Agilent 6500 Series Q-TOF LC/MS System
Agilent 6500 SeriesQ-TOF LC/MS systemMaintenance GuideResearch Use Only. Not for use in DiagnosticProcedures.Agilent Technologies
Notices Agilent Technologies, Inc. 2011WarrantyNo part of this manual may be reproduced inany form or by any means (including electronic storage and retrieval or translationinto a foreign language) without prior agreement and written consent from AgilentTechnologies, Inc. as governed by UnitedStates and international copyright laws.The material contained in this document is provided “as is,” and is subject to being changed, without notice,in future editions. Further, to the maximum extent permitted by applicablelaw, Agilent disclaims all warranties,either express or implied, with regardto this manual and any informationcontained herein, including but notlimited to the implied warranties ofmerchantability and fitness for a particular purpose. Agilent shall not beliable for errors or for incidental orconsequential damages in connection with the furnishing, use, or performance of this document or of anyinformation contained herein. ShouldAgilent and the user have a separatewritten agreement with warrantyterms covering the material in thisdocument that conflict with theseterms, the warranty terms in the separate agreement shall control.Manual Part NumberG2581-90065EditionRevision B, December 2011Printed in USAAgilent Technologies, Inc.5301 Stevens Creek Blvd.Santa Clara, CA 95051PatentsThis product is covered by U.S. patents6,107,628 and 6,803,565 licensed fromBattelle Memorial Institute.Safety NoticesTechnology LicensesThe hardware and/or software described inthis document are furnished under a licenseand may be used or copied only in accordance with the terms of such license.Restricted Rights LegendCAUTIONA CAUTION notice denotes a hazard. It calls attention to an operating procedure, practice, or the likethat, if not correctly performed oradhered to, could result in damageto the product or loss of importantdata. Do not proceed beyond aCAUTION notice until the indicatedconditions are fully understood andmet.WA R N I N GA WARNING notice denotes ahazard. It calls attention to anoperating procedure, practice, orthe like that, if not correctly performed or adhered to, could resultin personal injury or death. Do notproceed beyond a WARNINGnotice until the indicated conditions are fully understood andmet.U.S. Government Restricted Rights. Software and technical data rights granted tothe federal government include only thoserights customarily provided to end user customers. Agilent provides this customarycommercial license in Software and technical data pursuant to FAR 12.211 (TechnicalData) and 12.212 (Computer Software) and,for the Department of Defense, DFARS252.227-7015 (Technical Data - CommercialItems) and DFARS 227.7202-3 (Rights inCommercial Computer Software or Computer Software Documentation).Agilent 6500 Series Q-TOF LC/MS Maintenance Guide
Content1Basic Operation7Starting and Shutting Down 13To start the system in Standby modeTo change from Standby to On 18To change from On to Standby 18To shut down the instrument 1915Changing Ion Sources 21To remove an electrospray source 21To remove the ESI with Agilent Jet Stream Technology 22To remove a multimode source 22To remove an APCI or APPI source 23To remove a nano ESI source 24To remove a dual nano ESI source 25To install an electrospray source 26To install an APCI source 27To install an APPI source 28To install a nano ESI, dual nano ESI or multimode source or HPLC-Chip/MSinterface 28To install the Agilent Jet Stream inlet assembly 292Maintenance31Calibrant Delivery System and Divert Valve 32To prepare tuning mix 35To prepare the reference mass solution 40To check calibrant levels 43To fill a tuning mix or reference mix bottle 44To check for leaks 45To replace the LC filter elements 46To replace the MS selection valve rotor seal 47Agilent 6500 Series Q-TOF LC/MS Maintenance Guide3
ContentsElectrospray Ion Source 49To flush the nebulizer 49To clean the electrospray spray chamber daily 50To clean the electrospray spray chamber weekly 53To remove the electrospray nebulizer 57To replace the electrospray nebulizer needle in the analytical or the referencenebulizer sprayer 58To adjust the electrospray nebulizer needle 61To reinstall the electrospray nebulizer 63To remove the desolvation assembly 64To clean skimmer 1 (for 6520/6530/6538/6540) 66To reinstall the desolvation assembly 68ESI with Agilent Jet Stream Technology 69To flush the nebulizer daily 69To flush the nebulizer monthly 70To clean the spray chamber daily for the ESI with Agilent Jet Stream 71To clean the spray chamber weekly for the ESI with Agilent Jet Stream 74To remove the nebulizer for the ESI with Agilent Jet Stream 78To replace the nebulizer needle for the ESI with Agilent Jet Stream 79To adjust the nebulizer needle for the ESI with Agilent Jet Stream 83To reinstall the nebulizer for the ESI with Agilent Jet Stream 85APCI Source 86To clean the APCI spray chamber daily 86To clean the APCI spray chamber weekly 89To remove the APCI nebulizer 91To replace the APCI nebulizer needle 92To adjust the APCI nebulizer needle 95To reinstall the APCI nebulizer 97To clean the corona needle 98To replace the corona needle 100Multimode Source and HPLC-Chip/MS InterfaceTo clean the multimode source daily 1024102Agilent 6500 Series Q-TOF LC/MS Maintenance Guide
ContentsTo clean the multimode source weekly 104To adjust the multimode nebulizer 106To change HPLC-Chip capillaries 109Ion Transfer Capillary 113To remove the capillary 113To clean the capillary 115To reinstall the capillary 118To clean skimmer 1 (for 6520/6530/6538/6540)Manifold 121To open the manifold 121To close the manifold 122To clean the ion optics assembly119123High Pressure Ion Funnel (6550 only) 132To remove the high pressure ion funnel 132To clean the high pressure ion funnel 135To reinstall the high pressure ion funnel process138Vacuum System 139To check the rough pump fluid level 139To check the oil mist filter 141To add rough pump fluid 142To replace the rough pump fluid 144To replace the fuses 1463Reference149Safety 150Environmental ConditionsReplaceable Fuses 151Agilent 6500 Series Q-TOF LC/MS Maintenance Guide1515
Contents6Agilent 6500 Series Q-TOF LC/MS Maintenance Guide
Agilent 6500 Series Q-TOF LC/MSMaintenance Guide1Basic OperationStarting and Shutting Down 13Changing Ion Sources 21This chapter describes procedures for the basic operation of your Q-TOFLC/MS instrument.Flight tubeService panelSourceFront coverCDS coverPower switchFigure 16520 Q-TOF LC/MS covers. The main power switch is behind the service panel.Agilent Technologies7
1Basic OperationFlight tubeService panelCDS coverFront coverPower switchFigure 26530 with Agilent Jet Stream TechnologyFor more details, see the site preparation guide that is sent to customersbefore installation. If you move the instrument, you must follow and repeat thesteps detailed in the site preparation guide.8Agilent 6500 Series Q-TOF LC/MS Maintenance Guide
Basic Operation1Flight tubeService panelFront coverCDS coverPower switchFigure 36538/6540 Q-TOF LC/MSAgilent 6500 Series Q-TOF LC/MS Maintenance Guide9
1Basic OperationFlight tubeService panelFront coverCDS bottles for tuningand reference mixesPower switchFigure 4106550 Q-TOF LC/MSAgilent 6500 Series Q-TOF LC/MS Maintenance Guide
Basic Operation1LAN connectionFigure 56520/6530/6538/6540 gas, LAN, and power connections behind servicepanelAgilent 6500 Series Q-TOF LC/MS Maintenance Guide11
1Basic OperationPump expander box powerswitchFigure 6126550 power connections and pump expander box behind service panelAgilent 6500 Series Q-TOF LC/MS Maintenance Guide
Basic OperationStarting and Shutting Down1Starting and Shutting DownThis section describes how to start up your Q-TOF LC/MS and how to shut itdown.The Q-TOF LC/MS instruments have three standard modes of operation thatyou can select from the software.On ModeOn is the fully operational status of the system. The instrument and the sourceare on. The Q-TOF icon indicates the state of the instrument:Table 1Q-TOF icon color indicationColorStategreenidlebluerunning, injectingrederroryellownot readypurplepre-run, post-rundark grayofflinelight graystandbyTo put an individual device in the On mode, right click the image of the devicein the Instrument Status window and click On. To put all devices in the Onmode, click the On button in the Instrument Status window.Standby ModeIn Standby, the source interface is on, the drying gas remains heated, andnebulizer flows are maintained. The source and ion optics voltages are turnedoff, and the mass spectrometer is not sending spectra to the computer.However, the Q-TOF high voltage electronics are on.For APCI and MMI sources, the vaporizer gas heaters are turned down.For an instrument with Agilent Jet Stream inlet assembly, the sheath gastemperature, drying gas flow, and drying gas temperatures are reduced.Agilent 6500 Series Q-TOF LC/MS Maintenance Guide13
1Basic OperationStarting and Shutting DownThis mode lets the instrument remain idle for periods lasting from minutes todays. You should place the instrument in Standby mode when it is not in useor when you want to change the ion source.To put an individual device in the Standby mode, right click the image of thedevice in the Instrument Status window and click Standby.Powered OffStateWhen the system is in the powered off state, the system is vented and theinstrument is turned off to allow maintenance or to prepare for long periodswhen the instrument is not used.NOTEBefore you move the instrument to another location, maintain it, or expect itto be idle for long periods of time, turn off both the front switch and the mainpower breaker switch behind the service panel.CAUTION14If the Q-TOF LC/MS is planned to be shut down for longer than one day, unplug theinstrument from the wall outlet to prevent overheating of the turbo pump powersupplies.Agilent 6500 Series Q-TOF LC/MS Maintenance Guide
Basic OperationTo start the system in Standby mode1To start the system in Standby modeThis procedure brings the system from the powered off state to Standby mode.1 Check that nitrogen gas for the drying gas and for the collision cell areturned on.When you use an instrument with Agilent Dual Jet Stream Technology orAgilent Jet Stream Technology, the drying gas requirements are greaterthan when operating with ESI, APCI, APPI, or multimode sources. Thesupply line must have two hydrocarbon traps (part number BHT-4 orRMSN-4) plumbed in parallel to achieve these flows without triggeringerrors at the instrument. Refer to the Installation Guide for more details.2 Check that the rough pump is connected to the Q-TOF LC/MS. Check that the rough pump power cable is connected to the ForelinePump power receptacle behind the service panel of the Q-TOF LC/MS. For 6550: Check that the rough pump power cable is connected to theForeline Pump power receptacle and that the Ion Funnel pump isconnected to the Auxiliary Pump power receptacle in the pumpexpander box of the Q-TOF LC/MS. Check that the rough pump has the correct voltage rating for your ACpower (230 V or 208 V). For 6520/6530/6538/6540: Check that the rough vacuum tubing isconnected to the inlet part of the rough pump. For 6550: Check that the rough vacuum hose for the foreline pump isconnected to the foreline vacuum port and that the ion funnel roughvacuum hose is connected to the ion funnel rough pump inlet. Check that the switch on the rough pump is in the On position.Agilent 6500 Series Q-TOF LC/MS Maintenance Guide15
1Basic OperationTo start the system in Standby modeNOTEA silicone rubber septum is placed between the spray shield and the capillary for shipment.Make sure that this rubber septum is removed if you are starting the system for the firsttime.CAUTIONDo not connect the spray chamber exhaust bottle to the rough pump exhaust tubing orthe rough pump exhaust tubing to the spray chamber exhaust tubing. Doing so cancontaminate the instrument with rough pump fluid.3 Check that all pump and spray chamber exhausts are vented outside thelaboratory.CAUTIONVent all exhausts external to the building where they cannot be recirculated byenvironmental control systems. Do not vent exhaust into your laboratory. The exhaustfumes from the vacuum pumps and spray chamber contains trace amounts of thechemicals you analyze. Health hazards include chemical toxicity from solvents, buffers,samples and pump fluid vapor, as well as potentially biohazardous aerosols ofbiological samples.For oil-based rough pumps only: The oil mist filter must be installed on therough pump, and the ballast valve must be closed. Open the ballast valveperiodically (must be done on a weekly basis) to return any oil that hascondensed in the oil mist filter to the pump as needed.For dry pumps (Agilent TS800 or Edwards XDS351i), the ballast does notneed to be emptied regularly.4 Turn on the power for the computer and monitor.5 Check that the instrument is plugged into a power outlet.6 For 6550 only: Check that the power switch on the pump expander box isconnected to the wall outlet and is turned on. The switch is illuminatedgreen when the power is on.7 Turn on the front switch of the Q-TOF LC/MS.This starts the pumping system and the electronics.8 After Windows starts, click Start Programs Agilent MassHunterWorkstation Acq Tools Q-TOF Diagnostics to start the Q-TOFdiagnostics program.9 From the Connection menu, select Connect and click OK.16Agilent 6500 Series Q-TOF LC/MS Maintenance Guide
Basic OperationTo start the system in Standby mode110 Under System Turn-On, mark the check boxes for Pump Down and HVCondition.11 Click the Start button under System Turn-On.The system monitors the vacuum pressure. Once the vacuum pressurereaches 3 x 10-6 torr, the system will begin conditioning the high voltageelectronics.12 Once high voltage conditioning has completed, go to Start Programs Agilent MassHunter Workstation Data Acquisition to start the DataAcquisition program.The system will come up in Standby mode.By default, the source values are set to: Drying gas flow (non iFunnel systems): 3.5 L/minute Drying gas flow (6550): 12 L/minute Drying gas temperature: 300 C Nebulizing gas pressure: 20 psi Sheath gas flow: 3 L/minute Sheath gas temperature: 125 CNOTEYou will not be able to set the flows while the Q-TOF system is in a “Not Ready” state. Thesystem will remain in the Not Ready state while the high vacuum pressure is above 3.5 X10-6 torr.13 Allow the instrument to continue pumping down.The Rough Vac (rough pump) pressure should be about 1.75 to 2.5 torr. TheTOF Vac (flight tube region) pressure should be approximately 3x10-6 torrwithin two to three hours. The TOF Vac reading should be in the 10-7 torrrange after pumping overnight to several days.Leave the instrument in Standby.Agilent 6500 Series Q-TOF LC/MS Maintenance Guide17
1Basic OperationTo change from Standby to OnTo change from Standby to OnUse this procedure when the Q-TOF LC/MS is in Standby mode and you needto bring it into the On mode.Before you begin, check that: The Q-TOF LC/MS is in Standby mode In the Data Acquisition program, click On.You can only activate the Standby mode or On mode if the ion source ismounted and closed. You can now select parameters for your measurement.The instrument is now in the On mode.To change from On to StandbyPut the Q-TOF LC/MS in Standby mode when you have completed youranalysis of samples.Before you begin, check that: You have completed tuning and data acquisition and you have saved alldata as needed (described in later chapters). In the Data Acquisition program, click Standby.The drying gas flow, drying gas temperature, nebulizer pressure, vaporizertemperature, and sheath gas temperature are reduced when the instrumentis in Standby mode. The spray chamber high voltages are turned off inStandby mode. Voltages in the flight tube remain On in Standby mode tomaintain stable operating voltages. The mass spectrometer stops generatingspectra.The system is now in Standby mode.18Agilent 6500 Series Q-TOF LC/MS Maintenance Guide
Basic OperationTo shut down the instrument1To shut down the instrumentYou can turn off the Q-TOF LC/MS when the instrument will be idle for anextended time or when you must do maintenance.Before you begin, check that you have completed tuning and acquiring data,and that you have saved all data as needed.CAUTIONWhen you click Vent in the Q-TOF shortcut menu, the Q-TOF LC/MS does not turn off.You must follow the entire shutdown procedure.WA R N I N GThe spray shield and related spray chamber components are likely to be hot. Do nottouch them!1 Turn off the solvent flow.If you have analyte in any of the components in the sample delivery system,flush the delivery system with pure solvent before you continue.2 Check that the ballast valve on the rough pump is closed.3 In the Data Acquisition program, right-click the Q-TOF device pane andclick Vent.When you vent the system, these parts are turned off: spray chamber highvoltages, the drying gas heater, the nebulization flow, the detector, andother lens voltages. The drying gas flow is set to 3.5 L/minute. If the APCIsource is installed, the vaporizer heater is also turned off. If you have aninstrument with Agilent Jet Stream Technology, the sheath gas heater isalso turned off. The Rough Pump turns off when the turbo speed is below 20percent.4 Wait until the instrument completely vents (reaching 760 torr) to ensurethat the flight tube is filled with nitrogen. This protects the detector frommoisture damage.5 Turn off the front switch located in the lower left front corner of theinstrument.Agilent 6500 Series Q-TOF LC/MS Maintenance Guide19
1Basic OperationTo shut down the instrument6 Unplug the main power cable behind the service panel. This action preventsthe turbo pump components from overheating.7 At this point, you can also shut down the Data Acquisition program andcomputer. The system is now shut down.20Agilent 6500 Series Q-TOF LC/MS Maintenance Guide
Basic OperationChanging Ion Sources1Changing Ion SourcesThis section describes the steps to change from one ion source to another.First, you need to follow the set of steps to remove your current source. Then,you need to follow the steps to install the new source.To remove an electrospray sourceWA R N I N GThe spray chamber operates at very high temperatures. Let the spray chamber coolbefore you continue.1 Put the instrument in Standby mode.2 Slide open the nebulizer cover.3 Disconnect the LC nebulizer tubing and LC nebulizing gas tubing.4 Disconnect the Reference nebulizer tubing and Reference nebulizing gastubing.5 Open the spray chamber.6 Plug the reference nebulizer gas outlet on the side of the instrument, underthe service panel.7 Remove the spray chamber by lifting it along the axis of its hinges.Agilent 6500 Series Q-TOF LC/MS Maintenance Guide21
1Basic OperationTo remove the ESI with Agilent Jet Stream TechnologyTo remove the ESI with Agilent Jet Stream TechnologyWA R N I N GThe spray chamber operates at very high temperatures. Let the spray chamber coolbefore you continue.1 Put the instrument in standby mode.If the ESI with Agilent Jet Stream Technology is at operating temperature(for example 400 C, it may take 20 to 30 minutes to cool down to anacceptable temperature.2 Disconnect the LC tubing and LC nebulizing gas tubing.3 Disconnect the heater and high voltage cables.4 Disconnect the sheath gas line at the connector and unplug it.5 Open the spray chamber.6 Remove the spray chamber by lifting it along the axis of its hinges.7 Remove the Agilent jet stream spray cap.8 If you are changing to nanospray, also remove the capillary cap.To remove a multimode source1 Put instrument in Standby mode.2 Disconnect the electrical connectors to the multimode source.WA R N I N
Agilent 6500 Series Q-TOF LC/MS Maintenance Guide 15 Basic Operation 1 To start the system in Standby mode To start the system in Standby mode This procedure brings the system from the powered off state to Standby mode. 1 Check that nitrogen gas for the drying gas and for the collision cell are
Agilent 6200 Series TOF and 6500 Series Q-TOF LC/MS System Concepts Guide 11 Help for applications You can use one or more of the 6200 Series TOF or 6500 Series Q-TOF LC/MS systems in the following application areas (for example): † Combinatorial chemistry target compound analysis † Natural products screening
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Agilent 6224/6230 Series TOF LC/MS Maintenance Guide Agilent Technologies 1 Basic Operation Starting and Shutting Down 10 Changing Ion Sources 19 This chapter describes procedures for the basic operation of your TOF LC/MS instrument. Figure 1 6224 TOF LC/MS covers. The main power switch is located on the front lower left. Dual ESI Source CDS cover
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Agilent 6200 Series Accurate-Mass TOF LC/MS systems Agilent 6500 Series Accurate-Mass Q-TOF LC/MS systems NOTE N This manual gives links to most references. If you have an electronic copy of this manual, you can easily download the documents from the Agilent literature library. Look for and
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Tip 1: How to use Agilent 82357B USB/GPIB converter in NI’s MAX or LabVIEW? Figure 2. Typical setup for Agilent IO Libraries Suite. 1 Agilent I/O Libraries Each Agilent IO product is bundled with the Agilent I/O libraries. There are four I/O libraries included in Agilent IO libraries Suite: Agilent
