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Thermo Finnigan LTQ, Hardware Manual

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Summary of Contents for Finnigan LTQ

Page 1: ...Finnigan LTQ Hardware Manual 97055 97013 Revision B ...

Page 2: ...icio Sertram Planta 2 Modulo 3 ES 08038 Barcelona 34 093 223 0918 Sweden Pyramidbacken 3 S 141 75 Kungens Kurva Stockholm 46 08 556 468 00 United Kingdom Stafford House 1 Boundary Park Boundary Way Hemel Hempstead Hertfordshire HP2 7GE 44 01442 233 555 U S A 355 River Oaks Parkway San Jose CA 95134 1991 1 408 965 6000 Notes The country code is enclosed in square brackets The city code or area code...

Page 3: ...st Doc Clinical Toxicology Government lab Group Manager Drug Metabolism and Pharmacokinetics Medical Diagnostic lab Laboratory Manager Drug Discovery Pharmaceutical Manufacturing lab Purchasing Agent Environmental Research and Development lab Project Manager Pharmaceutical Research Institute Scientist Technical Expert Proteomics University College lab User Technician Research Veterinary lab Other ...

Page 4: ...AL PUBLICATIONS THERMO ELECTRON SAN JOSE 355 RIVER OAKS PARKWAY SAN JOSE CA 95134 1991 UNITED STATES OF AMERICA From _______________________________ ____________________________________ ____________________________________ fold fold ...

Page 5: ...hould be ordered from Thermo Electron or one of its authorized representatives FCC Compliance Statement Note This equipment has been tested and found to comply with the limits for a Class A digital device pursuant to part 15 of the FCC rules These limits are designed to provide reasonable protection against harmful interference when the equipment is operated in a commercial environment This equipm...

Page 6: ...an Jose instrument requires a team effort for lifting and or moving the instrument This instrument is too heavy and or bulky for one person alone to handle safely Notice on the Proper Use of Thermo Electron San Jose Instruments In compliance with international regulations If this instrument is used in a manner not specified by Thermo Electron San Jose the protection provided by the instrument coul...

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Page 9: ...ron Produkte zu identifizieren die unter diese RoHS Anweisung fallen finden Sie unter www thermo com WEEERoHS WEEE Compliance This product is required to comply with the European Union s Waste Electrical Electronic Equipment WEEE Directive 2002 96 EC It is marked with the following symbol Thermo Electron has contracted with one or more recycling disposal companies in each EU Member State and this ...

Page 10: ...plusieurs compagnies de recyclage dans chaque état membre de l union européenne et ce produit devrait être collecté ou recyclé par celles ci Davantage d informations sur la conformité de Thermo Electron à ces directives les recycleurs dans votre pays et les informations sur les produits Thermo Electron qui peuvent aider la détection des substances sujettes à la directive RoHS sont disponibles sur ...

Page 11: ...afety Precautions xvi Solvent and Gas Purity Requirements xviii Service Philosophy xix Level of Repair xix Reply Cards xx Introduction 1 1 1 1 Ion Polarity Modes 1 3 1 2 Ionization Techniques 1 4 Electrospray Ionization 1 4 Atmospheric Pressure Chemical Ionization 1 7 Atmospheric Pressure Photoionization 1 10 Nanospray Ionization 1 12 1 3 Scan Power and Scan Modes 1 13 MS Scan Mode 1 13 MS MS Scan...

Page 12: ...tor 2 7 Controls and Indicators 2 7 API Source 2 10 Ion Optics 2 15 Mass Analyzer 2 16 Ion Detection Systems 2 21 Vacuum System and Inlet Gasses Hardware 2 23 Cooling Fans 2 31 Electronic Assemblies 2 32 2 6 Data System 2 39 Computer Hardware 2 39 Data System MS Detector LC Interface 2 40 Data System Local Area Network Interface 2 41 Printer 2 42 Daily Operation 3 1 3 1 Things to Do Before Operati...

Page 13: ...plies 4 5 4 2 Frequency of Cleaning 4 6 4 3 API Source Maintenance 4 7 Flushing the Sample Transfer Line Sample Tube and API Probe 4 7 Flushing the Ion Sweep Cone and Ion Transfer Capillary 4 7 Removing and Cleaning the Ion Transfer Capillary 4 8 Maintaining the API Probes 4 10 Maintaining the PhotoMate Light Source 4 11 Maintaining the Ion Source Interface 4 11 4 4 Cleaning the Q00 Ion Guide 4 22...

Page 14: ... Multiplier 4 39 4 8 Replacing the Turbomolecular Pump Insert 4 43 4 9 Cleaning the Fan Filter 4 44 System Shutdown Startup and Reset 5 1 5 1 Shutting Down the System in an Emergency 5 2 5 2 Placing the System in Standby Condition 5 3 5 3 Shutting Down the System Completely 5 4 5 4 Starting Up the System after a Complete Shutdown 5 6 Starting Up the LC 5 6 Starting Up the Data System 5 6 Starting ...

Page 15: ...placeable Parts 7 1 7 1 MS Detector 7 2 ESI Source 7 3 APCI Source 7 6 Ion Source Interface 7 8 Q00 Ion Guide 7 10 Q0 and Q1 Ion Guides 7 11 Mass Analyzer 7 12 Electron Multiplier 7 12 Coil Module 7 12 Divert Inject Valve 7 12 Syringe Pump 7 12 Turbomolecular Pump 7 12 Forepump 7 12 Pressure Gauges 7 12 Vacuum Accessories 7 13 Vacuum Manifold O Rings 7 13 Vent Valve 7 16 Power Supplies 7 16 Printe...

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Page 17: ...stem Chapter 2 Functional Description describes the principal components of your LTQ system and their respective functions Chapter 3 Daily Operation describes the checks and cleaning procedures of the LTQ system that you should perform every day before you begin your first analysis and after your final analysis Chapter 4 MS detector Maintenance outlines the maintenance procedures that you should p...

Page 18: ... Manual _______________________ Changes to the Manual and Online Help To suggest changes to this manual or the online Help please send your comments to Editor Technical Publications Thermo Electron San Jose 355 River Oaks Parkway San Jose CA 95134 1991 U S A You are encouraged to report errors or omissions in the text or index Thank you ...

Page 19: ...ic pressure ionization ASCII American Standard Code for Information Interchange b bit B byte 8 b baud rate data transmission speed in events per second C degrees Celsius CD compact disc CD ROM compact disc read only memory cfm cubic feet per minute CI chemical ionization CIP carriage and insurance paid to cm centimeter cm3 cubic centimeter CPU central processing unit of a computer CRC cyclic redun...

Page 20: ...rd ft foot FTP file transfer protocol g gram G giga 109 GC gas chromatograph gas chromatography GC MS gas chromatograph MS detector GND electrical ground GPIB general purpose interface bus GUI graphical user interface h hour h height HPLC high performance liquid chromatograph HV high voltage Hz hertz cycles per second ICIS Interactive Chemical Information System ICL Instrument Control Language ID ...

Page 21: ...micro 10 6 m meter m milli 10 3 M mega 106 M molecular ion MB Megabyte 1048576 bytes MH protonated molecular ion min minute mL milliliter mm millimeter MS MS detector mass spectrometry MS MSn power where n 1 MS MS MSn power where n 2 MSn MSn power where n 1 through 10 m z mass to charge ratio n nano 10 9 NCBI National Center for Biotechnology Information USA NIST National Institute of Standards an...

Page 22: ...selected reaction monitoring SSQ single stage quadrupole TCP IP transmission control protocol Internet protocol TIC total ion current Torr torr TSQ triple stage quadrupole u atomic mass unit URL uniform resource locator V volt V ac volts alternating current V dc volts direct current vol volume w width W watt WWW World Wide Web Note Exponents are written as superscripts In the corresponding online ...

Page 23: ...itial letter of each word and by italicizing each word Input that you enter by keyboard is represented in bold face letters Titles of topics chapters and manuals also appear in bold face letters For brevity expressions such as choose File Directories are used rather than pull down the File menu and choose Directories Any command enclosed in angle brackets represents a single keystroke For example ...

Page 24: ...ou might need if you are having trouble Tip helpful information that can make a task easier Important critical information that can affect the quality of your data Caution information necessary to protect your instrument from damage CAUTION hazards to human beings Each CAUTION is accompanied by a CAUTION symbol Each hardware manual has a blue CAUTION sheet that lists the CAUTION symbols and their ...

Page 25: ...ns _________________________ Finnigan LTQ Hardware Manual______________________ xv 5IFSNP 530 03103 5 0 Topic Headings The following headings are used to show the organization of topics within a chapter Chapter 1 Chapter Name 1 2 Second Level Topics Third Level Topics Fourth Level Topics Fifth Level Topics ...

Page 26: ...APCI vaporizer might be very hot and might cause severe burns if they are touched Allow heated components to cool before you service them Place the MS Detector in Standby or Off Before You Open the Atmospheric Pressure Ionization API Source The presence of atmospheric oxygen in the API source when the MS detector is On could be unsafe LTQ automatically turns the MS detector Off when you open the A...

Page 27: ...minated if the API source drain tube and the blue forepump exhaust tubing are connected to the same fume exhaust system Your laboratory must be equipped with at least two fume exhaust systems Route the blue forepump exhaust tubing to a dedicated fume exhaust system Route the PVC drain tube from the API source to the waste container Vent the waste container to a dedicated fume exhaust system Use Ca...

Page 28: ...ed Deionized water contains chemicals and is not recommended The following is a list of international sources that can supply high quality solvents The LTQ MS detector uses helium as a collision gas The helium should be high purity 99 995 The required gas pressure is 135 70 kPa 20 10 psig Thermo Electron has found that particulate filters are often contaminated and are therefore not recommended Th...

Page 29: ...e the life of the system maximize the up time of your system and allow you to achieve optimum system performance Service not described in this manual should be performed only by a Thermo Electron Customer Support Engineer or similarly trained and qualified technical personnel Level of Repair Thermo Electron s service philosophy for the LTQ system calls for troubleshooting to the lowest part assemb...

Page 30: ...nctions First when you return the card you are placed on the Thermo Electron San Jose mailing list As a member of this list you receive application reports and technical reports in your area of interest and you are notified of events of interest such as user meetings Second it allows you to tell us what you like and do not like about the manual The Change of Location card allows us to track the wh...

Page 31: ... pump direct infusion Using the divert inject valve fitted with a sample loop and LC flow injection analysis Using the divert inject valve and HPLC fitted with a column LC MS In analysis by LC MS a sample is injected onto an LC column The sample is then separated into its various components The components elute from the LC column and pass into the MS detector where they are analyzed Analysis by di...

Page 32: ... analyzer The function of these lenses is controlled by an automatic gain control AGC that sets them to transmit the optimum number of ions to the mass analyzer The mass to charge ratios of the ions produced in the API source are measured by the mass analyzer Selected ions are ejected from the mass analyzer and reach the ion detection system where they produce a signal The signal produced is then ...

Page 33: ...the mass analyzer for mass analysis by changing the polarity of the potentials applied to the API source and ion optics The ion optics are located between the API source and the mass analyzer The information obtained from a positive ion mass spectrum is different from and complementary to that obtained from a negative ion spectrum Thus the ability to obtain both positive ion and negative ion mass ...

Page 34: ...for mass analysis for example heat labile compounds or high molecular weight compounds can be analyzed by the use of ESI ESI can be used to analyze Note Because APCI ESI APPI and NSI use the same ion source interface that is the portion of the API source that is under vacuum you can switch between these three ionization techniques in just a few minutes Switching ionization techniques merely involv...

Page 35: ...dle sprays the sample solution into a fine mist of droplets that are electrically charged at their surface 3 The electrical charge density at the surface of the droplets increases as solvent evaporates from the droplets 4 The electrical charge density at the surface of the droplets increases to a critical point known as the Rayleigh stability limit At this critical point the droplets divide into s...

Page 36: ...ely charged needle is used to analyze negative ions 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 In ESI the buffer and the buffer strength both have a noticeable effect on sensitivity Therefore it is important to choose these variables correctly In the case of h...

Page 37: ...t system Atmospheric Pressure Chemical Ionization Atmospheric pressure chemical ionization APCI is a soft ionization technique APCI is used to analyze nonpolar compounds and compounds of medium polarity that are relatively low in molecular weight and have some volatility In APCI ions are produced and analyzed as follows 1 The APCI nozzle sprays the sample solution into a fine mist of droplets 2 Th...

Page 38: ...ion formation are shown below Primary ion formation e N2 N2 2e Secondary ion formation N2 H2O N2 H2O H2O H2O H3O HO Proton transfer H3O M M H H2O In negative ion mode M H is typically formed by the abstraction of a proton by OH APCI is typically used to analyze small molecules with molecular weights up to about 2000 u APCI is a very robust ionization technique It is not affected by minor changes i...

Page 39: ...n positive ions Although in general fewer negative ions are produced than positive ions negative ion polarity is sometimes the mode of choice This is because the negative ion polarity mode sometimes generates less chemical noise than does the positive mode Thus selectivity might be better in the negative ion mode than in the positive ion mode Figure 1 4 APCI process in the positive ion polarity mo...

Page 40: ...nteracts with the light from the PhotoMate light source The analyte molecule M is ionized to a molecular ion M if the ionization potential of the analyte is less than the photon energy hν M hν M 4 In the presence of protic solvents the analyte ion may extract a hydrogen to form an MH ion M S MH S H 5 The analyte ions pass through the ion transfer capillary enter the MS detector and are analyzed Mo...

Page 41: ...ration of selective photoionization Photoionization Gases in air solvent molecules Fragment ion thresholds Molecular ion thresholds Drugs and other compounds Energy Photoionization hν Threshold H2O CO2 O2 N2 Drugs Steroids MeOH AcCN Chlorinated solvents Ionized Not Ionized Agricultural compounds Threshold H2O CO2 O2 N2 Drugs Drugs Steroids MeOH AcCN Chlorinated solvents Ionized Not Ionized Agricul...

Page 42: ... of typical compounds and solvents Nanospray Ionization Nanospray ionization NSI is a technique for performing electrospray ionization on amounts of liquid as small as 1 µL for time periods of greater than 30 min Stable mass spectra can be obtained for very small amounts of biomolecules such as proteins peptides oligonucleotides and oligosaccharides For more information on NSI refer to the manual ...

Page 43: ... n 1 and n 10 The higher the scan power the more structural information is obtained about the analyte The scan powers supported by LTQ in its standard configuration are as follows MS scan mode n 1 MS MS scan mode n 2 MSn scan mode n 3 to 10 MS Scan Mode The MS or mass spectrometry scan mode corresponds to a single stage of mass analysis that is a scan power of n 1 The MS scan mode involves only pa...

Page 44: ...udes the following Single stage full scan Two stage full scan Single Stage Full Scan The single stage full scan type has one stage of mass analysis n 1 scan power With single stage full scan type the ions formed in the ion source are stored in the mass analyzer Then these ions are sequentially scanned out of the mass analyzer to produce a full mass spectrum Single stage full scan experiments can b...

Page 45: ...oduct reaction you are looking for before you can perform an experiment Thus for SRM you might use one stage full scan type to determine the parent mass spectrum and two stage full scan type to determine the product mass spectra for parent ions of interest Then you might use SRM to do routine quantitative analysis of the compound Selected Ion Monitoring Selected ion monitoring SIM is a single stag...

Page 46: ...ry rapid analysis of trace components in complex mixtures However because you are monitoring pairs of ions one product ion for each parent ion the specificity obtained in SRM can be much greater than that obtained in SIM Thus you are very unlikely to get a false positive result with SRM To get a false positive result the interfering compound must do the following First it must form a parent ion of...

Page 47: ...eases as the number of consecutive reactions that you monitor increases However the sensitivity decreases as the number of consecutive reactions that you monitor increases especially if there are many fragmentation pathways available to the ion ZoomScan The determination of the mass of an ion from its mass to charge ratio may be complicated by the fact that the charge state of the ion may be unkno...

Page 48: ...ing intervals The intensity at each sampling interval is displayed with the intensities connected by a continuous line In general the profile scan data type is used when you tune and calibrate the MS detector so that you can easily see and measure mass resolution Centroid Data Type In the centroid data type the mass spectrum is displayed as a bar graph In this scan data type the intensities of eac...

Page 49: ...of your analyte s of interest In a General MS MS quantitation experiment you need to specify a parent precursor ion that fragments into distinctive product ions In a General MSn quantitation experiment you need to specify the mass to charge ratios of all the parent ions of interest The LTQ can then collect data on the ions in the range or on the product ions of the parent ion s that you specify If...

Page 50: ...n the experiment should be to collect even more data For example in a Data Dependent Triple Play experiment for a mixture of compounds the LTQ can decide which parent ion to isolate the charge state of the parent ion and the molecular weight of the compound Ion Mapping experiments can be Data Dependent The Total Ion Map Neutral Loss Ion Map and Parent Ion Map experiments are not Data Dependent The...

Page 51: ...ollowing Identify low level impurities in high purity compounds Data Dependent MS MS Identify metabolites in a complex mixture Chromatographic Separation with Data Dependent MS MS Build a custom library of composite MSn spectra Ion Tree You can use a Data Dependent MSn experiment to identify process impurities In the quality assurance process for aspirin for example the LTQ can identify impurities...

Page 52: ...ng you can get product ion scans on every parent ion However a Neutral Loss Ion Map identifies which parent ions lost a neutral fragment of a particular mass For example you can specify a neutral loss of 80 u as in the case of a phosphorylated peptide in a tryptic digest A Neutral Loss Ion Mapping experiment can step through each product mass in the mixture The experiment searches for evidence of ...

Page 53: ...um the LTQ selects and fragments the most intense ion of the MS MS spectrum This results in an MS3 spectrum the level specified as the maximum depth for this example The LTQ then backs up one level and fragments the second most intense ion of the MS MS spectrum creating more product ions on the level of MS3 from this parent ion This process is then repeated for the second most intense ion in the M...

Page 54: ......

Page 55: ...tted with a loop and an LC flow injection analysis Using a divert inject valve and LC fitted with a column LC MS In analysis by LC MS a sample is injected onto an LC column The sample is then separated into its various components The components elute from the LC column and pass into the MS detector where they are analyzed Upon entering the API source sample molecules are ionized by electrospray io...

Page 56: ..._________ Finnigan LTQ Hardware Manual _______________________ Figure 2 1 Functional block diagram of the LTQ system The broad single headed arrows represent the flow of sample molecules through the instrument The narrow double headed arrows represent electrical connections ...

Page 57: ...iate instrument button in the Instrument Configuration window which is available by choosing Start Programs Xcalibur Instrument Configuration Refer to the Xcalibur online Help for a description of Instrument Configuration You can also set up monitor and control the autosampler from the data system computer from the Instrument Setup window which is available by choosing Start Programs Xcalibur Xcal...

Page 58: ...LC TSP P2000 TSP P4000 and Agilent 1100 LCs and the corresponding UV detectors can be controlled directly from the LTQ data system computer Refer to Finnigan LTQ Getting Connected for information on connecting an LC to the LTQ You can configure the Xcalibur data system for your LC and UV detector from the data system computer You specify the model name and model number by selecting the appropriate...

Page 59: ... into the sample transfer line as the plunger is depressed The syringe is held in place by a syringe holder Refer to Finnigan LTQ Getting Started for instructions on setting up the syringe pump You can start and stop the syringe pump from the Syringe Pump dialog box which can be reached from the Tune Plus window which is available by choosing Start Programs Xcalibur LTQ Tune You can also specify t...

Page 60: ...ing Connected You can control the divert inject valve from the data system You specify the parameters of the divert inject valve in the Divert Inject Valve dialog box which can be reached from the Tune Plus window or the Divert Valve page which can be reached from the Instrument Setup window Refer to the online Help for instructions on operating the divert inject valve from the data system You can...

Page 61: ...MS MS MS and MSn scan modes Full scan SIM SRM CRM and ZoomScan scan types Data Dependent Ion Mapping and Ion Tree experiments The MS detector includes the following components Controls and indicators API source Ion optics Mass analyzer Ion detection system Vacuum system and inlet gasses hardware Cooling fans Electronic assemblies Controls and Indicators Five light emitting diodes LEDs are located ...

Page 62: ...ty interlock switch on the API source is depressed that is the door on the Ion Max ion source is closed If the LED labeled Vacuum is not illuminated high voltage is not applied to LTQ components The LED labeled Communication is illuminated yellow when the MS detector and the data system are trying to establish a communication link The Communication LED is illuminated green when the communication l...

Page 63: ... circuit breaker switch labeled Main Power is located on the power panel which is located at the lower right corner of the right side panel of the MS detector See Figure 2 6 In the Off O position the circuit breaker removes all power to the MS detector including the vacuum pumps In the On position power is supplied to the MS detector In the standard operational mode the circuit breaker is kept in ...

Page 64: ...ation on resetting the MS detector API Source 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 interface between the LC and the MS detector You can operate the API source using either the electrospray ionization ESI atmospheric pressure chemical ionization APCI atmospheric pressure phot...

Page 65: ... by the ion optics into the mass analyzer where they are separated according to their mass to charge ratio The Ion Max ion source housing allows you to quickly switch between ionization modes without the need for specialized tools The ventilation of the ion source housing ensures that the housing is always cool and easy to handle Pressure in the ion source housing is kept at atmospheric levels whi...

Page 66: ...sensor vent prevent ball ion sweep cone tube lens and skimmer See Figure 2 8 and Figure 2 9 The ion transfer capillary assists in desolvating ions that are produced by ESI APCI NSI or APPI The capillary is an elongated 2 5 in cylindrical tube made of metal that has a hole bored through the center of its long axis Two heater cartridges are embedded in the heater block The heater block surrounds the...

Page 67: ... the skimmer When you tune the LTQ you adjust the tube lens offset voltage to maximize sensitivity by balancing desolvation with fragmentation Ions from the tube lens pass through the skimmer and move toward the Q00 quadrupole The skimmer acts as a vacuum baffle between the higher pressure ion source interface region at 1 Torr and the lower pressure Q00 ion guide region at 50 mTorr of the vacuum m...

Page 68: ...FSNP 530 03103 5 0 2 14 ______________________________________ Finnigan LTQ Hardware Manual_________________________________________________ Figure 2 9 Internal under vacuum components of the MS detector ...

Page 69: ...will increase the translational kinetic energy of the ions Typical values of the Q00 offset voltage are 4 V to 4 V The lens L0 is a metal cylinder with a small hole in one end through which the ion beam can pass A potential of between 0 and 5 V negative for positive ions and positive for negative ions is applied to lens L0 to aid in ion transmission Lens L0 also acts as a vacuum baffle between the...

Page 70: ...yzer The mass analyzer is the site of mass analysis that is ion storage ion isolation collision induced dissociation and ion scan out This section describes the components of the mass analyzer the voltages applied to the mass analyzer electrodes the presence of helium damping gas in the mass analyzer cavity and the operation of the mass analyzer during mass analysis Components of the Mass Analyzer...

Page 71: ...analysis LTQ applies a potential of 14 V to the center rod section during both ion storage and mass analysis For negatively charged ions the polarity of the dc axial trapping voltages are reversed Main RF Voltage In each quadrupole rod section rods opposite each other in the array are connected electrically Ac voltages are applied to the rods and these voltages are ramped during the scan Voltages ...

Page 72: ...Waveform Voltage Resonance Excitation RF Voltage and Resonance Ejection RF Voltage Applied to the Exit Rods The ion isolation waveform voltage resonance excitation RF voltage and resonance ejection RF voltage are ac voltages that are applied to the exit rods to stimulate motion of the ions in the direction of the ion detection system The voltages applied to the exit rods are equal in amplitude but...

Page 73: ...er cavity contains helium that is used as a damping gas and a collision activation partner The helium damping gas enters the mass analyzer cavity through a gap between the quadrupole rods The flow of gas 1 mL min into the mass analyzer cavity is regulated by a pressure regulator and a capillary restrictor The flow of gas out of the mass analyzer cavity and into the turbomolecular pump is restricte...

Page 74: ... source are trapped in the mass analyzer if the ions have mass to charge ratios greater than the minimum storage mass to charge ratio Next for SIM SRM CRM or MSn n 1 full scan the ion isolation waveform voltage is applied to the exit rods in combination with a ramp of the main RF voltage to a new storage voltage to eject all ions except those of the selected mass to charge ratio Then for SRM CRM o...

Page 75: ...cles 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 The electron multiplier is mounted on the top cover plate of the vacuum manifold next to the mass analyzer See Figure 2 11 and Figure 2 1...

Page 76: ...oportional to the number of secondary particles striking the cathode Typically the electron multiplier is set to a gain of about 3 105 i e for each ion or electron that enters 3 105 electrons exit The current that leaves the electron multiplier via the anode is converted to a voltage by the electrometer circuit and recorded by the data system Refer to the topic Ion Detection System Electronic Asse...

Page 77: ...re produced The increase in conversion efficiency is more pronounced for more massive ions than for less massive ions 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 reduced Vacuum System and Inlet Gas...

Page 78: ... sweep gas and air during venting into the MS detector The inlet gasses hardware includes the following components Vent gas valve Damping gas inlet assembly Sheath gas valve Auxiliary gas valve Sweep gas valve A functional block diagram of the vacuum system and inlet gasses hardware is shown in Figure 2 13 Figure 2 12 Vacuum manifold with top cover plate and turbomolecular pump Turbomolecular Pump...

Page 79: ...cuated to 50 mTorr by the third inlet in the molecular drag section of the triple inlet turbomolecular vacuum pump The region inside the third chamber called the Q0 ion guide region is evacuated to 1 mTorr by the interstage port of the turbomolecular vacuum pump The region inside the fourth chamber called the analyzer region is evacuated to less than 10 5 Torr by the high vacuum port of the turbom...

Page 80: ...e ion gauge The removable top cover plate of the vacuum manifold holds the Q0 and Q1 ion guides mass analyzer and two electron multipliers one part of the ion detection system Thus removal of the top cover plate allows easy access to these assemblies Two handles on the top and four guide posts on the underside of the top cover plate facilitate its removal and installation An electrically conductiv...

Page 81: ...gh the top cover plate Two 4 pin and two 8 pin feedthroughs for the RF and DC voltages for the ion optics Two feedthroughs for the high voltage for the cathodes of the electron multipliers A feedthrough for the ion current signal from the dual anode of the electron multipliers Figure 2 15 Top cover plate of the vacuum manifold topside 4 Pin Feedthroughs 8 Pin Feedthroughs Electron Multiplier High ...

Page 82: ...mp mounts onto the bottom of the vacuum manifold The turbomolecular pump has three pumping inlets see Figure 2 17 A 400 L s high vacuum inlet at the top of the rotor stack which evacuates the analyzer chamber An 300 L s interstage inlet about half way down the rotor stack which evacuates the Q0 ion guide chamber A 25 L s third inlet in the molecular drag section of the pump which evacuates the Q00...

Page 83: ...ower to and control of the turbomolecular pump The turbomolecular pump status temperature rotational speed etc is sent from the Turbomolecular Pump Controller to the embedded computer over a serial line Power to the turbomolecular pump is shut off if the foreline pressure as measured by the Convectron gauge is too high or if the turbomolecular temperature is too high Forepump An Edwards E2M30 fore...

Page 84: ... 342 mini ion gauge The ion gauge produces energetic electrons that cause the ionization of molecules in the ion gauge Positive ions formed in the ion gauge are attracted to a collector The collector current is related to the pressure in the vacuum manifold The ion gauge is also involved in vacuum protection Vent Valve The vent valve allows the vacuum manifold to be vented to air that has been fil...

Page 85: ...itrogen gas of the API probe that sprays nebulizes the sample solution into a fine mist as it exits the sample tube The auxiliary gas is the outer coaxial nitrogen gas that assists the sheath gas in the nebulization and evaporation of sample solutions The Sweep gas flows out from behind the sweep cone in the ion source interface Sweep gas aids in solvent declustering and adduct reduction Dry nitro...

Page 86: ...e power filters it and provides it to various components of the MS detector The Power Entry Module includes the following components Main power circuit breaker switch Line filter Electronics service switch Interlock PCB A functional block diagram of the Power Entry Module and MS detector power distribution is shown in Figure 2 18 Line power 230 V ac 10 15 A 50 60 Hz single phase enters the power p...

Page 87: ... Interlock PCB and distributes it to the 300 V power supply the 8 KV power supply and the conversion dynode electron multiplier power supply Power supply PS1 provides 5 V dc 15 V dc for analog and digital circuits and 60 V dc for the heater that heats the ion transfer capillary Power supply PS2 provides 24 V dc for the turbomolecular pump fans vent valve divert inject valve syringe pump 8 KV power...

Page 88: ...ERVICE 220 V ac 220 V ac 24 36 28 V POWER SUPPLY PS2 300 V POWER SUPPLY INTRLK 24 V 300 150 V SOURCE PCB 5 15 V 60 24 V ION GAUGE GAS FLOW VALVES DIVERT INJECT VALVE SYRINGE PUMP SERVICE 220 V ac 220 V ac 220 V ac 220 V ac 220 V ac 15 V 24 V 24 V 15 V 180 V 8 KV POWER SUPPLY INTRLK 24 V 0 TO 8 KV API SOURCE SERVICE INTRLK 220 V ac 24 V FANS VENT VALVE TURBOMOLECULAR PUMP INTRLK 24 V CONVERSION DYN...

Page 89: ...e divert inject valve control circuit controls and monitors the divert inject valve The API source control circuit controls and monitors the high voltage that is applied to the ESI needle the APCI corona discharge needle and the NSI capillary The electron multiplier control circuit sends a signal to the electron multiplier power supply that is proportional to the voltage to be applied to the elect...

Page 90: ...or more of the following conditions arise The pressure in the ion transfer capillary skimmer region is above 3 Torr The pressure in the analyzer region is above 5 10 4 Torr The high voltage safety interlock switch on the API source is open that is the door to the Ion Max ion source is open The LED labeled Vacuum on the front panel of the LTQ is illuminated green whenever the vacuum protection circ...

Page 91: ... the mass analyzer The RF voltage detector senses the 0 to 10 000 V RF voltage signal applied to the rods of the mass analyzer and converts this sensed signal into a 0 to 10 V dc output signal The integrating amplifier also called an error amplifier produces the 0 to 10 V dc RF modulation signal that is used by the RF Voltage Amplifier PCB The magnitude of the RF modulation signal is proportional ...

Page 92: ...ltage to the cathodes of the electron multipliers The high voltage set control signal for the electron multiplier power supply comes from the Analog PCB This signal controls a feedback control circuit and is proportional to the final high voltage to be applied to the electron multiplier cathode The electron multiplier voltage is lowered by the Analog during sample ionization to prolong the life of...

Page 93: ...r _______________________ Finnigan LTQ Hardware Manual _____________________ 2 39 5IFSNP 530 03103 5 0 Figure 2 19 Functional block diagram of the ion detection system electronic assemblies ANALOG PCB ELECTRON MULTIPLIER AND CONVERSION DYNODE POWER SUPPLY ELECTROMETER PCB POWER SIGNAL DISTRIBUTION PCB DATA SYSTEM ...

Page 94: ...ory RAM High capacity hard disk drive Recordable rewriteable CD drive Primary Ethernet adapter data system to MS detector Secondary Ethernet adapter data system to local area network 1 44 MB 3 5 in diskette drive Integrated video graphics card with 48 MB RAM 19 in 1280 1024 resolution flat panel LCD monitor Keyboard and mouse For more information about the computer refer to the manuals that come w...

Page 95: ...n the data system and the MS pump is established by way of an RS232 connection A synchronization cable assembly is used to coordinate the run control signals between the LC modules and the MS detector Refer to Finnigan LTQ Getting Connected for information on connecting the LTQ with other LC modules Figure 2 20 Cable diagram for the Surveyor LC system with an MS pump LTQ MS detector and data syste...

Page 96: ...not involved in data system MS detector or LC communications You can use this secondary Ethernet adapter to access your local area network Printer A high resolution laser printer is available with the LTQ as an option The printer communicates with the PC via the local area network Refer to the manual supplied by the manufacturer for details about the printer You set up the printer from the Print S...

Page 97: ...ity of the ion signal You need to tune and calibrate the LTQ that is optimize the tune and calibration parameters perhaps once a quarter Refer to the Automatic Tuning and Calibrating in the ESI MS Mode chapter in Finnigan LTQ Getting Started for a procedure for tuning and calibrating the LTQ To check the tuning and calibration follow the procedure described in the topic Testing the Operation of th...

Page 98: ... MS detector is between 200 and 350 kPa 30 to 50 psig If necessary adjust the pressure with the tank pressure regulator 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 100 cubic feet per day nitrogen on 24 hours per day If necessary replace the tank Verify t...

Page 99: ...he ESI Probe on page 2 7 of the Finnigan Ion Max API Source Hardware Manual 2 Loosen the sample inlet fitting 3 Gently pull back on the sample tube to free it from the fitting 4 Push the sample tube forward so that it extends beyond the end of the electrospray needle 5 Use a fused silica cutting tool to cut off a small length of sample tube Ensure that you cut the end of the sample tube squarely 6...

Page 100: ...system within the last 30 to 60 minutes wait an additional 30 minutes and recheck the pressure If the pressure is decreasing with time check the pressure periodically until it is within the typical pressure range of the MS detector If the pressure remains high your system may have an air leak If you suspect an air leak shut down the system as described in the topic Shutting Down the System Complet...

Page 101: ...tart Programs Xcalibur Xcalibur choose Actions Check Disk Space to open the Disk Space dialog box The Disk Space dialog box lists the following Current drive and directory for example C Xcalibur system programs Number of Mbytes that are available free on the current drive Percentage of the current drive that is available Total capacity of the current drive 2 To select another disk drive so that yo...

Page 102: ...gh the API source To flush the sample transfer line sample tube and API probe proceed as follows 1 Wait until data acquisition if any is complete 2 Make sure that the lid to the API chamber in closed and secured 3 Choose Start Programs Xcalibur LTQ Tune to open the LTQ Tune Plus window 4 From the Tune Plus window choose Control On or click on the On Standby button to toggle it to On to turn on the...

Page 103: ... 5 In the ESI Source dialog box enter 5 in the Aux Gas Flow Rate text box d Set the sweep gas flow rate to 0 In the ESI Source dialog box enter 0 in the Sweep Gas Flow Rate text box e Set the ESI spray voltage to 0 In the ESI Source dialog box enter in the Spray Voltage text box f Click on OK 7 Set up and start a flow of 50 50 methanol water solution from the LC to the API source as follows a In t...

Page 104: ...lary Flushing the Ion Sweep Cone and Ion Transfer Capillary You need to clean the ion sweep cone or spray cone and the ion transfer capillary on a regular basis to prevent corrosion and to maintain optimum performance of your API source A good practice is to flush the ion sweep cone and ion transfer capillary at the end of each operating day after you flush the sample transfer line sample tube and...

Page 105: ...y salt or other contaminants that may have been deposited on the ion sweep cone or spray cone If necessary remove the Ion Max ion source and clean the ion sweep cone or spray cone as follows a Remove the Ion Max ion source from the front of the MS detector as described in the topic Removing the Ion Max Ion Source on page 4 12 b Remove the ion sweep cone if it is installed as follows i Put on a pai...

Page 106: ...beaker of 50 50 methanol water ii Sonicate it for 15 min iii Dry the ion sweep cone d Clean the spray cone with a Kimwip soaked in methanol e Reinstall the ion sweep cone as follows i Note the location of the sweep gas supply port in the API cone seal The gas inlet on the ion sweep cone is placed in this port See Figure 3 1 and Figure 3 2 Figure 3 1 Sweep gas supply port in the API cone seal Sweep...

Page 107: ...pic Purging the Oil in the Rotary Vane Pump Purging the Oil in the Rotary Vane Pump You need to purge decontaminate the oil in the rotary vane pump on a daily basis to remove water and other dissolved chemicals from the pump oil Water and other chemicals in the rotary vane pump can cause corrosion and decrease the lifetime of the pump A good time to purge the oil is at the end of the working day a...

Page 108: ...tector in Standby Ensure that a septum seals the entrance to the ion transfer capillary 3 Open the gas ballast valve on the rotary vane pump by turning it to position Refer to the manual that came with the pump for the location of the gas ballast valve 4 Allow the pump to run for 30 min with the gas ballast valve open 5 After 30 min close the gas ballast valve by turning it to position O Go on to ...

Page 109: ...lar basis This chapter describes routine MS detector maintenance procedures that must be performed to ensure optimum performance of the instrument Most of the procedures involve cleaning For example procedures are provided for cleaning the API source ion guides mass analyzer and ion detection system Procedures are also presented for replacing the API sample tube ion transfer capillary and API sour...

Page 110: ... window If VUV lamp window is dirty Finnigan Ion Max API Source Hardware Manual Ion source interface Clean tube lens and skimmer As needed1 Page 4 13 Cooling fans Clean fan filters Every 4 months Page 4 44 Q00 ion guide Clean Q00 quadrupole and lens L0 As needed1 Page 4 22 ESI probe Trim sample tube If polyimide coating on the end of the sample tube has elongated Page 3 3 APCI or ESI probe Replace...

Page 111: ...discolored Manufacturer s documentation Ion detection system Replace electron multiplier assembly2 If noise in spectrum is excessive or proper electron multiplier gain can not be achieved Page 4 39 Turbomolecular pump Replace turbomolecular pump insert2 Every 20 000 to 30 000 hours or if bearings fail Page 4 43 Electronic modules Replace electronic module2 If electronic module fails Diagnostics an...

Page 112: ... maintenance Cleaning the Q00 ion guide Cleaning the Q0 ion guide Cleaning the mass analyzer Cleaning the ion detection system Replacing the electron multiplier Replacing the turbomolecular pump insert Cleaning the fan filters Note The keys to success with the procedures in this chapter are Proceed methodically Always wear clean lint free gloves when handling the components of the API source ion g...

Page 113: ...ll point Allen also referred to as ball drivers 00025 03025 Hex ball Driver 3 16 in 00025 01700 Hex ball Driver 7 64 in 00025 01800 Hex ball driver 5 16 in 9 5 in long 00025 10015 Hex ball driver 5 32 7 4 in long 00025 10020 Ion transfer capillary removal tool 70111 20258 Screwdriver slot head large Screwdriver slot head small Screwdriver Phillips small Fused silica cutting tool Spray bottle Beake...

Page 114: ...an the API probe ion sweep cone and ion transfer capillary The Q00 quadrupole and lens L0 require cleaning less often than the tube lens and skimmer Refer to the topic Cleaning the Q00 Ion Guide on page 4 22 The Q0 quadrupole Q1 octapole and lenses of the Q0 and Q1 ion guides become dirty at a rate significantly slower than the API source and Q00 ion guide Refer to the topic Cleaning the Q0 and Q1...

Page 115: ...I Probe You should flush the sample transfer line sample tube and API probe at the end of each working day or more often if you suspect they are contaminated by flowing a 50 50 methanol distilled water solution from the LC through the API source To flush the sample transfer line sample tube and API probe follow the procedure described in the topic Flushing the Sample Transfer Line Sample Tube and ...

Page 116: ...eck the Convectron gauge pressure in the Vacuum dialog box of the Tune Plus window To display the Tune Plus window choose Start Programs Xcalibur LTQ Tune Choose Setup Vacuum to display the Vacuum dialog box To remove and clean the ion transfer capillary do the following 1 Turn off the flow of liquid from the LC or other sample introduction device to the API source To turn off the flow of liquid f...

Page 117: ...terclockwise with the custom removal tool P N 70111 20258 until you can pull it free from the ion source interface 6 Soak the ion transfer capillary in a dilute solution of nitric acid to remove contaminants 7 Sonicate the ion transfer capillary in distilled water 8 Clean the ion sweep cone by wiping the inside and outside with methanol and a Kimwipe 9 Remove clean with methanol and inspect the 0 ...

Page 118: ... Max ion source requires a minimum of maintenance If the sample tube becomes obstructed with salt precipitates or is broken you need to replace it Also you may need to disassemble an API probe so you can clean it or to replace a part Refer to the Finnigan Ion Max API Source Hardware Manual for procedures for maintaining the API probes Caution Be careful not to bend the ion transfer capillary Rotat...

Page 119: ...ep cone and the bore of the ion transfer capillary at the end of each working day with a 50 50 methanol water solution Refer to the topic Flushing the Ion Sweep Cone and Ion Transfer Capillary on page 3 9 The ion transfer capillary can be easily removed for cleaning or replacement without venting the system Refer to the topic Removing and Cleaning the Ion Transfer Capillary on page 4 8 To access t...

Page 120: ...he ion source housing locking levers 90º to release the ion source housing from the ion source mount assembly 3 Remove the ion source housing by pulling straight off of the ion source mount assembly and place the housing in a safe location for temporary storage Go on to the next topic Removing the Ion Source Interface Note If an ion source probe is still installed in the ion source housing the ext...

Page 121: ... clean the tube lens and skimmer go on to the next topic Cleaning the Tube Lens and Skimmer Cleaning the Tube Lens and Skimmer An accumulation of chemicals on the surfaces of the tube lens and skimmer forms an insulating layer that can modify the electrical fields that control ion transmission The tube lens and skimmer require cleaning less often than the ion sweep cone and the ion transfer capill...

Page 122: ...LC grade methanol and a cotton tipped applicator swab Note Wear clean gloves when you handle the tube lens and skimmer Caution Take care not to scratch or nick the skimmer cone Note For most cleaning applications HPLC grade methanol is the solvent of choice However use of buffers or salt solutions may require that you use an acidic aqueous solution If you need to use a solvent other than methanol ...

Page 123: ...ry heater assembly proceed as follows 1 Remove the ion transfer capillary by turning it counterclockwise until you can pull it free from the ion source interface 2 Disconnect the capillary heater cable from the connector 3 Disconnect the grounding wire 4 Loosen the two screws that hold the capillary heater mount to the ion source interface housing 5 Remove the capillary heater assembly 6 To instal...

Page 124: ...dware Manual_________________________________________________ Figure 4 5 Exploded view of the ion source interface front Ion Sweep Cone Guide Pin Ion Transfer Capillary 0 3 in O Ring Spray Cone 2 033 in O Rings Spray Cone Seal Graphite Seal Capillary Heater Mount Cage Contact Socket ...

Page 125: ...______ Finnigan LTQ Hardware Manual ________________________________________ 4 17 Figure 4 6 Exploded view of the ion source interface rear Skimmer Tube Lens Contact Ring Plunger Balls Capillary Heater Capillary Heater Mounting Cage Vented Screws 2 625 in O Ring ...

Page 126: ...______ Finnigan LTQ Hardware Manual _______________________ Figure 4 7 Wiring diagram for the ion source interface Skimmer Brown Ion Transfer Tube Red Tube Lens Orange RTD Ret RTD Heater 2 Ret Heater 1 Ret Hea ter 2 Heater 1 Pin 1 2 9 RTD Right RTD Ret Left Heater 1 Heater 1 Ret Heater 2 Heater 2 Ret ...

Page 127: ...install the source drain tube as follows a Connect the 1 in ID Tygon tubing P N 00301 22922 to the ion source housing drain fitting b Attach the free end of the hose to a waste container Ideally the waste container should be vented to a fume exhaust system Go on to the next topic Starting Up the System Caution Prevent solvent waste from backing up into the ion source and mass spectrometer Always e...

Page 128: ...ce JOOJHBO 52 5IFSNP 530 03103 5 0 4 20 ______________________ Finnigan LTQ Hardware Manual _______________________ Figure 4 8 Rear view of the Ion Max ion source housing Guide Pin Holes Ion Source Housing Drain Ion Source Housing Locking Levers ...

Page 129: ... Finnigan LTQ Hardware Manual _____________________ 4 21 5IFSNP 530 03103 5 0 Starting Up the System Start up the system as described in the topic Starting Up the System After a Complete Shutdown in the System Shutdown Startup and Reset chapter Figure 4 9 Ion source mount showing ion source housing guide pins Ion Source Housing Guide Pins ...

Page 130: ...d vent the system Remove the Ion Max ion source Remove the ion source interface Remove the Q00 ion guide Disassemble the Q00 ion guide Clean Q00 quadrupole and lens L0 Reassemble the Q00 ion guide Reinstall Q00 ion guide Reinstall the ion source interface Reinstall the Ion Max ion source Start up the system Shutting Down the System Shut down and vent the system as described in the topic Shutting D...

Page 131: ... 13 Go on to the next topic Removing the Q00 Ion Guide Removing the Q00 Ion Guide To remove the Q00 ion guide proceed as follows 1 Reach into the opening in the vacuum manifold where the ion source interface was and disconnect the electrical connector to the Q00 ion guide 2 Loosen the three mounting bolts that hold the Q00 ion guide housing to the vacuum manifold See Figure 4 10 3 Carefully remove...

Page 132: ...de cage Lens L0 is secured to the Q00 ion guide cage by plunger balls See Figure 4 12 for the location of the Q00 ion guide components 3 Remove the Q00 quadrupole from the front of the Q00 ion guide cage The Q00 quadrupole is secured to the Q00 ion guide cage by plunger balls Go on to the next topic Cleaning the Q00 Ion Guide Components Note Prepare a clean work area by covering the area with lint...

Page 133: ...__________ Finnigan LTQ Hardware Manual ________________________________________ 4 25 Figure 4 12 Exploded view of the Q00 ion guide Lens L0 2 148 in O Ring Q00 Quadrupole Contact Ring Plunger Ball 3x Plunger Ball 6x Threaded Guide Post 2x Q00 Ion Guide Cage ...

Page 134: ...s 7 Inspect each part for contamination and dust If necessary repeat the cleaning procedure Go on to the next topic Reassembling the Q00 Ion Guide Reassembling the Q00 Ion Guide Reassemble the Q00 ion guide as follows 1 Insert the Q00 quadrupole through the front of the Q00 ion guide cage until it seats in the cage 2 Insert lens L0 through the rear of the Q00 ion guide cage until it seats in the c...

Page 135: ...next topic Reinstalling the Ion Source Interface Reinstalling the Ion Source Interface Reinstall the ion source interface as described in the topic Reinstalling the Ion Source Interface on page 4 19 Go on to the next topic Reinstalling the Ion Max Ion Source Reinstalling the Ion Max Ion Source Reinstall the Ion Max ion source as described in the topic Reinstalling the Ion Max Ion Source on page 4 ...

Page 136: ...he vacuum manifold Remove the Q0 and Q1 ion guides Clean the Q0 quadrupole Q1 octapole lens L1 and gate lens Reinstall the Q0 and Q1 ion guides Reinstall the top cover plate of the vacuum manifold Reinstall the top cover of the MS detector Start up the system Shutting Down the System Shut down and vent the system as described in the topic Shutting Down the System Completely in the System Shutdown ...

Page 137: ...fferential between the vacuum manifold and atmospheric pressure Six cables are connected to the top cover plate See Figure 4 12 To remove the top cover plate proceed as follows 1 Disconnect the electron multiplier high voltage coaxial cables that come from the electron multiplier power supply 2 Disconnect the electrometer cable from the Electrometer PCB If necessary use a small screw driver to loo...

Page 138: ... 52 5IFSNP 530 03103 5 0 4 30 ______________________ Finnigan LTQ Hardware Manual _______________________ Figure 4 13 Electrical connections to the top cover plate of the vacuum manifold Electron Multiplier High Voltage Cables Electrometer Cable Top Cover PCB Cables ...

Page 139: ...you remove it 2 Disconnect the electrical leads to the Q0 quadrupole lens L1 gate lens and Q1 octapole 3 Hold the Q0 quadrupole and lens L1 with one hand loosen and remove the two thumb screws that hold the Q0 ion guide mounting bracket to the top cover plate of the vacuum manifold See Figure 4 14 4 Remove the Q0 quadrupole and lens L1 5 Hold the Q1 octapole and gate lens with one hand loosen and ...

Page 140: ...n from the Q0 quadrupole Q1 octapole lens L1 and the gate lens Clean each part in turn After cleaning place each part on a clean lint free surface Figure 4 14 Exploded view of the Q0 and Q1 ion guides Q1 Octapole Gate Lens Mounting Bracket Thumb Screw Lens L1 Q0 Quadrupole Mounting Bracket Baffle Caution Take care not to bump or jar the Q0 quadrupole and Q1 octapole Note When you clean the ion gui...

Page 141: ...all ion optics and mass analyzer parts are clean and dry go on to the next topic Reassembling the Ion Optics and Mass Analyzer Reinstalling the Q0 and Q1 Ion Guides Two adjustable mounting brackets hold the Q0 and Q1 ion guides in position against the baffle on the top cover plate of the vacuum manifold See Figure 4 14 Use the following procedure to reinstall the Q0 and Q1 ion guides on the top co...

Page 142: ...mounting bracket so that the quadrupole is held between the mounting bracket and the lens L1 c Tighten the two thumb screws that hold the Q0 ion guide mounting bracket to the top cover plate 3 Reconnect the electrical leads to the Q0 quadrupole lens L1 gate lens and Q1 octapole according to the wiring diagram shown in Figure 4 15 Go on to the next topic Cleaning the Ion Detection System Caution Be...

Page 143: ...5IFSNP 530 03103 5 0 _____________________________________________ Finnigan LTQ Hardware Manual ________________________________________ 4 35 Figure 4 15 Wiring diagram for the Q0 and Q1 ion guides ...

Page 144: ...the vacuum manifold 2 Check the O ring that surrounds the opening for signs of wear and replace it if necessary P N 97055 40005 Make sure that the O ring is seated properly 3 Carefully lift the top cover plate up by its two handles and turn it over Orient the top cover plate such that the electron multiplier is over the conversion dynode Carefully insert the guide posts on the underside of the top...

Page 145: ...er over the MS detector such that the front of the cover is about 1 2 cm 0 5 in in front of the front of the MS detector 3 Slide the cover back until it is flush with the front doors when they are closed 4 Tighten the two fasteners to secure the top cover to the chassis 5 Close the front door of MS detector Tighten the Allen screw on the right side of the door with an Allen wrench or hex head ball...

Page 146: ...he mass analyzer requires cleaning very rarely if ever A wiring diagram for the mass analyzer is shown in Figure 4 16 Caution The hyperbolic rods of the mass analyzer are precision aligned at the factory Due to the delicate nature of the mass analyzer mass analyzer maintenance should be performed only by a Thermo Electron Field Service Engineer Figure 4 16 Wiring diagram for the mass analyzer ...

Page 147: ...he Ion Detection System dialog box which can be reached from the Tune Plus window by choosing Setup Ion Detection System If you are having problems with the ion detection system you need to replace the electron multiplier assembly To replace the electron multiplier assembly proceed as follows 1 Shut down and vent the system as described in the topic Shutting the System Down Completely in the Syste...

Page 148: ... 9 Install a new dual anode P N 97055 20018 in the anode feedthrough in the top cover plate Secure the dual anode with the socket head screw 10 Reinstall the anode shield over the dual anode 11 With one hand holding the high voltage tube and the other hand holding the electron multiplier support install the new electron multiplier P N 96000 60036 on the top cover plate Ensure that the high voltage...

Page 149: ...r plate of the vacuum manifold over the opening in the vacuum manifold as described in the topic Reinstalling the Top Cover Plate of the Vacuum Manifold on Reinstalling the Top Cover Plate of the Vacuum Manifold on page 4 36 15 Reinstall the top cover of the MS detector as described in the topic Reinstalling the Top Cover of the MS Detector on page 4 37 16 Start up the LTQ system as described in t...

Page 150: ...n to set the electron multiplier voltage to 800 V g Click on the OK button to return to Tune Plus 18 Calibrate the electron multiplier voltage as follows a Allow the system to pump down for at least one hour before you turn on the high voltages b Set up for the infusion of the tuning solution into the MS detector as described in LTQ Getting Started c From the Tune Plus window choose Control Calibr...

Page 151: ...ps 1 Shutting down the system 2 Removing the left front panel 3 Disconnecting the power cable from the turbomolecular pump 4 Disconnecting the foreline from the turbomolecular pump 5 Loosening and removing the six 4 mm socket head screws that hold the insert to the pump 6 Removing the insert 7 Reinstalling a new inset 8 Installing and tightening the six screws that hold the insert to the pump 9 Co...

Page 152: ... months The fan filters is located on the rear of the MS detector on the right side To clean the fan filters proceed as follows 1 Remove the fan filter from the rear of the MS detector by pulling it up and out of the fan filter bracket 2 Wash the fan filters in a solution of soap and water 3 Rinse the fan filters with tap water 4 Squeeze the water from the fan filters and allow them to air dry 5 R...

Page 153: ...tion the LTQ can be placed in Standby if the system is not to be used for 12 hours or more In this chapter procedures are provided to do the following Shut down the system in an emergency Place the system in standby condition Shut down the system completely Start up the system after a complete shutdown Reset the MS detector Reset the tune and calibration parameters to their default values Reset th...

Page 154: ...O position This turns off all power to the MS detector including the vacuum pumps Although removing power abruptly will not harm any component within the system this is not the recommended shutdown procedure to follow Refer to the Shutting Down the System Completely topic on page 5 4 for the recommended procedure To turn off the LC autosampler and computer in an emergency use the on off switches o...

Page 155: ...u choose Control Standby the LTQ turns off the electron multipliers conversion dynodes 8 kV power to the API source main RF voltage and ion guide RF voltages LTQ also turns off the auxiliary and sheath gas flows See Table 5 1 on page 5 14 for the On Off status of MS detector components when the MS detector is in the standby condition The System LED on the front panel of the MS detector is illumina...

Page 156: ...s 3 Place the electronics service switch located on the power panel see Figure 5 1 on page 5 2 in the Service position Power to the non vacuum system electronics is turned off when you place the electronics service switch in the Service position 4 Place the main power circuit breaker switch located on the power panel Figure 5 1 in the Off O position When you place the main power circuit breaker sw...

Page 157: ... Computer option button and then click on Yes to start the Windows XP shutdown procedure b When the Windows XP shutdown procedure tells you that it is safe to turn off the computer turn off the monitor and computer by using the on off switches 10 Turn off the optional printer by using the on off switch 11 Turn off the optional autosampler by using the main power on off switch Note If you are plann...

Page 158: ...quid flow to the MS detector Starting Up the Data System Use the following procedure to start up the data system 1 Turn on the monitor computer and printer 2 Observe the Windows XP startup procedure on the monitor 3 Press Ctrl Alt Del when you are prompted to do so Then click on OK or enter your password if you have one in the Logon Information dialog box to complete the start up procedure Startin...

Page 159: ...r several more seconds the Communication LED is illuminated green to indicate that the data system and the MS detector have established a communication link Ensure that the instrument console window is active Software for the operation of the MS detector is then transferred from the data system to the MS detector After 3 minutes the System LED is illuminated yellow to indicate that the software tr...

Page 160: ...uge is around 1 Torr Compare the values of the other parameters in the status panel with values that you recorded previously 4 Set up for ESI APCI APPI or NSI operation as described in Finnigan LTQ Getting Started Note Air in the helium line must be purged or given sufficient time to be purged for normal LTQ performance Note You do not need to calibrate or tune the LTQ each time you restart the LT...

Page 161: ...omplete Shutdown on page 5 6 To reset the MS detector press the Reset button located on the power panel for 3 s Make sure the Communication LED is extinguished before releasing the Reset button When you press the Reset button for 3 s the following occurs An interrupt on the embedded computer causes the CPU to reboot All LEDs on the front panel of the MS detector are off except the Power LED After ...

Page 162: ...ance To reset the LTQ tune and calibration parameters to their default values proceed as follows 1 In the Tune Plus window choose File Restore Factory Calibration to restore the default calibration parameters or choose File Restore Factory Tune Method to restore the default tune parameters 2 To optimize the LTQ system parameters that is to calibrate or tune the system perform the calibration or tu...

Page 163: ...e Restart The Computer option button and then click on Yes to start the Windows XP shutdown and restart procedure 3 Observe the Windows XP shutdown and restart procedure on the monitor 4 Press Ctrl Alt Del when you are prompted to do so Then click on OK or enter your password if you have one in the Logon Information dialog box to complete the shutdown and restart procedure Resetting the Data Syste...

Page 164: ...wn and restart procedure 4 When the shutdown and restart procedure has completed choose Start Programs Xcalibur LTQ Tune to display the Tune Plus window Note The communications link between the data system and the MS detector should be automatically reestablished after you reset the data system When this occurs the Communication LED on the front panel of the MS detector is illuminated yellow and t...

Page 165: ...n when it is not in use Choose Control Standby or toggle the On Standby button from the Tune Plus window to place the MS detector in Standby Place the MS detector in the Off condition The Off condition is similar to Standby except all high voltage components of the MS detector are turned off Choose Control Off from the Tune Plus window to place the MS detector in the Off condition Place the electr...

Page 166: ... multipoles RF voltages Off Off Off Off Ion optics multipoles dc offset voltages On Off Off Off Ion optics lens On Off Off Off Tube lens On Off Off Off Ion transfer capillary heater On On Off Off Ion transfer capillary dc offset On Off Off Off Corona discharge needle Off Off Off Off APCI vaporizer Off Off Off Off ESI needle Off Off Off Off Sheath gas Off Off Off Off Auxiliary gas Off Off Off Off S...

Page 167: ...30 03103 5 0 Power supply 300 V dc On Off Off Off Fan turbomolecular pump On On On Off Fan RF coil On On Off Off Fans electronics tower On On On Off Convectron gauge On On Off Off Ion gauge On On Off Off Table 5 1 On Off Status of MS Detector Components Voltages and Gas Flows continued MS detector component Standby Off Electronics service switch in Service position Main power circuit breaker switc...

Page 168: ......

Page 169: ... LTQ system calls for troubleshooting to the lowest part assembly PCB or module listed in the Replaceable Parts chapter You should replace LTQ components when indicated by the LTQ diagnostics by Thermo Electron Technical Support or by a Thermo Electron Customer Support Engineer This chapter covers the following topics Running the LTQ diagnostics Replacing a fuse in the MS detector Replacing a powe...

Page 170: ...u change the system s configuration cables or peripherals just before the problem occurred If the answer is yes to the first item above there is the possibility of a hardware failure and running the diagnostics is appropriate If the answer is yes to one of the last two items above the problem is probably mechanical not electrical Reverify that alignment configurations and cable connections are cor...

Page 171: ...hronological log of all diagnostic tests in the Testing text box Once testing for a specific subsystem is completed LTQ displays either Pass or Fail in the Results group box If the LTQ diagnostics indicates a problem perform the maintenance procedure indicated by the LTQ diagnostics by Thermo Electron Technical Support or by a Thermo Electron Customer Support Engineer For more information on the L...

Page 172: ...and current rating of the various fuses are listed in Table 6 1 Check fuses when power is lost to a fused subsystem CAUTION Always shut down the system and disconnect the power cord before you replace fuses Table 6 1 MS detector fuses Location Fuse Circuit Description P N Interlock PCB F1 F3 APCI vaporizer heater 3 15 A Type F 5 x 20 mm 250 V 00006 10510 Interlock PCB F2 F4 220 Vac 6 3 A 250 V 000...

Page 173: ...ower supply To replace the PS1 power supply P N 97055 60014S PS2 power supply P N 97055 60015S 300 V power supply P N 97055 98001 or the 8 kV power supply P N 97055 60033 proceed as follows 1 Shut down and vent the system as described in the topic Shutting Down the System Completely in the System Shutdown Startup and Reset chapter 2 Open the right front door of the MS detector by loosening the All...

Page 174: ...air Center in San Jose Be sure to note the apparent problem or symptoms on the enclosed forms 7 Slide the new power supply into the space occupied by the old power supply Push carefully on the power supply to seat the connectors in the rear 8 Tighten with a Phillips screwdriver the fastener that holds the power supply to the tower 9 If necessary reinstall the vertical beam if you removed it in ste...

Page 175: ...he system Due to the complexity of removing and reinstalling many of the LTQ PCBs we recommend that a Thermo Electron Field Service Engineer replace the electronic assemblies PCBs and assemblies in the MS detector are shown in Figure 6 3 CAUTION Shutdown the system and unplug the power cord before you access PCBs and electronic assemblies Caution To prevent damage to the electronics due to electro...

Page 176: ......

Page 177: ... equivalent This chapter contains part numbers for the following MS Detector Data system hardware Manuals Accessory kit Metal needle kits Fittings ferrules and sample loops Note Not all parts are available for purchase separately Some parts may be available for purchase only as part of a kit or assembly Note Some parts are also available as exchange parts An exchange part is a refurbished part tha...

Page 178: ...ctor Replaceable parts are available to support the following ESI source APCI source Ion source interface Ion guides Mass analyzer Divert inject valve Syringe pump Turbomolecular pump Forepump Pressure gauges Vacuum system assemblies Vacuum manifold O rings Vent valve Power supplies Printed circuit boards PCBs RF control detection assemblies Cables Fans ...

Page 179: ...50 00990 O ring 00 438ID 1 16 in Viton 00107 05575 Connector receptacle high voltage shielded 00004 89626 Ferrule 012ID KEL F HPLC 00101 18116 Fitting Fingertight 2 Upchurch 00101 18195 Fitting plug 1 4 28 TEFZEL HPLC 00101 18075 O ring 0 676 ID 1 16 TH VI 00107 05710 O ring 00 125ID 1 16TH VI 00107 02550 Assembly resistor contact ESI probe 97055 60058 Sleeve resistor 97055 20147 Resistor FXD CC 1...

Page 180: ...2 5IFSNP 530 03103 5 0 7 4 _______________________ Finnigan LTQ Hardware Manual _______________________ Figure 7 1 Exploded view of the ESI probe 97055 20215 97055 60058 00950 00952 00004 21402 00950 00990 00107 05710 97055 20146 97055 20217 ...

Page 181: ..._____________________ MS Detector _________________________ Finnigan LTQ Hardware Manual ____________________ 7 5 5IFSNP 530 03103 5 0 Figure 7 2 Replaceable parts for the ESI probe 00107 05575 00107 05710 00004 89626 00101 18075 00101 18116 00101 18116 00109 00304 00101 18195 ...

Page 182: ...APCI probe OPTON 20012 APCI probe nozzle assembly 97055 60089 Ferrule 016ID PEEK HPLC 00101 18120 Tubing fused silica 150U X 390U 00106 10498 O ring 239 1 16th Viton 00107 04000 O ring 00 312 ID 5 16 1 16 00107 04500 O ring 00 500 ID 1 16TH VI 00107 05600 Fitting 10 32 male nut PEEK 70005 20220 Fitting APCI flange 70005 20250 Nozzle APCI probe 97055 20221 ...

Page 183: ...ware Manual ____________________ 7 7 5IFSNP 530 03103 5 0 Figure 7 3 APCI Probe Assembly OPTON 20012 APCI Nozzle Assembly Flat Side Retention Flange Retention Flange Guide Pin Vaporizer Heater Cable Socket Figure 7 4 APCI probe nozzle assembly P N 97055 60089 00107 04500 97055 20221 00107 05600 00106 10468 7005 20220 00101 18120 00107 04000 70005 20250 ...

Page 184: ...cket 2 56 x 3 16 ss 00419 25603 Screw 4 40 x 3 8 SHCS vented stainless steel 00419 44014 Screw socket 6 32 x 1 ss 00419 63216 Screw set socket 6 32 x 7 8 alloy A574 00451 63278 Screw 2 56 x 3 32 socket head stainless steel 00452 25612 Seal graphite source heater 70111 20216 Thumbnut knurled 6 32 97055 20033 Seal API cone 97055 20034 Cone API source sweep cone 97055 20035 Ring contact support 97055...

Page 185: ...52 ___________________________________________________________________ MS Detector _________________________ Finnigan LTQ Hardware Manual ____________________ 7 9 5IFSNP 530 03103 5 0 Figure 7 5 Ion source interface part numbers ...

Page 186: ...ger ball 20 x 0 53 4lb 00201 11716 Plunger ball 6 40 x 0 31 1lb 00201 11719 Screw socket HD CAP 4 40 x 3 8 ss 00419 44010 Screw socket 6 32 x ss 00419 63204 Lens L1 mount 97055 20026 Rod threaded guide 97055 20050 Cage outer contact support 97055 20053 Manifold API gas inlet 97055 20067 Quadrupole Q00 large R0 97055 20106 Latch block probe housing 97055 20128 Cage Contact Ring Assembly 97055 63082...

Page 187: ..._____________________ Finnigan LTQ Hardware Manual ___________________ 7 11 5IFSNP 530 03103 5 0 Q0 and Q1 Ion Guides Thumb screws 10 32 97000 20235 Lens L1 97055 20022 Gate lens 97055 20023 Multipole bracket 97055 20054 Q1 octapole 97055 60034 Q0 quadrupole 97055 60035 Figure 7 7 Q0 and Q1 ion guides part numbers ...

Page 188: ...ringe pump 97055 98006 Turbomolecular Pump Turbomolecular pump insert Leybold TW 400 300 25 EX00108 10022 Turbomolecular pump controller Leybold TDS 00108 10012 Forepump Forepump Kit 70111 62014 Forepump mechanical pump E2M30 650 L3 min 220V AC 00108 02655 Vacuum hardware clamp KF 20 25 00102 10020 Pump hardware centering ring 00108 02011 Mist Filter 00108 02 00002 Hose clamp band 00201 03810 PVC ...

Page 189: ...3 port 1 5 in 97055 20222 Flange NW40 long 00108 02 00003 Clamp NW32 40 swing 00108 02 00004 Ring centering 00108 02 00005 Adaptor pump roughing line 70111 20210 Hose clamp band 00201 03810 Pump hardware centering ring 00108 02011 Vacuum hardware clamp KF 20 25 00102 10020 Vacuum Manifold O Rings O ring 0 31 in ID 1 16 00107 05000 O ring 4 5 in ID 1 8 Viton 00107 14500 O ring 6 48 in ID 1 8 Viton ...

Page 190: ...Replaceable Parts MS Detector JOOJHBO 52 5IFSNP 530 03103 5 0 7 14 ______________________ Finnigan LTQ Hardware Manual _______________________ Figure 7 8 Vacuum manifold O rings part numbers ...

Page 191: ... ___________________________________________________________________ MS Detector _________________________ Finnigan LTQ Hardware Manual ___________________ 7 15 5IFSNP 530 03103 5 0 Figure 7 9 Vacuum manifold O rings part numbers ...

Page 192: ...ircuit Boards PCBs Source PCB available as exchange 70111 61053S Interlock PCB 70111 61060S Digital PCB available as exchange 97055 61010S Distribution PCB 97055 61020S Analog PCB available as exchange 97055 61030S Top Cover PCB available as exchange 97055 61040S I O PCB 97055 61070S Front Panel PCB 97055 61110S Electrometer PCB 97055 61190S RF Detector PCB available as exchange 97055 61200S Diver...

Page 193: ...al Dynode Electron Multiplier Supply to Power Signal Distribution PCB 97055 63036 Elcon Power to Power Signal Distribution PCB 97055 63038 Elcon System Signals to Power Signal Distribution PCB 97055 63040 PS2 to Elcon Connector Sled 97055 63042 PS1 to Elcon Connector Sled 97055 63044 Coax WFM RF Signal Analog to LPF 97055 63046 Analog PCB to Top Cover PCB 97055 63048 Interlock AC Power Module to S...

Page 194: ...21509 Fuse 3 15 A 250 V Interlock PCB fuses F1 and F3 4 each 00006 10510 Fuse 4 A 250 V Source PCB fuse F3 4 each 00006 11420 Fuse 6 3 A 250 V Interlock PCB fuses F2 and F4 4 each 00006 11450 Cable serial 00012 51086 Fitting Swagelok Adapt M 1 8 x 1 4 in 00101 01740 Fitting ferrule HPLC reducer 1 8 x 16 in 00101 02 00002 Fitting Swagelok bulkhead 1 8 in 00101 02102 Fitting ferrule Swagelok Back 1 ...

Page 195: ...05 mm ID 0 19 mm OD deactivated 00106 10502 Tubing fused silica 0 11 mm ID 0 4 mm OD deactivated 00106 10504 O ring 2 5 in Viton 00107 01 00002 O ring 0 218 in Viton 2 each 00107 01 00004 O ring 2 033 in Viton 00107 01 00006 O ring 3 16 in 6 each 00107 01 00009 O ring 0 926 in Viton 00107 01 00013 O ring 0 101 ID Viton 6 each 00107 02456 O ring 0 174 ID Viton 00107 02464 O ring 0 125 ID Viton 2 ea...

Page 196: ...301 22912 Hose poly spiral PVC superflex 1 5 ft 00301 24168 Cable shield 22 gauge 24 ft 00302 01800 Wrench L hex 4 mm 00725 00034 Troubleshooting guide HPLC 00920 05914 Seal STD Needle 5000 Series 00950 00952 Needle D Point 26 gauge 2 in long 0 24D washer 00950 00990 Corona needle APCI 5 each 70005 98033 Seal API source heater graphite 70111 20216 Tool ion transfer capillary removal 70111 20258 Ki...

Page 197: ...28 Upchurch 70111 20233 Blunt tip 34 gauge 30 µm ID stainless steel needle 70111 20288 7 5 Fittings Ferrules Sample Loops and Tubing Ferrule Fingertight 2 Upchurch for PEEK tubing and Teflon tube 00101 18196 Ferrule 0 016 in ID PEEK Upchurch for Fused silica capillary infusion line 00101 18120 Ferrule 0 012 in ID Kel F Upchurch for High flow metal needle and low flow metal needle 00101 18114 Ferru...

Page 198: ... 39 mm OD fused silica capillary APCI sample tube 00106 10498 Tubing 0 10 mm ID 0 19 mm OD fused silica capillary ESI sample tube 00106 10499 Tubing 0 05 mm ID 0 19 mm OD fused silica capillary low flow ESI 200 µL min 00106 10502 Tubing 0 1 mm ID 0 363 mm OD fused silica capillary infusion line 00106 10504 Tubing 0 075 mm ID 0 3193 mm OD fused silica capillary low flow ESI 00106 10511 Teflon tube ...

Page 199: ...4 selective photoionization figure 1 11 autosampler description 2 3 startup 5 7 TSP AS 2 3 auxiliary gas description 2 31 flow rates APCI 2 31 flow rates ESI 2 31 on off status table 5 14 B Breadth Focus in Ion Tree experiment discussion 1 23 C cables replaceable parts 7 16 calibration checking note 3 1 frequency note 3 1 capillary skimmer region vacuum manifold description 2 25 cathode electron m...

Page 200: ...ce 2 41 LAN interface 2 42 LC interface 2 41 personal computer 2 40 primary Ethernet adapter 2 41 resetting 5 11 shutdown 5 5 startup 5 6 data types defined 1 18 Depth Focus in Ion Tree experiment discussion 1 23 detector system description 2 21 disk space checking 3 5 divert inject valve button and LEDs figure 2 9 button location figure 2 6 control circuitry 2 35 description 2 6 Divert inject Val...

Page 201: ...ngle stage defined 1 14 two stage defined 1 15 Functional description LCQ Advantage system 2 1 functional description autosampler 2 3 data system 2 40 divert inject valve 2 6 liquid chromatograph LC 2 4 mass analyzer 2 16 MS detector 2 7 syringe pump 2 5 fuses MS detector replacing 6 4 replacing CAUTION 6 4 table 6 4 G gate lens description 2 16 guide posts location figure 2 27 2 28 H hard drive c...

Page 202: ...2 ionization potentials figure 1 12 ionization technique switching note 1 4 L LCQ Advantage system functional description 2 1 LCs 2 4 leaks checking for 3 4 LEDs Communication LED 2 8 Communication LED MS detector reset 5 9 Communication LED MS detector startup 5 7 divert inject valve LEDs 2 9 Power LED 2 7 Power LED MS detector reset 5 9 Power LED MS detector startup 5 7 Scan LED 2 8 syringe pump...

Page 203: ...wer Entry Module description 2 32 metal needle kits replaceable parts 7 21 monitors 2 35 mounts 2 28 MS detector API source 2 10 calibration note 5 8 covers caution 2 31 damping gas valve 2 31 data types 1 18 description 2 16 electronic assemblies 2 32 electronics service switch 2 32 emergency shutdown 5 2 Failure condition 2 8 fans 2 31 features 2 7 frequency of cleaning 4 6 functional descriptio...

Page 204: ...ersion dynode power supply description 2 38 electron multiplier power supply description 2 38 location figure 6 5 on off status table 5 14 replaceable parts 7 16 replacing 6 5 pressure pressure readings table 3 4 pressure levels checking 3 4 printer setting up 2 42 product ions defined 1 13 profile scan defined 1 18 PS1 power supply location figure 6 5 PS2 power supply location figure 6 5 pumps fo...

Page 205: ...can data types centroid scan 1 18 profile scan 1 18 Scan LED description 2 8 scan modes consecutive reaction monitoring CRM 1 16 scan power defined 1 13 scan types defined 1 14 full scan 1 14 selected ion monitoring SIM 1 15 selected reaction monitoring SRM 1 16 single stage full scan 1 14 two stage full scan 1 15 ZoomScan 1 17 section 2 16 2 17 selected ion monitoring SIM defined 1 15 selected re...

Page 206: ...troller description 2 29 V Vacuum LED description 2 8 note 5 7 vacuum levels checking 3 4 vacuum manifold cleaning 4 36 description 2 25 electrical feedthroughs 2 27 figure 2 26 interior figure 2 26 pressure readings table 3 4 top cover plate figure 4 30 top cover plate description 2 26 top cover plate reinstalling 4 36 top cover plate removing 4 29 Vacuum pumps forepump 2 29 vacuum pumps turbomol...

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