described in Clearing Access to the Source Block Assembly on page 81 CAUTION The corona needle is very sharp Do not attempt to remove the entrance cone or the cone wash nozzle before you turn the corona pin knob to its vertical position See Figure 62 Figure 62 View of the front side of the source block with the cone wash nozzle turned away from the entrance cone 1 Corona pin knob ZP iw Entrance cone Cone wash nozzle 2 Being careful to handle the cone wash nozzle by its base rotate the cone wash nozzle away from the entrance cone See Figure 62 CAUTION The tip of the cone wash nozzle is very fragile so take care to handle the cone wash nozzle by its base See Figure 66 on page 85 3 Place a lint free cloth over the drainage holes in the bottom of the source enclosure Tip It is easy to drop small objects such as the entrance cone and the cone wash nozzle into the drain at the bottom of the source enclosure Temporarily blocking the drainage holes in the bottom of the source enclosure prevents small objects from falling into the drainage tubing 4 Turn the entrance cone clockwise and pull forward to remove it Note The entrance cone assembly is reverse threaded Therefore to remove it turn it clockwise To install it turn it counterclockwise 82 MSQ Plus Mass Detector Hardware Manual Thermo Scientific 5 Routine and Preve
102. into the probe until it is flush with the PEEK sleeve c Visually check that the capillary is protruding from the tip of the probe As Figure 45 shows the capillary should protrude from the tip of the probe 64 MSQ Plus Mass Detector Hardware Manual Thermo Scientific 5 Routine and Preventive Maintenance Maintaining the ESI Probe Figure 45 Capillary inserted into the ESI probe mount Z Internal bottom of Z ESI probe mount ESI probe mount Capillary 4 Depending on whether the capillary protrudes from the tip of the probe do one of the following e Ifthe capillary protrudes from the probe tip go to step 5 e Ifthe capillary does not protrude from the tip of the probe turn the probe upside down and gently shake the capillary assembly out of the probe Adjust the position of the graphite ferrule so that it is closer to the end of the PEEK insert and repeat step 2 and step 3 of this procedure Continue to adjust the position of the graphite ferrule until the capillary protrudes from the tip of the probe when you insert the capillary assembly into the probe 5 Screw the capillary retaining nut adapter into the ESI probe until finger tight and visually verify that the capillary protrudes from the probe tip Figure 46 shows the capillary protruding from the probe tip Thermo Scientific MSQ Plus Mass Detector Hardware Manual 65 5 Rou
103. iption Reference Inlet System Figure 10 Microinjection switching valve in the Load position RECH Grounding union UK To API probe Connection To waste to LC t 7 Nitrogen line e y Clip Waste reservoir Reference inlet reservoir Figure 11 Microinjection switching valve in the Inject position AC 500 uL sample loop Connection to LC o Grounding union UK To waste To API probe ee 7 lt Nitrogen line a Clip Waste reservoir Reference inlet reservoir Thermo Scientific MSQ Plus Mass Detector Hardware Manual 17 2 Functional Description Mass Detector Mass Detector The MSQ Plus Mass Detector provides sample ionization and mass analysis of samples injected with an autosampler or samples infused with the reference inlet system The MSQ Plus Mass Detector uses a quadrupole mass analyzer with an API source external to the mass analyzer This section describes the following components of the MSQ Plus Mass Detector e Front Panel Status Indicator e Back Panel Controls and Connections e Connection Between LC and Mass Detector e API Sources e RF dc Prefilter e Mass Analyzer e Jon Detection System e Vacuum System es Inlet Gas Hardware Front Panel Status Indicator One light emitting diode LED is located at the upper right corner of the front panel of the MSQ Plus Mass Detector as shown in Figure 12 Table lists the states of the
104. it in the following solvents a 1 v v solution of formic acid distilled water b 100 distilled water c 100 methanol 3 Clean the extraction cone as follows a Place the extraction cone with the cone side facing upwards into a beaker CAUTION Exercise great care when handling the extraction cone Use tweezers to handle the extraction cone and ensure that the cone side faces upwards when you place the extraction cone on a solid surface b Fill the beaker with 10 v v solution of formic acid and then sonicate for approximately 15 minutes c Decant the formic acid fill the beaker with methanol and then sonicate again for approximately 15 minutes d Examine the entrance cone under magnification to be certain that the entrance is circular with sharp edges If the entrance cone is damaged you might be able to repair the damage using the technique in Repairing the Entrance Cone Repairing the Entrance Cone Thermo Scientific You can temporarily repair the MSQ Plus Mass Detector entrance cone part number 60111 60049 pending replacement of the entrance cone Li Ze 1 To temporarily repair the entrance cone Remove the entrance cone and clean according to standard procedures sonicate in water and then methanol and blow dry with compressed air or nitrogen Using a microscope set to 30x magnification examine the cone The tip must be circular with a sharp edge The inner diameter specification is 300
105. it is referred to as RF voltage The ratio of RF voltage to dc voltage determines the resolving power of the quadrupole and the ability of the mass detector to distinguish between ions of different mass to charge ratios 26 MSQ Plus Mass Detector Hardware Manual Thermo Scientific 2 Functional Description Mass Detector Mass Analysis The mass analyzer in the MSQ Plus Mass Detector is a square array of round rods The rods are charged with a variable ratio of RF voltage and dc voltage These potentials give rise to an electrostatic field that gives stable oscillations to ions with a specific mass to charge ratio and unstable oscillations to all others The mass range for the MSQ Plus Mass Detector is 17 to 2000 Da at unit resolution At any given instant one particular set of RF and dc voltage values is being applied to the mass analyzer rods Under these conditions only ions of one mass to charge ratio for example m z 180 are maintained within bounded oscillations as their velocity carries them through the mass analyzer During this same time all other ions undergo unbounded oscillations These ions strike one of the rod surfaces become neutralized and are pumped away by the vacuum system See Figure 19 Figure 19 Schematic of the RF dc prefilter mass analyzer and ion detector Source entrance cone Square Source quadrupole Quadrupole lon extraction RF dc prefilter mass analyzer detector cone
106. itch 20 21 maintenance schedule 55 manuals available 126 mass analyzer components of 27 purpose 26 Thermo Scientific Index H mass scale calibration how to perform 16 steps performed in 15 when to perform 16 MCA data type 9 menu bar of Tune window 42 methanol 5 84 128 methylene chloride 134 mobile phase pH 129 mobile phrase additives 128 M path region 31 32 MSQ Plus Mass Detector additives compatible with 129 components of 1 2 18 connecting API probe 51 connection to data system computer 2 connection to liquid chromatograph 2 connection to nitrogen source 22 data types provided by 8 emergency shutdown 99 integration with LC system 12 ion detection system 28 ion polarity modes 2 maintenance schedule 55 mass analyzer in 26 mass range of 27 parts in 111 power supply requirements for 21 procedures to perform after operation 47 procedures to perform before operation 45 resetting 108 restarting after shutdown 105 106 scan types in 7 turning off 48 99 from Tune window 103 from Xcalibur data system 101 non routine maintenance 104 types of ionization performed 2 MSQ Plus Mass Detector Calmix Kit 136 MSQ Plus Mass Detector Chemical Kit 135 multiply charged ions 7 needle voltage 42 negative ion polarity mode 2 5 7 25 130 nitric acid 134 nitrogen gas 23 32 36 100 Nitrogen Gas On Off toggle button 34 nitrogen generator parts 125 nitrogen source 22 nitrogen supply 45 MSQ Plus Mass Detector Hardware Manua
107. king plate on the APCI probe clockwise to the open position Insert the APCI probe into the probe heater as shown in Figure 33 Then turn the locking plate counterclockwise to the closed position Figure 32 MSQ Plus Mass Detector setup for the APC mode Locking plate in locked position Probe heater Probe mount Corona pin knob Source housing Figure 32 shows the MSQ Plus Mass Detector setup for the APCI mode Figure 33 shows the corona pin in the operational position for the APCI mode 52 MSQ Plus Mass Detector Hardware Manual Thermo Scientific 4 Switching Probes Switching from APCI to ESI Figure 33 View of the corona pin in the operational position for the APC mode 8 Turn the corona pin knob 90 degrees to its horizontal position 9 Insert the PEEK fingertight fitting into the APCI probe and screw in 10 Adjust the nitrogen gas pressure to 310 kPa 45 psi Switching from APCI to ESI Follow these steps to connect an ESI probe to the MSQ Plus Mass Detector To switch from APCI mode to ESI mode CAUTION Allow the probe heater to cool before you remove the APCI probe 1 Turn off the LC pump flow If you are using the cone wash pump turn it off 2 Turn the nitrogen gas ion optics and probe heater off by doing one of the following e From the Status page in the Information view in the Xcalibur data system right click the MSQ Plus listing to display a shortcut menu and choose Turn Device Off from
108. l 141 Index 0 non volatile salts 129 normal phase solvents 128 0 oil mist filter 46 48 49 O rings 83 84 113 P Peak Display 43 PEEK delivery tube 16 PEEK tube insert 60 70 PEEK tubing color coding 134 cone wash system 37 connections for cone wash system 37 description 134 plumbing system with 134 PEEK union 22 Per Method Parameters table 43 phosphate buffers 131 phosphoric acid 130 Pirani gauge 32 positive ion polarity mode 2 5 7 25 130 positive negative ion polarity mode 2 5 7 power circuit breaker switch 21 power source for forepump 21 power supply requirements for MSQ Plus Mass Detector 21 Print Setup dialog box 44 printer 44 probe heater cleaning 77 installing 78 94 maintaining 74 removing 74 replacing detent screw insulator 77 probe heater assembly 123 Probe Heater Repair Kit 74 77 probe temperature 41 profile data type 8 protonated molecules 4 7 PUMP OUT outlet 32 PUMP OUT power source for forepump 20 21 Q quadrupole rod assembly 26 142 MSQ Plus Mass Detector Hardware Manual raw files acquiring data to 41 MCA 10 Rayleigh stability limit 3 reference inlet reservoir 16 32 reference inlet system components of 16 purpose 15 Reset button 20 22 108 reverse phase LC solvents 128 RF lens bias 25 RF voltage 26 28 RF dc prefilter cleaning 87 deep cleaning 88 disassembly 89 purpose 25 Rheodyne microinjection switching valve 16 Roadmap view 39 S safety precautions xvii Scan Event
109. le calibration Note Perform a mass scale calibration by selecting either the Full System Autotune or the Mass Scale Calibration option from the Instrument Tuning and Calibration wizard The reference inlet system consists of a reference inlet reservoir a waste reservoir nitrogen pressurization line a PEEK delivery tube and a Rheodyne microinjection switching valve One end of the PEEK tubing is inserted into the reference reservoir and the other end of the tubing is attached to port 5 of the Rheodyne microinjection valve Pressuring the reference reservoir with nitrogen gas and switching the valve to the load position forces the calibrant solution through the tubing into a 500 uL sample loop as shown in Figure 10 After the sample loop is filled the valve switches to the inject position allowing mobile phase to push the calibrant out of the sample loop and through the API probe as shown in Figure 11 CAUTION The union that connects the Rheodyne microinjection switching valve to the API probe is a grounding union Do not connect port 3 of the Rheodyne microinjection directly to the inlet of the API probe Bypassing the grounding union could lead to instrument damage and personal injury Note Thermo Fisher Scientific recommends that you avoid using the reference inlet for sample introduction This inlet is used exclusively for autotune 16 MSQ Plus Mass Detector Hardware Manual Thermo Scientific 2 Functional Descr
110. losure drain The cone wash system consists of a cone wash pump PEEK tubing and a cone wash nozzle Red 0 005 in ID PEEK tubing connects the cone wash pump to the MSQ Plus Mass Detector Inside the MSQ Plus Mass Detector the red PEEK tubing is connected to one end of a union Green 0 030 in ID PEEK tubing is connected to the other end of the union The green PEEK tubing is connected to the back of the source block behind the cone wash nozzle When you are using the cone wash system adjust the cone wash nozzle so that solvent flowing out its tip just touches the orifice of the entrance cone as it falls towards the drain See Figure 26 When you are not using the cone wash system adjust the cone wash nozzle so that it faces away from the entrance cone Storing the cone wash nozzle in the 12 o clock to 2 o clock position helps to prevent its blockage CAUTION The corona needle is very sharp Do not attempt to adjust the position of the cone wash nozzle before you turn the corona pin knob to its vertical position Instructions for connecting the cone wash pump to the mass detector are included in the MSQ Plus Mass Detector Getting Connected Guide The Xcalibur data system controls the modules of the LC MS system The Server software handles the communication between the MSQ Plus Mass Detector and the data system computer The Xcalibur data system also processes data that is acquired by the MSQ Plus Mass Detector Information about the status of
111. low rate as listed in Table 19 Table 19 LC columns and flow rates Column ID Flow rate 4 6 mm 1 0 mL min 3 9 mm 0 5 mL min 2 1 mm 0 2 mL min 1 0 mm 40 50 L min Capillary lt 10 uL min Thermo Scientific MSQ Plus Mass Detector Hardware Manual 127 D Optimizing the LC Conditions LC Solvents and Mobile Phase Additives The different ionization modes require different flow rates and column IDs The following guidelines apply when using the MSQ Plus Mass Detector e Electrospray can operate at all the flow rates described in Table 19 e APCI cannot operate at flow rates below 0 2 mL min Therefore suitable column IDs are 2 1 mm 3 9 mm and 4 6 mm LC Solvents and Mobile Phase Additives LC Solvents The choice of solvents for LC is dictated primarily by the separation requirements but you must follow some guidelines when performing LC MS analyses Water acetonitrile and methanol are the solvents that are the most compatible with the MSQ Plus Mass Detector These common reverse phase LC solvents are ideal for LC MS When you use high percentages of water you usually need to raise the probe temperature to aid desolvation Less commonly used solvents include normal phase solvents alcohols such as isopropanol 2 methoxyethanol and ethanol and dimethyl sulfoxide DMSO Normal phase solvents such as dichloromethane hexane and toluene are most suitable for use in APCI Alcohols have all been used with LC MS but t
112. lvent trap connected to the detector s exhaust port from being drawn into the detector Depending on the API mode and whether the instrument is in use the nitrogen consumption is as follows e ESI mode consumes approximately 720 L hr e APCI mode consumes approximately 480 L hr e Standby mode consumes approximately 20 to 50 L hr Cone Wash System 36 The API source on the MSQ Plus Mass Detector includes a self cleaning solvent delivery system called the cone wash system Figure 25 shows an example of this system It makes the source robust and productive greatly increasing the number of samples that can be analyzed before maintenance is required Figure 25 Front of the cone wash pump The self cleaning API source delivers a constant low flow of solvent to the edge of the inlet orifice See Figure 26 This low flow of wash solvent prevents the build up of non volatile components during LC MS analysis that occurs with typical chromatographic buffers for example phosphates and ion pairing agents and dramatically extends the length of time possible for analyses 1 Image of the Scientific Systems Inc single piston pump from the Series 1 Pump Operators Manual 90 2518 Rev D by Scientific Systems Inc MSQ Plus Mass Detector Hardware Manual Thermo Scientific Data System Thermo Scientific 2 Functional Description Data System Figure 26 Source enclosure Entrance cone Cone wash nozzle Source enc
113. molecules with a discharge needle operating at a constant current of 2 to 10 pA in the positive polarity mode or 5 to 30 uA in the negative polarity mode 24 MSQ Plus Mass Detector Hardware Manual Thermo Scientific Ride Prefilter Thermo Scientific 2 Functional Description Mass Detector The newly formed ions then enter the focusing region through the entrance cone and pass into the RF dc prefilter region See Figure 16 Figure 16 Principal components and the pressure regions used by the APC probe LC eluent Nebulizing gas N2 8 Sheath gas Nz Probe heater l l l l Corona pin RF dc prefilter Entrance cone l l l l l l l l og Insert See J l capillary zz Wei l l l l l sg Extraction fone Atmospheric M path RF df prefilter pressure region vacuum region vacuum region 1 torr 107 torr Forepump The RF dc prefilter focuses the ions produced in the API source and transmits them to the mass analyzer The RF dc prefilter is a square array of square profile rods that acts as an ion transmission device and as a wide band pass mass filter as shown in Figure 17 During ion transmission the offset voltage is positive for the positive ion polarity mode and negative for the negative ion polarity mode Increasing the offset voltage increases the kinetic energy of the ions along the axis of the quadrupole through the differential aperture Allowable values for the RF lens bi
114. mp and vent the vacuum If the system is not under vacuum the menu contains the Pump command Choose Pump to pump down the system The Edwards forepump is not turned off by venting the system To turn off the Edwards forepump without turning off the mass detector set the On Off switch on the forepump to the Off position e Choose Exit to close the server The MSQ Plus Mass Detector Tune window allows you to optimize the mass detector parameters manually tune for your analytes and acquire data to a raw raw file When you finish tuning your mass detector for a compound of interest you save the current values of the tuning parameters in a tune tune file In ESI you empirically determine the optimal probe temperature needle voltage and cone voltage for each application In APCI you empirically determine the optimal probe temperature corona current and cone voltage for each application Tip There are three ways to open the Tune window e Start the Xcalibur data system Then double click the Server icon that appears in the system tray of the Windows taskbar e Double click the Tune icon on the Windows desktop Then double click the Server icon that appears in the system tray of the Windows taskbar e From the Windows 7 taskbar choose Start gt Tune Then double click the Server icon that appears in the system tray of the Windows taskbar MSQ Plus Mass Detector Hardware Manual Ai 2 Functional Description Data System
115. n you are in Acquisition mode that is when you are acquiring data to file from the Tune window A spinning icon indicates that communication is working correctly Use the Tune Scan Events table or Peak Display controls to define all the scan events that you want to acquire when performing a manual tune Per Method Parameters Table Peak Display Status Bar Thermo Scientific Use the Tune Per Method Parameters table to enter values and define the settings for the per method tuning parameters The table also provides individual tuning parameter readbacks You can adjust the tuning of the MSQ Plus Mass Detector by altering the values of these tuning parameters In ESI you optimize the probe temperature and the needle voltage for your application In APCI you optimize the probe temperature and the corona current for your application The Tune Peak Display displays a real time view of each tuning peak as defined by an enabled scan event row in the Tune Scan Events table Use the Peak Display to monitor the tuning peaks for both peak form and intensity particularly when optimizing the MSQ Plus Mass Detector during a manual tune Using the parameters available in the Scan Events table you can change the number of peaks displayed in the Peak Display and their appearance The status bar at the bottom of the Tune window displays information on the current status of the MSQ Plus Mass Detector MSQ Plus Mass Detector Hardware Manual 4
116. need to turn off the mass detector in an emergency place the main power circuit breaker switch in the Off O position as shown in Figure 78 The main power switch which is labeled MAINS ON OFF is located on the back panel of the mass detector in the lower right quadrant Turning the main power switch to the Off position turns off all power to the mass detector including the forepump Although removing power abruptly does not harm any component within the system it is not the recommended shutdown procedure to follow See Shutting the System Down for Non Routine Maintenance on page 104 for the recommended procedure MSQ Plus Mass Detector Hardware Manual 99 6 System Shutdown Turning Off the Nitrogen Gas To turn off your LC devices and your data system computer in an emergency use their ON OFF switches Figure 78 MAINS ON OFF circuit breaker switch ele O MAINS ON OFF Power switch in OFF position o PUMP OUT Dy Power supply for forepump MAINSIN Je Turning Off the Nitrogen Gas Connection to line power If you are performing intermittent analyses throughout the day and you want to conserve nitrogen you can turn off the nitrogen gas between analyses To turn off the nitrogen gas 1 If you are using the optional cone wash pump turn it off by turning the external cone wash pump switch to the Off position 2 Turn off the flow from your LC pump a Ifyour LC pump is controlled from the Xcalibur data
117. ng Access to the Source Block Assembly 0000000 e eee 81 Removing the Entrance Cone and the Cone Wash Nozzle 82 Cleaning the Entrance Cone and the Cone Wash Nozzle 83 Removing the Source Block Assembly sty s ERR ARC i sieenew sees 86 Cleaning the RF dc Prefilter os owes Eed 87 Cleaning the Extraction Cone and the Source Block 89 Repairing the Entrance EE 91 Assembling the Source Block Assembly 2 cio ERKENNEN de E en A 92 Installing the Source Block Assembly 0 0 0 0 cece eee ee 93 Maintaining the Forepump eege dreit E dear Late ithe abe da cdekaad 95 Maintaining the Turbomolecular Pump 96 Removing the Turbomolecular Pump Lubricant Reservoir 96 Replacing the Turbomolecular Pump Lubricant Reservoir 98 Chapter6 System Shutdown cece eect e eee eee e eens 99 Shutting Down the System in an Emergency 2 0 00 eee eee 99 Turning ENEE 100 Placing the System in the Off ergeet arias dp Aas ole AN 101 Turning Off the Mass Detector from the Xcalibur Data System 101 Turning Off the Mass Detector from the Tune Window 103 Shutting the System Down for Non Routine Maintenance 104 Restarting the System Following a Complete Shutdown 105 Checking the System Connections 2030 ERR eieaee wee eS 105 Restarting the MSQ Plus Mass Detector 0 0 0 eee e eee eee ee 106 Resetting the MSQ Plus Mass Detector 22 isos aw
118. ning nut P N 6070119 P N FM102590 122 MSQ Plus Mass Detector Hardware Manual Thermo Scientific 7 Replaceable Parts Spares Probe Heater Assembly Table 14 lists the parts in the probe heater assembly Table 14 Probe heater assembly parts Item Part number Probe heater assembly 60111 60023 Detent screw insulator FM102585 Spring screw FM102583 Spring cup FM102584 Probe screw sleeve FM102582 O ring 18 77 mm ID x 1 78 mm THK BS018 5711035 BLK Viton Figure 88 shows the probe heater assembly Figure 89 shows the components of the Probe Heater Repair Kit part number 60111 62010 Figure 88 Probe heater assembly with a view of the O rings O ring BS018 18 77 mm ID x 1 78 mm THK P N 5711035 Detent screw insulator P N FM102585 O ring BS006 2 9 mm ID x 1 78 THK P N TORNO03 Thermo Scientific MSQ Plus Mass Detector Hardware Manual 123 7 Replaceable Parts Spares Figure 89 Components of the Probe Heater Repair Kit part number 60111 62010 LI Vacuum Spares Spring screw P N FM102583 Not provided in the kit Spring cup P N FM102584 Probe screw sleeve P N FM102582 Detent screw insulator P N FM102585 Table 15 lists the vacuum spare parts Table 15 Vacuum spare parts Item Part number Oil wick Pfeiffer replacement FM104398 Oil Edwards pump 1 L bottle 00301 15102 Seal vacuum hous
119. not remove the contamination sonicate the cone in a 10 v v aqueous solution of formic acid rinse with distilled water and then rinse with 100 methanol 3 Using a microscope set to 30x magnification inspect the inside of the cone to ensure cleanliness Also inspect the outside of the cone to verify that the opening is circular and has a sharp edge See Repairing the Entrance Cone on page 91 for information on temporarily repairing the cone See Figure 65 Figure 65 View of the inside back of the entrance cone Orifice in the center of the entrance cone CAUTION Because solvent and acid can damage them do not sonicate O rings CAUTION Take care when handling the cone wash nozzle Its tip is extremely fragile 4 If the cone wash nozzle requires cleaning remove its O ring and then sonicate the nozzle in 100 methanol If methanol does not remove the contamination sonicate the nozzle in a 10 v v aqueous solution of formic acid rinse with distilled water and then rinse with 100 methanol Figure 66 shows the cone wash nozzle For O ring part numbers see Figure 84 on page 115 84 MSQ Plus Mass Detector Hardware Manual Thermo Scientific 10 Thermo Scientific 5 Routine and Preventive Maintenance Maintaining the Source Block Assembly Figure 66 Cone wash nozzle assembly part number FM102521 Fragile tip O ring BS007 3 68 mm ID x 1 78 mm THK part number FM101464 If you removed the O rings
120. nt Screw Insulator Use the parts supplied in the Probe Heater Repair Kit part number 60111 62010 to repair the probe heater See Figure 89 on page 124 To replace a broken detent screw insulator 1 Disassemble the detent screw assembly a Using a flat blade screwdriver loosen and remove the spring screw Figure 59 Slot in the top of the spring screw Spring screw Spring cup Probe screw sleeve b Remove the spring from the spring cup and set the spring aside Because the spring is reusable it is not provided in the repair kit c Pull the probe screw sleeve off the detent screw insulator d Pull the detent screw insulator out the underside of the probe heater body See Figure 60 Thermo Scientific MSQ Plus Mass Detector Hardware Manual 71 5 Routine and Preventive Maintenance Maintaining the Probe Heater Figure 60 Partially disassembled probe heater Spring screw Spring Spring cup Probe screw sleeve Detent screw insulator 2 Using the parts supplied in the repair kit rebuild the assembly a Insert a new detent screw insulator into the underside of the probe heater body b Slide the probe screw sleeve over the top of the detent screw insulator c Insert the spring that you removed from the broken assembly into the spring cup d Align the bottom of the spring cup with the probe screw sleeve e Insert the spring screw into the spring cup and tighten the assembly with a flat blade screwdriver In
121. ntific This chapter describes the principal components of the MSQ Plus Mass Detector and their functions See Figure 7 Contents Liquid Chromatograph Reference Inlet System Mass Detector Cone Wash System Data System MSQ Plus Mass Detector Hardware Manual 11 2 Functional Description Figure 7 Accela LC MSQ Plus Mass Detector cone wash pump forepump and data system Accela LC system MSO Plus Mass Detector Ethernet Reference inlet switchbox system inside Data system front door computer Monitor User supplied printer Cone wash pump EJS Solvent C Waste container for Forepump with trap LC system oil mist filter A functional block diagram of the LC MS integrated system with an Accela LC pump Accela Autosampler and the MSQ Plus Mass Detector is shown in Figure 8 12 MSQ Plus Mass Detector Hardware Manual Thermo Scientific 2 Functional Description Figure 8 Functional block diagram of the LC MS system Autosampler Reference inlet system MSQ Plus Mass Detector _ ee _ _ Ee zm zm Data system Printer Instrument Mass e control Personal analyzer detection electronic computer system assemblies lon optics Source Video monitor Vacuum system
122. ntive Maintenance Maintaining the Source Block Assembly CAUTION Take care when handling the entrance cone Always store the entrance cone with its cone facing upwards as shown in Figure 63 Figure 63 Entrance cone with cone facing upwards N Cone facing upwards 5 Taking care to handle it by its base carefully remove the cone wash nozzle from the source block CAUTION Because its tip is fragile take care when handling the cone wash nozzle 6 Proceed to one of the following e For instructions on cleaning the entrance cone go to the next procedure Removing the Entrance Cone and the Cone Wash Nozzle e For instructions on cleaning the internal components of the source block assembly go to Removing the Source Block Assembly on page 86 Cleaning the Entrance Cone and the Cone Wash Nozzle The cone wash nozzle requires cleaning only if it becomes blocked To clean the entrance cone and the cone wash nozzle 1 Use a 2 5 mm flat blade screwdriver to remove the O ring on the back of the entrance cone Figure 64 shows the location of the O ring For O ring part numbers see Figure 84 on page 115 Figure 64 Back of the entrance cone showing its O ring BSO10 O ring BS010 6 07 mm ID x 1 78 mm THK Thermo Scientific MSQ Plus Mass Detector Hardware Manual 83 5 Routine and Preventive Maintenance Maintaining the Source Block Assembly 2 Sonicate the entrance cone in 100 methanol If methanol does
123. nto the gas phase lon Desolvation Mechanism Thermo Scientific To produce gas phase ions in ESI the following sequence of events occurs 1 The ESI capillary to which a high voltage is applied sprays sample solution into a fine mist of droplets that are electrically charged at their surface 2 The electrical charge density at the surface of the droplets increases as solvent evaporates from the droplets until it reaches a critical point known as the Rayleigh stability limit At this critical point the droplets divide into smaller droplets because the electrostatic 1 Refer to the following papers for more information on the electrospray process Fenn J B Mann M Meng C K Wong S F Whitehouse C M Mass Spectrometry Reviews 1990 9 37 Smith R D Loo J A Edmonds C G Barinaga C J Udseth H R Anal Chem 1990 62 882 Ikonomou M G Blades A T Kebarle P Anal Chem 1991 63 1989 MSQ Plus Mass Detector Hardware Manual 3 1 Introduction lonization Techniques repulsion is greater than the surface tension The process repeats itself forming smaller and smaller droplets 3 From the very small highly charged droplets the force of electrostatic repulsion ejects sample ions into the gas phase 4 The charged ESI capillary attracts gas phase ions of opposite charge and repels gas phase ions of the same charge The low vacuum of 1 torr produced by the forepump draws both ionized molecules re
124. oarse ee ae kines 8 Centroid Data JE gaer SES nates eRe 9 MCA Data Type Eege TEE RTE DESEE wheats 9 Functional Description de n uss EES Ed ENEE EEN 11 Liquid Chromatograph Zeg KEE hens dee EELER eeh eee cho 14 Reference Inlet Systemi ioe ida vee hehe be ede sends EE ae EE 15 Mass RE 18 Front Panel Status Indicator ag ENNEN A cohen ce EEN ona ced 18 Back Panel Controls and Connections 00 c ee eee eee eee 20 Connection Between LC and Mass Detector 0000 c cece eee ee 22 API SOULCES 4 5 sv aded dee ae LAG edad oe eet Nae eee Sata e ee 22 LE E EE EE 25 Wass Padre E EE EE EE E EE He Jon Detection System 28 Vacuum Syst me d ANE idence geet ee ects 30 EE 32 Cone Wash Systemi sre sobs ci nehan dae bre WEE gg EE 36 MSQ Plus Mass Detector Hardware Manual xi Contents DatasSystem ger ia i ec ante ented dete antes Aa gated oA 37 Computer Hard wate y s cut xunkcae Aerer Age nen Ges a wl 38 KE EE 38 MSQ Plus Mass Detector Server 40 RTE 41 Printer eebe Waster tin eens EE incase at ea arial kees atk 44 Chapter3 Daily Operatiits Si cc dude EE ENN AN Ed ANEN e cae EE dE te 45 Before Operating the Mass Detector d Vert gute e 45 Checking the Nitrogen Supply 2 cies ae ried awn EE EE eee 45 Checking the Disk Space sis ve as vi tt Mat raw wade eas 45 Checking the Oil Level in the Oil Mist Pier 46 After Operating the Mass Detectors a hee ege kee ee 47 Flushing EE 47 Placing the System in the OF Modes nin cieu sds shawls bias eee ee
125. oblems with electrospray because the ionization relies on the evaporation of ions from the surface of a droplet Therefore the detergent suppresses the evaporation of other ions Use surfactants only when they are being analyzed themselves not as additives to HPLC mobile phases Cone Wash System Thermo Scientific Historically LC MS has only been compatible with volatile buffer systems using modifiers such as trifluoroacetic acid formic acid and acetic acid Phosphate buffers although extensively used in LC separations were not suited to LC MS because of the rapid blocking of the ion sampling region caused by the deposition of non volatile phosphate salts The self cleaning API source provided by the cone wash system of the MSQ Plus Mass Detector allows routine LC MS with chromatographic buffers such as phosphates or ion pairing agents and samples in dirty matrices The cone wash system consists of a cone wash nozzle internal tubing and a cone wash pump Refer to the MSQ Plus Mass Detector Getting Connected Guide for instructions on connecting the cone wash pump to the MSQ Plus Mass Detector The recommended flow rate for the cone wash solvent is 200 l min and the recommended cone wash solvent is 50 50 methanol water v v Note Use the cone wash only for dirty matrices or with non volatile buffers Choose the cone wash solvent to give the most effective solubility for the expected contaminants The cone wash can be used for a sho
126. of the latching plate might compromise the ability of the plate to lock the probe down so Thermo Fisher Scientific recommends that you avoid filing these edges unless pin breakage becomes a common problem To clean or repair the probe heater follow these procedures e Removing the Probe Heater e Cleaning the Probe Heater or Replacing the Detent Screw Insulator e Installing the Probe Heater Removing the Probe Heater Follow these instructions to remove the probe heater from the probe mount To remove the probe heater from the probe mount 1 Remove the ESI or APCI probe See Removing the ESI Probe on page 57 or Removing the APCI Probe on page 68 CAUTION Wait for the probe heater to cool before you remove it 2 Rotate the black knobs of the probe heater outwards 90 degrees so that they face away from each other See Figure 55 and Figure 56 74 MSQ Plus Mass Detector Hardware Manual Thermo Scientific Thermo Scientific 5 Routine and Preventive Maintenance Maintaining the Probe Heater Figure 55 Probe heater and its connections to the front panel of the mass detector Grounding Green cable thermocouple connector White power connector Probe heater knobs in Probe mount locked position Figure 56 Probe heater knobs in the removal position Probe heater knobs in removal position MSQ Plus Mass Detector Hardware Manual 75 5 Routine and Preventive Maintenance Maintaining the Probe Heater
127. on 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 Conditions of Sale which Terms and Conditions of Sale shall govern all conflicting information between the two documents Release history Revision A September 2013 Software version Thermo MSQ Plus Mass Detector 2 0 or later Xcalibur 2 2 SP1 or later Foundation 2 0 SP1 2 1 3 0 or later For Research Use Only Not for use in diagnostic procedures Regulatory Compliance Thermo Fisher Scientific performs complete testing and evaluation of its products to ensure full compliance with applicable domestic and international regulations When the system is delivered to you it m
128. or Hardware Manual Thermo Scientific 5 Routine and Preventive Maintenance Maintaining the ESI Probe Cleaning or Replacing the ESI Capillary Follow this procedure to clean or replace the ESI capillary To clean or replace an ESI capillary 1 Remove the ESI probe from the probe heater as described in Removing the ESI Probe on page 57 2 Remove the ESI capillary from the probe as described in Removing the ESI Capillary on page 59 3 If the capillary is reusable clean its surface with 50 50 methanol water 4 Reinstall the clean capillary or a new capillary as described in Installing the ESI Capillary on page 63 Figure 40 Partially disassembled ESI probe with capillary removed ESI ceramic mount Locking plate ESI probe tip ESI probe ceramic sleeve PEEK tube insert ESI probe mount Graphite ferrule Capillary retaining nut M3 x 10 cap head Stainless steel screws Replacing the Ceramic Sleeve of the ESI Probe If you break the ceramic sleeve of the ESI probe replace it See Figure 86 on page 121 for the part numbers of the ESI probe components To replace the ceramic sleeve of the ESI probe 1 Remove the ESI probe from the mass detector as described in Removing the ESI Probe on page 57 Thermo Scientific MSQ Plus Mass Detector Hardware Manual 61 5 Routine and Preventive Maintenance Maintaining the ESI Probe 2 Disassemble the ESI probe and
129. ories This symbol also appears on the instrument For details about the hazard refer to the instrument manual When the safety of a procedure is questionable contact Technical Support for Thermo Scientific San Jose products VORSICHT Stromschlaggefahr Dieses Ger t arbeitet mit Spannungen die Stromschlage und oder Personenverletzungen verursachen k nnen Vor Wartungsarbeiten muss das Ger t abgeschaltet und vom Netz getrennt werden Betreiben Sie das Ger t nicht mit abgenommenen Abdeckungen Nehmen Sie die Schutzabdeckungen von Leiterplatten nicht ab Gefahr durch Chemikalien Tragen Sie beim Umgang mit toxischen karzinogenen mutagenen atzenden oder reizenden Chemikalien Schutzhandschuhe und weitere geeignete Schutzausrtistung Verwenden Sie bei der Entsorgung von verbrauchtem OI und beim Umgang mit medienberithrenden Komponenten die vorgeschriebenen Beh lter und wenden Sie ordnungsgem e Verfahren an Hei e Oberfl chen Lassen Sie hei e Komponenten vor der Ber hrung abk hlen Gefahr durch entz ndbare Substanzen Beachten Sie die einschl gigen Vorsichtsma nahmen wenn Sie das System in Gegenwart von entztindbaren Substanzen betreiben Augenverletzungsrisiko Verspritzte Chemikalien Schwebstoffpartikel oder scharfe Objekte k nnen Augenverletzungen verursachen Scharfe Objekte die Kunden m glicherweise im Ger t installieren sind z B Quarzglas Kapillaren die Nadel des Autosamplers usw Tragen Sie b
130. ou wait approximately 10 minutes for the source to equilibrate There is an allowable 2 5 tolerance on the readback 9 Turn on the flow from the LC pump Resetting the MSQ Plus Mass Detector If communication between the mass detector and data system computer is lost it might be necessary to reset the mass detector by using the Reset button on the power panel Pressing the Reset button creates an interrupt on the CPU PCB of the embedded computer causing the embedded computer to restart into a known default state You might hear a high or low tone that confirms the reset when you open the Tune window The procedure given here assumes that the mass detector and data system computer are both powered on and operational If the mass detector data system computer or both are off See Restarting the MSQ Plus Mass Detector on page 106 To reset the mass detector press the Reset button located on the mass detector s back panel as shown in Figure 83 108 MSO Plus Mass Detector Hardware Manual Thermo Scientific 6 System Shutdown Resetting the MSQ Plus Mass Detector Figure 83 View of the upper right corner of the mass detector s back panel USB O START IN START IN USER 1 0 d O READY OUT READY OUT RESET Thermo Scientific MSQ Plus Mass Detector Hardware Manual 109 E Replaceable Parts This chapter lists the parts most commonly used in the course of working
131. ource Block Assembly Cleaning the RF dc Prefilter See Table 4 to determine the frequency at which you need to clean the RF dc prefilter Table 4 Cleaning schedule for RF dc prefilter Sample Solvent Type Cleaning Frequency Pure samples and solvents 6 months Standard samples 3 to 6 months Complex matrices for example crude 1 to 4 weeks with operation of cone wash plasma and urine Non volatile buffer Weekly with operation of cone wash To clean the RF dc prefilter IMPORTANT You must wear non powdered gloves to handle the quadrupole 1 Support the quadrupole as you unscrew the hexapole screws at the base of the RF dc prefilter to disconnect it from the source block Tools are not required to remove the quadrupole See Figure 68 Figure 68 Source block assembly with the three screws connecting the RF dc prefilter to the source block Three hexapole screws 2 Carefully slide the RF dc prefilter into a 500 mL graduated glass cylinder containing 100 methanol See Figure 69 Thermo Scientific MSQ Plus Mass Detector Hardware Manual 87 5 Routine and Preventive Maintenance Maintaining the Source Block Assembly A 5 7 Li Ze 1 2 88 MSQ Plus Mass Detector Ha Figure 69 Cleaning the RF dc prefilter Sonicate the cylinder for 15 minutes Carefully remove the RF dc prefilter from the graduated cylind
132. pelled by the charge on the capillary and neutral molecules in the gaseous phase into the mass detector through the entrance cone Figure 2 shows the steps in the formation of gas phase ions from highly charged droplets Figure 2 Positive ion electrospray mechanism Positively charged capillary 3 to 5 kV Step 1 Step 2 Step 3 Step 4 D Negative ions attracted back to the capillary gay A _ t cb SE rE TE Ee Positive ions TA A ejected from S the surface Fine spray Large droplet lons moving towards the surface Spectral Characteristics In ESI mode ionization takes place in the liquid phase Polar compounds of low molecular weight lt 1000 Da typically form singly charged ions by the loss or gain of a proton Basic compounds for example amines can form a protonated molecule M HIT which can be analyzed in the positive ion polarity mode to give a peak at an m z value of M 1 where M equals the mass of the original molecule Acidic compounds for example sulphonic acids can form a deprotonated molecule M HIT which can be analyzed in the negative ion polarity mode to give a peak at an m z value of M 1 Because electrospray is a very soft ionization technique there is usually little or no fragmentation and the spectrum contains only the protonated or deprotonated molecule Preformed ions can also include adducts Adduct ions are produced by th
133. portant to clear access to the source block assembly to prevent damage to its parts To clear access to the source block assembly 1 To open the front door of the mass detector depress the door latch on the left side of the detector as you pull the door forward 2 Remove the API probe from the probe heater a Remove the PEEK fingertight fitting from the probe b Turn the locking plate clockwise to the open position and then carefully pull the API probe out of the probe heater CAUTION Exercise care when handling the API probe The ceramic sleeve of the ESI probe and the capillaries of both probes are fragile and can be damaged easily 3 Rotate the black knobs of the probe heater so that they face away from each other and then pull the probe heater out of the source mount See Figure 56 on page 75 4 Store the probe heater in the holder to the left of the source compartment 5 If your MSQ Plus Mass Detector is set up in the APCI mode rotate the corona pin knob downward to its vertical position Thermo Scientific MSQ Plus Mass Detector Hardware Manual 81 5 Routine and Preventive Maintenance Maintaining the Source Block Assembly Removing the Entrance Cone and the Cone Wash Nozzle Follow these steps to remove the entrance cone and the cone wash nozzle To remove the entrance cone and the cone wash nozzle 1 If you have not already done so vent the mass detector as described in Preparing the LC MS System for Ma
134. probe components To remove the capillary from the ESI probe 1 Remove the ESI probe from the mass detector as described in Removing the ESI Probe on page 57 2 Using the 2 5 mm Allen key unscrew the M3 x 10 cap head stainless steel screw from the probe clamp and then remove the probe clamp and the locking plate as shown in Figure 37 Figure 37 Removing the probe clamp and locking plate Locking plate M3 x 10 cap head stainless steel screw 3 Using the front end of the probe clamp unscrew the capillary retaining nut adapter and remove it from the ESI probe See Figure 38 Thermo Scientific MSQ Plus Mass Detector Hardware Manual 59 5 Routine and Preventive Maintenance Maintaining the ESI Probe Figure 38 Removing the capillary retaining nut adapter Probe clamp Capillary retaining nut adapter 4 Place a lint free cloth on the workbench and then gently shake the ESI capillary part number FM102598 graphite ferrule part number 6070119 and PEEK tube insert part number FM102591 assembly out of the ESI probe onto the cloth as shown in Figure 39 Figure 39 Removing the capillary graphite ferrule and PEEK insert assembly from the probe ESI capillary Graphite ferrule oo PEEK insert CAUTION Because the ESI capillary is fragile and can be damaged easily exercise care when handling it 5 Pull the ESI capillary out of the PEEK tube insert 60 MSQ Plus Mass Detect
135. r diameters and internal volume of five of the most commonly used colors Table 23 1 16 in OD PEEK tubing color coding Color Inner diameter Internal volume in mm uL in Green 0 030 0 75 11 577 Orange 0 020 0 50 5 146 Blue 0 010 0 25 1 288 Yellow 0 007 0 18 0 632 Red 0 005 0 13 0 323 To plumb your system with PEEK tubing 1 Cut PEEK tubing with a polymeric tubing cutter to ensure a square cut to prevent distortion of the tubing and to avoid creating burrs that will constrict flow Thermo Fisher Scientific recommends a polymeric tubing cutter that is engineered with guide holes for 1 16 in and 1 8 in OD tubing The following instructions apply to the 134 MSQ Plus Mass Detector Hardware Manual Thermo Scientific Optimizing the LC Conditions Chemical Kit Upchurch Scientific Model A18 Polymeric Tubing Cutter and are provided courtesy of Upchurch Scientific a Squeeze the tabs at the back of the cutter together to raise the blade b Insert your tubing through the appropriate guide hole c Release the tabs allowing the blade of the cutter to rest on the tubing d Holding the tubing spin the cutter around the tubing to begin the cut For PEEK tubing spin the cutter two to three times remove the tubing and snap the tubing at the cut 2 Slip a fitting over the end of the tubing 3 As you insert PEEK tubing into a port ensure that the end of the tubing makes contact with the bottom of the por
136. rds forepump Purge the oil on a regular basis as described in Draining the Oil Mist Filter and Purging the Pump Oil on page 48 Maintaining the Turbomolecular Pump A turbomolecular pump creates the vacuum for the mass detector The lubricant reservoir of this pump may occasionally need to be replaced to keep the pump operating optimally Removing the Turbomolecular Pump Lubricant Reservoir Follow the steps in this section to remove the existing lubricant reservoir before replacing it Figure 75 shows the parts and tools involved in replacing the lubricant reservoir of the turbomolecular pump Figure 75 Parts needed to replace the lubricant reservoir of the turbomolecular pump 6 End cover 7 Lubricant reservoir 48 O ring E Special tool PV M40 569 To remove the turbomolecular pump lubricant reservoir CAUTION Always wear protective gloves Contaminants in the oil are extremely hazardous 1 Leave the system pumping for at least a half an hour before starting the removal procedure 1 Image of the turbomolecular pump from the Compact Turbo TurboDrag Pump TMH TMU 261 Manual PM 0470 BE O 0709 by Pfeiffer Vacuum 96 MSQ Plus Mass Detector Hardware Manual Thermo Scientific 5 Routine and Preventive Maintenance Maintaining the Turbomolecular Pump 2 Vent the mass detector Using a No 1 point Pozidriv screwdriver remove the pump access plate securing screws A Lu Remove the access plate
137. rged ions its use is limited to small molecules with molecular weights up to about 2000 Da Because the APCI process takes place in the gas phase minor changes in most variables such as changes in buffer or buffer strength have no effect You can use APC in the positive negative or positive negative switching ion polarity mode For most molecules the positive ion mode produces a stronger ion current especially for molecules with one or more basic nitrogen or other basic atoms Exceptions to the general rule are molecules with acidic sites such as carboxylic acids and acid alcohols which produce more negative ions than positive ions Although the negative ion polarity mode generates fewer ions it also generates less chemical noise than does the positive mode making it more selective Spectral Characteristics Scan Types Full Scan Like electrospray APCI is a soft ionization technique and forms singly charged ions either the protonated M HI or deprotonated M HI molecule depending on the selected ion polarity mode Unlike electrospray however APCI does not produce multiply charged ions so it is unsuitable for the analysis of high molecular weight compounds such as proteins or peptides Because APCI uses a heated probe to aid the desolvation process it is not suitable for thermally labile unstable compounds which can fragment in the ion source The MSQ Plus Mass Detector provides two scan types full scan and s
138. rogen gas pressurizes the reference inlet reservoir Pressurizing the reference inlet reservoir pushes the calibrant out of the reference inlet reservoir bottle and into the 500 uL sample loop attached to the microinjection valve of the mass detector After the sample loop fills with calibrant the microinjection valve switches to the inject position With the valve in the inject position the sample loop is open to the mobile phase stream from the LC pump The stream pushes the calibrant out of the sample loop and through the API probe After the microinjection valve switches to the inject position the third solenoid valve switches to the On position allowing the nitrogen gas to vent to the atmosphere and depressurizing the reference inlet reservoir The first restrictor allows a constant low flow of nitrogen gas to the API probe when the first solenoid valve is turned off See dashed line shown in Figure 22 on page 33 The second restrictor shown in Figure 22 on page 33 limits the flow of sheath gas and acts as a split flow regulator by forcing the majority of the gas flow to the API probe through the tubing for the nebulizing gas Thermo Scientific MSQ Plus Mass Detector Hardware Manual 35 2 Functional Description Cone Wash System Note There is a constant low flow of nitrogen gas through the mass detector when it is not in use This low flow of nitrogen gas maintains a positive pressure in the source compartment preventing fumes from the so
139. rt duration at the beginning of the LC analysis and turned off after the void volume of the LC column is cleared Figure 90 shows the back of the cone wash pump including the inputs MSQ Plus Mass Detector Hardware Manual 131 A Optimizing the LC Conditions Cone Wash System Figure 90 Back of the cone wash pump imac a anan The pump s inputs are on the 10 pin terminal board connector Table 22 shows the pinouts of the cone wash pump Table 22 Pinout of the cone wash pump Pin Function VOLTAGE COM VOLTAGE IN FREQ IN ENABLE IN PUMP RUN PUMP STOP No connection No connection ATI GB AI WN AINI o No connection COM To optimize the position of the cone wash nozzle 1 Turn the cone wash nozzle counterclockwise until the tip of the nozzle is just above the top of the entrance cone 2 Turn the cone wash pump on by turning its On Off switch to On 132 MSQ Plus Mass Detector Hardware Manual Thermo Scientific Optimizing the LC Conditions Controlling the Cone Wash Pump Through Timed Events 3 Adjust the nozzle so that the drops of solvent just touch the tip of the entrance cone as they fall to the drain at the bottom of the source chamber CAUTION Do not leave the cone wash running when the source heater is turned off because this can lead to cone wash solvents condensing on the RF dc prefilter Controlling the Cone Wash Pump Through Timed Events Thermo Scient
140. s Connection Kits Electronic Spares Table 18 lists the electronic spare parts Table 18 Electronic spare parts Item Part number Assembly power supply low voltage MSQ FM103098 PCB assembly status 60111 61090 PCB 2000 RF Digital control 60111 61050S or EXFM102818 PCB electrometer 60111 61020 PCB source 60111 61030 PCB RF generator 60111 61040 PCB digital 60111 61050 PCB RF dc prefilter Replacement requires 60111 61080 redipping the transfer lens coil Call Field Services Connection Kits For information on the connection kits available refer to the manuals stored on the LC devices CD that is part of the media kit Manuals The following manuals are available on the instrument software DVD e MSQ Plus Mass Detector Preinstallation Guide e MSQ Plus Mass Detector Getting Connected Guide e MSQ Plus Mass Detector Getting Started Guide e MSQ Plus Mass Detector Hardware Manual e MSQ Plus Mass Detector Calmix Kit Preparation Guide 126 MSO Plus Mass Detector Hardware Manual Thermo Scientific Optimizing the LC Conditions This appendix includes information that you might find helpful for optimizing the LC system and the cone wash system Contents Flow Rates Flow Rates LC Solvents and Mobile Phase Additives Cone Wash System Flow Splitting PEEK Tubing Chemical Kit In general the LC column employed determines the choice of flow rate Each column has an optimum f
141. s and the probe heater by doing one of the following e In the Per Method Parameters table of the Tune window click the Nitrogen Gas On Off toggle button to Off or e Open the Status page of the Information view in the Xcalibur data system Right click the MSQ Plus listing to open a shortcut menu and choose Turn Device Off from the shortcut menu Ifthe MSQ Plus Mass Detector is under vacuum vent it Right click the Server icon and choose Vent from the shortcut menu 80 MSQ Plus Mass Detector Hardware Manual Thermo Scientific 5 Routine and Preventive Maintenance Maintaining the Source Block Assembly Venting the MSQ Plus Mass Detector turns off the turbomolecular pump It does not turn off the Edwards forepump 5 Wait two or more minutes before proceeding so that the system has time to vent CAUTION It takes approximately two minutes for the vacuum rotor to decelerate after you choose Vent To avoid damaging the vacuum pump allow time for this deceleration process before you turn off the power to the vacuum pump 6 Turn off the Edwards forepump by doing one of the following e Turn off the power to the MSQ Plus Mass Detector by placing its MAINS ON OFF switch to the Off position or e Flip the power switch on the Edwards forepump to the Off position CAUTION Wait for the source block and probe heater to cool before performing any maintenance Clearing Access to the Source Block Assembly It is im
142. s et lors de la manipulation des pi ces de l instrument en contact avec l eau Surface chaude laisser refroidir les composants chauff s avant toute manipulation Danger li aux substances inflammables agir avec pr caution lors de l utilisation du syst me en pr sence de substances inflammables Risque de l sion oculaire les projections chimiques les particules en suspension dans l air et les objets tranchants peuvent entra ner des l sions oculaires Les objets tranchants pouvant tre install s par les clients dans l instrument comprennent les tubes en silice fondue les aiguilles du passeur automatique etc Porter des lunettes de protection lors de toute manipulation de produit chimique ou intervention sur l instrument Danger d ordre g n ral 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 plus de d tails sur ce danger potentiel se reporter au manuel de l instrument Si la s ret d une proc dure est incertaine contacter l assistance technique pour les produits Thermo Scientific San Jose CAUTION Symbol gt oeeo CAUTION Laser hazard This instrument uses a laser that is capable of causing personal injury This symbol also appears on the instrument For details about the hazard refer to the instrument manual Ultra violet light hazard Do not look directly at the ultra violet UV light or into the UV source
143. s not open open it by double clicking the Xcalibur icon X on the Windows desktop Thermo Scientific MSQ Plus Mass Detector Hardware Manual 101 6 System Shutdown Placing the System in the Off Mode 3 If the Information view is not displayed choose View gt Info View to display it Then click the Status tab to open the Status page 4 To turn off the flow from the LC pump do one of the following e Ifyour LC pump is controlled from the Xcalibur data system right click the pump listing on the Status page and choose Turn Device Into Standby from the shortcut menu shown in Figure 79 or e Ifyour LC pump is not controlled from the Xcalibur data system turn it off from its control keypad Figure 79 Status of the Accela MS pump and its shortcut menu shown on the Status page of the Information view Status Acquisition Queue Run Manager Ready To Download Sequence Sample Name Working On Position Raw File Inst Method Accela AS Ready to Download Accela Pump Ready to Download T m Device On ME taming oft the Ready to Download Turn Device Off pump flow 5 Right click the MSQ Plus listing on the Status page and choose Turn Device Off from the shortcut menu to place the mass detector in the Off mode as shown in Figure 80 The status LED on the front of the MSQ Plus Mass Detector turns yellow 102 MSQ Plus Mass Detector Hardware Manual Thermo Scientific 6 System Shutdown Placing the S
144. s table 43 selected ion monitoring SIM 7 Sensitivity Kit 136 Server icon 37 40 41 103 105 107 Server icon shortcut menu 41 105 Server software 37 sheath gas 23 24 Signal to Noise Calculator program 39 singly charged ions 4 7 solenoid valve 34 solvent path spare parts 125 source block 89 source block assembly assembling 92 cleaning cone wash nozzle 83 cleaning entrance cone 83 clearing access to 81 installing 93 maintaining 79 parts in 117 preparing LC MS system 80 removing 86 removing cone wash nozzle 82 removing entrance cone 82 repairing entrance cone 91 source manifold 20 22 spare parts 116 Thermo Scientific split flow tee 13 status bar of Tune window 43 sulfuric acid 130 surfactants 129 131 survey link xx T tetrahydrofuran THF 130 134 TF terminals 133 Thermo Foundation Instrument Configuration dialog box 14 Timed Events page 133 title bar of Tune window 42 toluene 128 toolbar of Tune window 43 triethylamine TEA 129 130 trifluoroacetic acid TFA 129 131 Tune Comms Indicator 43 tune file default 25 displaying name in Tune window 42 importing 42 saving values of tuning parameters in 41 Tune icon 41 43 100 103 Tune window Acquisition icon 43 features of 42 menu bar 42 opening 41 Peak Display 43 Per Method Parameters table 43 Scan Events table 43 status bar 43 title bar 42 toolbar 43 Tune Comms Indicator 43 Tune icon 43 turning off the mass detector from 103 turbomolecular pump
145. second dedicated fume exhaust system Consult local regulations for the proper method of exhausting the fumes from your system Do not vent the PVC drain tube or any vent tubing connected to the waste container to the same fume exhaust system that is connected to the forepump The forepump exhaust contains pump oil which can seriously contaminate the analyzer optics of the mass spectrometer xviii MSQ Plus Mass Detector Hardware Manual Thermo Scientific Preface Solvent and Gas Purity Requirements Solvent and Gas Purity Requirements Contacting Us Thermo Scientific Because the MSQ Plus Mass Detector is extremely sensitive to solvent impurities use the highest purity solvents available Use liquid chromatography grade or higher solvents and buffers Because deionized water contains chemicals that the MSQ Plus Mass Detector can detect use distilled water The following table lists international sources that can supply high quality solvents Solvent source Telephone or fax number Mallinckrodt Baker Inc Tel 800 582 2537 Fax 908 859 9370 Burdick amp Jackson Inc Tel 800 368 0050 Fax 616 725 6216 E M Science Inc Tel 800 222 0342 Fax 800 336 4422 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 soft
146. stalling the Probe Heater This section describes how to install the probe heater To install the probe heater 1 If you removed the O ring from the underside of the probe heater base reinstall it See Figure 61 78 MSQ Plus Mass Detector Hardware Manual Thermo Scientific 5 Routine and Preventive Maintenance Maintaining the Source Block Assembly Figure 61 View of O ring installed in the underside of the probe heater base Heater tube O ring BS018 18 77 mm ID x 1 78 mm THK 2 If you disconnected the grounding strap from the probe heater reconnect it to the probe heater See Figure 58 on page 76 CAUTION Make sure that the grounding strap is connected to the probe heater before you insert the probe heater into the probe mount 3 Rotate the black knobs of the probe heater so that they face away from each other See Figure 56 on page 75 A Insert the tube portion of the probe heater into the probe mount 5 Rotate the black knobs of the probe heater forward to their locking position See Figure 55 on page 75 6 Plug the green connector and the white connector into their respective receptacles located above the probe mount See Figure 55 Maintaining the Source Block Assembly Thermo Scientific The entrance cone is the only component of the source block assembly that requires frequent cleaning The cone wash nozzle rarely requires cleaning because it is used to spray the entrance cone with cleaning solvent
147. status LED 18 MSQ Plus Mass Detector Hardware Manual Thermo Scientific Thermo Scientific 2 Functional Description Mass Detector Figure 12 Front view of the MSQ Plus Mass Detector Status LED Table 1 States of MSQ Plus Mass Detector Status LED Instrument status Light Vented Red Venting Red Pumping down Flashing yellow Under vacuum above vacuum trip Red Under vacuum ready for use Yellow Operate On MSQ Plus Mass Detector in use Green Initially when a Thermo Fisher Scientific service engineer installs the MSQ Plus Mass Detector and turns on the forepump the status LED is red As the system pumps down the LED flashes yellow After the vacuum reaches 10 torr and the turbomolecular pump reaches its operating speed the LED turns solid yellow If you vent the system for a brief period of less than two hours for example to perform maintenance on the source block wait 15 minutes after pumping down the system to place the mass detector in Operate mode If the system has been in a vented state for more than a brief period pump the system down and then wait a minimum of eight hours before operating the system MSQ Plus Mass Detector Hardware Manual 19 2 Functional Description Mass Detector Back Panel Controls and Connections The back panel of the MSQ Plus Mass Detector is shown in Figure 13 The back panel controls and connections include the following e MAINS ON OFF e PUMP OUT e MAINS
148. sts the ion evaporation process This highly efficient desolvation process close to the entrance cone enables the routine use of high LC flow rates up to 2 mL min with the ESI technique Drawn in by the low vacuum produced by the forepump the desolvated ions enter the M path region through the entrance cone As the ions exit the focusing region they pass into the RF dc prefilter Figure 15 shows the components used in electrospray MSQ Plus Mass Detector Hardware Manual 23 2 Functional Description Mass Detector Figure 15 Principal components and the pressure regions used by the ESI probe LC eluent Nebulizing gas N2 i gas N2 g Sheath Probe heater RF dc prefilter Insert capillary O Po Entrance cone o 2 CH CT l Exitcone l l Atmospheric M path RF df prefilter pressure region vacuum region vacuum region 1 torr 10 torr Forepump Atmospheric Pressure Chemical lonization APCI In contrast to electrospray APCI is a gas phase ionization technique The sample is carried to a spray region through a stainless steel insert capillary The action of both the nebulizing gas and the heated probe lead to the formation of an aerosol The desolvation process is assisted by a second concentric flow of nitrogen gas called the sheath gas Ionization occurs as the aerosol leaves the heated nebulizer region A corona pin which is mounted between the heated region and the entrance cone ionizes the sample
149. t Then tighten the fitting fingertight See Figure 93 Note 1 Tubing that is not properly seated can add dead volume to a chromatographic system 2 Never over tighten PEEK fittings because this can cause leaks Figure 93 Poor connections result if tubing is not bottomed in the port A or is not cut square B A Courtesy of the Rheodyne Web site Chemical Kit To prepare the MSQ Plus Mass Detector calibration solution for autotune and mass calibration you can either prepare it yourself using the instructions in the Calibrant Solution section of the MSQ Plus Mass Detector Getting Started Guide or you can use the MSQ Plus Mass Detector Chemical Kit part number 60111 62023 shown in Figure 94 This kit contains calibration qualification and sensitivity chemicals for the MSQ Plus Mass Detector Specifically it contains the following Thermo Scientific MSQ Plus Mass Detector Hardware Manual 135 A Optimizing the LC Conditions Chemical Kit e MSQ Plus Mass Detector Calmix Kit part number 60111 62021 shown in Figure 95 which includes the following items MSQ Plus Mass Detector Calmix Kit Preparation Guide part number 60111 97200 This document contains the same information as the Preparing the MSQ Plus Mass Detector Calibration Solution section in the MSQ Plus Mass Detector Getting Started Guide Certificate of Analysis which verifies that the Calmix solution actually contains the specifie
150. the Per Method Parameters table Probe Temperature Setpoint box Description Readback Setpoint Tune Control Probe Temperature C 0 334 Needle Io 0 0 3 0 Acquisition Control Operate toggle Retention Time mins 0 00 n a zg button General Control Operate n a Nitrogen Gas n a off py lonization Mode n a ESI Nitrogen Gas toggle button vi y a H i CN a a 0 o Je D a D 2 ae Thermo Scientific MSQ Plus Mass Detector Hardware Manual 107 6 System Shutdown Resetting the MSQ Plus Mass Detector 6 Turn on the nitrogen gas by clicking the Nitrogen Gas On Off toggle button in the General Control group of the Per Method Parameters table shown in Figure 82 The On Off toggle button turns from gray to green and the text to the left of the button changes from Off to On Within a few seconds you hear the nitrogen supply to the API source turn on Put the instrument into the Operate mode by clicking the Operate On Off toggle button shown in Figure 82 on page 107 The button turns from gray to green and the text changes from Off to On To set the probe temperature click the Probe Temperature Setpoint box shown in Figure 82 and type an appropriate value for your application The MSQ Plus Mass Detector is ready to use as soon as the probe temperature readback value approaches that in the setpoint box although for most stable operation Thermo Fisher Scientific recommends that y
151. the Source Block Assembly 11 Lock the probe heater in place by turning its black knobs forward 90 degrees See Figure 55 on page 75 12 Reinsert the API probe into the probe heater and reattach the PEEK fingertight fitting to the probe See Figure 35 on page 58 Removing the Source Block Assembly You must clean the entire source block assembly on a regular basis if you inject complex sample matrices or use highly buffered mobile phases To clean the source block assembly you must remove it from the instrument and disassemble it To remove the source block assembly from the mass detector CAUTION Wait for the source block and probe heater assembly to cool before carrying out any maintenance 1 If you have not already done so do the following e Prepare your LC MS system for maintenance as described in Preparing the LC MS System for Maintenance on page 80 e Remove the probe and the probe heater as described in Clearing Access to the Source Block Assembly on page 81 e Remove the entrance cone and the cone wash nozzle as described in Removing the Entrance Cone and the Cone Wash Nozzle on page 82 2 Loosen the thumbscrews on the source block and pull the source block assembly out of the mass detector See Figure 67 Figure 67 Source block assembly being removed from the mass detector 86 MSQ Plus Mass Detector Hardware Manual Thermo Scientific 5 Routine and Preventive Maintenance Maintaining the S
152. the profile data type you can see the shape of the spectral peaks in the mass spectrum as shown in Figure 4 Figure 4 Spectrum of D raffinose shown in profile peak format in full scan 100 503 275 300 325 350 375 400 425 450 475 500 525 Each atomic mass unit is divided into approximately 15 sampling intervals The intensity of the ion current is determined at each of the sampling intervals The intensity at each sampling interval is displayed with the intensities connected by a continuous line In general the profile data type is used when you tune and calibrate the mass detector so that you can easily see and measure mass resolution 8 MSQ Plus Mass Detector Hardware Manual Thermo Scientific 1 Introduction Data Types Centroid Data Type In the centroid data type the mass spectrum appears as a bar graph as shown in Figure 5 In this data type the Xcalibur data system sums the intensities for each 15 point sampling interval and displays the summed intensities versus the integral center of mass of the sampling interval To increase the scan speed and reduce the disk space requirements use the centroid data type for data acquisition Data processing is also much faster for centroid data Figure 5 Spectrum of pentachlorophenol shown as centroid peak type in full scan 265 100 MCA Data Type The third type of full scan acquisition is MCA shown in Figure 6 Such data can be thought of
153. tific has contracted with one or more recycling or disposal companies in each European Union EU Member State and these companies should dispose of or recycle this product See www thermoscientific com rohsweee for further information on Thermo Fisher Scientific s compliance with these Directives and the recyclers in your country WEEE Konformitat Dieses Produkt muss die EU Waste Electrical amp Electronic Equipment WEEE Richtlinie 2002 96 EC erf llen Das Produkt ist durch folgendes Symbol gekennzeichnet Thermo Fisher Scientific hat Vereinbarungen mit Verwertungs Entsorgungsfirmen in allen EU Mitgliedsstaaten getroffen damit dieses Produkt durch diese Firmen wiederverwertet oder entsorgt werden kann Mehr Information ber die Einhaltung dieser Anweisungen durch Thermo Fisher Scientific ber die Verwerter und weitere Hinweise die n tzlich sind um die Produkte zu identifizieren die unter diese ROHS Anweisung fallen finden sie unter www thermoscientific com rohsweee Thermo SCIENTIFIC 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 Punion europ enne et ce produit devrait tre collect ou recycl par celles ci Davantage d informations sur la conformit de Thermo Fish
154. tine and Preventive Maintenance Maintaining the ESI Probe Figure 46 ESI probe with the capillary retaining nut screwed in finger tight Capillary retaining nut Capillary LLL protruding m ESI probe mount from the ESI J d probe tip tee Y 6 Using the probe clamp tighten the capillary retaining nut by one half turn Do not overtighten the nut Overtightening the nut can cause solvent leakage and it may collapse the ESI capillary 7 Finish reassembling the ESI probe a Place the locking plate and probe clamp in position b Insert the M3 x 10 cap head stainless steel screw part number FM103046 and tighten with the 2 5 mm Allen key c The capillary must protrude from the probe tip In addition to visually checking the protrusion depth of the capillary you can use the ESI spacer plate The ESI spacer plate is 0 64 mm thick If you can see or feel the capillary protruding through the hole in the center of the plate the capillary protrudes from the probe tip by more than 0 64 mm 8 Optional Using the ESI spacer plate confirm that the capillary protrudes from the tip of the probe Figure 47 shows the ESI spacer being used to check the protrusion depth of the capillary 66 MSQ Plus Mass Detector Hardware Manual Thermo Scientific 5 Routine and Preventive Maintenance Maintaining the APCI Probe
155. ugh an LC column under high pressure An autosampler introduces a measured quantity of sample into this solvent stream As the solvent stream passes through the LC column the sample separates into its chemical components The rate at which the components of the sample elute from the column depends on their relative affinities to the liquid mobile phase solvent and the solid particles that make up the column packing As the separated chemical components exit the LC column they pass through a transfer line and enter the MSQ Plus Mass Detector The MSQ Plus Mass Detector consists of an atmospheric pressure ionization API source a transfer lens a mass analyzer and an ion detection system A vacuum manifold encloses part of the API source the M path the transfer lens the mass analyzer and the ion detection system Mass detectors can detect only ionized molecules The MSQ Plus Mass Detector provides two techniques atmospheric pressure chemical ionization APCI and electrospray ESI In APCI mode molecules ionize in the gaseous phase as they enter the API source In ESI mode molecules ionize in the liquid phase before they enter the ion source For both ionization techniques the mass detector can place either a positive or negative charge on the capillary of the API probe at any point in time During a chromatographic run the mass detector can switch the charge applied to the capillary By repelling ions of like charge towards the entrance of t
156. ur system a Turn on the power to the MSQ Plus Mass Detector by turning the MAINS IN switch to the On position 106 MSQ Plus Mass Detector Hardware Manual Thermo Scientific 6 System Shutdown Restarting the System Following a Complete Shutdown b Turn on the power to your LC devices Wait for the LC devices to complete their initialization before proceeding c Turn on the Edwards forepump by setting its power switch to the On position 2 Turn on the data system computer Wait until Windows is running From the Windows desktop double click the Xcalibur icon 3 Pump down the instrument a Right click the Server icon 5 06 pm_ in the system tray of the Windows taskbar and choose Pump from the shortcut menu b Wait for the MSQ Plus Mass Detector to reach high vacuum c When system reaches the appropriate vacuum pressure the server light changes from flashing amber to solid amber Reaching high vacuum takes approximately 10 minutes If the MSQ Plus Mass Detector has not reached vacuum after 30 minutes the server light might still be red or flashing amber See Table 1 on page 19 to check for leaks in the system 4 Open the Tune window by double clicking the Server icon in the system tray of the Windows taskbar 5 If the Per Method Parameters table is not open open it by clicking the Expand icon on the right side of the Tune window as shown in Figure 82 Figure 82 Per Method Parameters table Click to open
157. valve on the Edwards forepump by turning it six rotations counterclockwise 4 Operate the Edwards forepump for approximately 15 minutes with the gas ballast valve open The oil in the oil mist filter returns to the forepump quickly The prescribed time period of 15 minutes for ballasting is for the removal of volatile contaminants such as water 5 After ballasting the forepump for a period of approximately 15 minutes close the gas ballast valve by turning the gas ballast knob clockwise until you feel resistance Note Operating the forepump with the gas ballast valve open increases the rate of oil loss from the pump During normal operations run the forepump with the gas ballast valve closed Emptying the Solvent Waste Bottles Waste solvents are produced by both the MSQ Plus Mass Detector and the LC system In the MSQ Plus Mass Detector waste solvent flows from the drain port at the bottom of the source enclosure out the back of the detector through the exhaust manifold and into a solvent trap Autosamplers such as the Accela Autosampler perform a flush operation after each injection The flush solution drains to a solvent waste bottle Dispose of the solvent waste in accordance with local and federal regulations Thermo Scientific MSQ Plus Mass Detector Hardware Manual 49 Switching Probes This chapter describes how to connect an atmospheric pressure ionization API probe to the MSQ Plus Mass Detector Contents e S
158. vents See Flushing the API Probes on page 47 Replace the capillary if it becomes clogged See Maintaining the ESI Probe on page 56 or Maintaining the APCI Probe on page 67 Clean the probe if it becomes contaminated See Maintaining the ESI Probe on page 56 or Maintaining the APCI Probe on page 67 Drain the oil from the oil mist filter and purge the oil in the forepump as described in Draining the Oil Mist Filter and Purging the Pump Oil on page 48 Monthly Clean the probe heater See Maintaining the Probe Heater on page 74 Check the oil level and color in the rotary pump and add oil if necessary See Maintaining the Forepump on page 95 Refer to the manual that ships with the rotary pump for instructions on changing the oil 3 to 6 months Replace the rotary pump oil after 3000 hours of operation Refer to the manual that ships with the pump gt 6 months Clean the RF dc prefilter See Cleaning the RF dc Prefilter on page 87 Perform maintenance of the turbo pump every two years Maintaining the ESI Probe Flushing the probe on a regular basis helps to prevent contamination and blockage of its capillary But even with the best preventive maintenance occasionally the capillary can become blocked and the internal components can become contaminated A significant increase in LC pump backpressure that is up to 300 psi at a flow rate of 1 mL min
159. w Take the system out of Operate mode by clicking the Operate toggle button and then turn off the nitrogen gas by clicking the Nitrogen Gas toggle button Wait for the source block and the probe heater of the mass detector to cool Unscrew and remove the PEEK fingertight fitting shown in Figure 35 from the ESI probe MSQ Plus Mass Detector Hardware Manual 57 5 Routine and Preventive Maintenance Maintaining the ESI Probe Figure 35 ESI probe installed in the probe heater PEEK fingertight fitting Locking plate in locked position Probe heater CAUTION Because its capillary tip and ceramic sleeve are fragile exercise care when you remove the ESI probe from the probe heater 5 Turn the locking plate clockwise to the open position and then carefully remove the ESI probe from the probe heater See Figure 36 Figure 36 Removing the ESI probe from the probe heater Co gt Locking plate in open position A Probe heater e y e gt S a Source housing 58 MSQ Plus Mass Detector Hardware Manual Thermo Scientific 5 Routine and Preventive Maintenance Maintaining the ESI Probe Removing the ESI Capillary To clean or replace the ESI capillary or to replace the ceramic sleeve you must remove the ESI capillary from the probe See Figure 86 on page 121 for the part numbers of the ESI
160. ware 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 get local contact information for sales or service Go to www thermoscientific com wps portal ts contactus MSQ Plus Mass Detector Hardware Manual xix To copy manuals from the Internet Go to mssupport thermo com agree to the Terms and Conditions and then click Customer Manuals in the left margin of the window To suggest changes to documentation or to Help e Fill out a reader survey online at www surveymonkey com s PQM6P62 e Send an e mail message to the Technical Publications Editor at techpubs lcms thermofisher com Introduction The MSQ Plus Mass Detector is an advanced analytical instrument that includes a mass detector forepump data system and an optional cone wash pump Integrated with an LC system the MSQ Plus Mass Detector provides the separation capability of an HPLC and the detection capability of a single quadrupole mass detector See Figure 1 Contents e Overview e Jon Polarity Modes e Ionization Techniques e Scan Types e Data Types Figure 1 MSQ Plus Mass Detector and the Accela LC system Thermo Scientific MSQ Plus Mass Detector Hardware Manual 1 1 Introduction Overview Overview In a typical LC MS analysis an analytical pump pushes solvent thro
161. wash nozzle P N FM102521 Es Plug sealing P N FM102277 O ring 3 0 mm ID x 1 0 mm THK P N 5711933 O ring BS225 47 2 mm ID x 3 5 mm THK P N FM 103048 ox O Exit cone P N FM102263 ei La BS014 12 42 mm ID x 1 78 mm THK P N FM101522 Hexapole screw insulator P N FM102248 O ring 9 0 mm ID x 3 0 mm THK Plug source P N 00107 01 0026 block sealing P N FM101460 0 ring BS207 13 87 mm ID x 3 53 mm THK P N FM101417 Circlip provided in MSQ Plus Hardware and O ring Kit part number 60111 62018 Thermo Scientific MSQ Plus Mass Detector Hardware Manual 119 Spares 7 Replaceable Parts Spares ESI Probe Assembly Table 12 lists the parts in the ESI probe assembly Table 12 ESI probe assembly parts Item Part number Assembly ESI probe FM102595 ESI probe capillary FM102598 ESI ceramic sleeve FM103394 Ferrule GVF 16 graphite Vespel 6070119 O ring 9 25 mm ID x 1 78 mm THK BS012 FM100231 BLK Viton O ring 5 28 mm ID x 1 78 mm THK BS009 5711020 BLK Viton PEEK tube insert FM102591 Screw M3 x 8 cap head stainless steel N A Screw M3 x 10 cap head stainless steel FM103046 Capillary retaining nut FM102590 Figure 86 shows an exploded view of the ESI probe assembly 120 MSQ Plus Mass Detector Hardware Manual Thermo Scientific Figure 86 Exploded view of ESI probe assembly O ring BS009 P N 5711020 ESI ceramic mount ESI capillary P N FM10259
162. witching from ESI to APCI e Switching from APCI to ESI Switching from ESI to APCI Follow these steps to connect an APCI probe to the MSQ Plus Mass Detector To switch from ESI mode to APCI mode CAUTION Allow the probe heater to cool before you remove the ESI probe 1 Turn off the LC pump flow If you are using the cone wash pump turn it off 2 Turn the nitrogen gas ion optics and probe heater off by doing one of the following e From the Status page in the Information view in the Xcalibur data system right click the MSQ Plus listing to display a shortcut menu and choose Turn Device Off from the menu or e Open the Per Method Parameters table in the Tune window Take the system out of Operate mode by clicking the Operate On Off toggle button and then turn off the nitrogen gas by clicking the Nitrogen Gas On Off toggle button 3 Allow the probe heater to cool 4 Unscrew and remove the PEEK fingertight fitting from the ESI probe Thermo Scientific MSQ Plus Mass Detector Hardware Manual 51 4 Switching Probes Switching from ESI to APC 5 Turn the locking plate on the ESI probe clockwise to the open position Then pull the ESI probe out of the probe heater 6 Remove the APCI probe from the holder located in the door of the MSQ Plus Mass Detector and replace it with the ESI probe CAUTION Take care not to damage the capillary of the probe as you insert the APCI probe into the probe heater 7 Turn the loc
163. with and maintaining your MSQ Plus Mass Detector The parts are categorized as follows e Consumables Keep a stock of each of these parts because you might need to replace them frequently e Spares You can order these parts as required e Connection Kits Use these interface kits to connect an LC system to your mass detector You do not need an interface kit to connect an Accela LC to your MSQ Plus Mass Detector The manuals for the MSQ Plus Mass Detector are provided on the software DVD Contents e Consumables e Spares e Connection Kits e Manuals Consumables The MSQ Plus Annual Maintenance kit part number 60111 62014 contains all the consumables required for the upkeep of your MSQ Plus Mass Detector The parts contained in this kit are listed in Table 6 Table 6 Parts in the MSQ Plus Annual Maintenance Kit Sheet 1 of 3 Item Part number MSO Plus Annual Maintenance kit 60111 62014 Adapter capillary retainer nut FM102590 APCI probe capillary 3 each FM102594 Thermo Scientific MSQ Plus Mass Detector Hardware Manual 111 7 Replaceable Parts Consumables Table 6 Parts in the MSQ Plus Annual Maintenance Kit Sheet 2 of 3 Item Part number Entrance skimmer assembly titanium 1 each 60111 60049 ESI probe capillary 3 each FM102598 ESI ceramic sleeve 1 each FM103394 Exit cone extraction cone 1 each FM102263 Ferrule SGE 1 16 graphite Vespel 10 per 6070119 package Kit hardware
164. ystem in the Off Mode Figure 80 Shortcut menu for the MSQ Plus Mass Detector on the Status page of the Information view Status Acquisition Queue Run Manager Ready To Download Sequence Sample Name Working On Position Raw File Inst Method Accela AS Ready to Download Accela Pump Stand By IEE Turn Device On Turn Device into Standby Turing off el the mass detector Turning Off the Mass Detector from the Tune Window Another way to turn off the MSQ Plus Mass Detector is to use the Tune window To turn off the MSO Plus Mass Detector from the Tune window 1 If you are using the optional cone wash pump turn it off by turning its power switch to the Off position 2 Turn off the flow from the LC pump e Ifyour LC pump is controlled from the Xcalibur data system turn it off from its respective Direct Control dialog box or place it in the Standby mode from the Status page of the Information view or e Ifyour LC pump is not controlled from the Xcalibur data system turn it off from its keypad control panel 3 If the Tune window is not open open it a Double click the Tune icon fl on the Windows desktop The Server icon appears in the Windows taskbar b Double click the Server icon to open the Tune window 4 If the Per Method Parameters table is not open open it by clicking the Expand icon on the right side of the Tune window Thermo Scientific MSQ Plus Mass

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