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1 Specifications and Operating Modes

March 14, 2014, 715004387 Rev. B

MassLynx v4.1

MassLynx software acquires, analyzes, manages, and distributes mass

spectrometry, ultraviolet (UV), evaporative light scattering, and analog data.
OpenLynx

and TargetLynx

application managers are included as

standard software with MassLynx.
See the MassLynx v4.1 user documentation and online Help for information

about using MassLynx software.
You configure settings, monitor performance, run diagnostic tests, and

maintain the system and its modules via the MassLynx Instrument Console

application.
The Instrument Console software, which functions independently of

MassLynx software, does not recognize or control data systems.
See the online Help for the Instrument Console system for details.

UNIFI v1.6

UNIFI software integrates mass spectrometry, UPLC chromatography, and

informatics data work flows.
See UNIFI v1.6 user documentation and online Help for more information

about using UNIFI software.

Summary of Contents for Xevo TQD

Page 2: ...ii March 14 2014 715004387 Rev B...

Page 3: ...document consult the Waters Web site waters com Trademarks ACQUITY ACQUITY UltraPerformance LC ACQUITY UPLC Alliance Connections INSIGHT ESCi MassLynx nanoACQUITY nanoACQUITY UPLC nanoTile THE SCIENC...

Page 4: ...emoval or disposal of any Waters product You can reach us via the Internet telephone or conventional mail Safety considerations Some reagents and samples used with Waters instruments and devices can p...

Page 5: ...nalysis assuming a maximum leak into the laboratory atmosphere of 10 LC eluate Warning To avoid electric shock use the SVT type power cord in the United States and HAR type or better in Europe The mai...

Page 6: ...ge caused by spilled solvent do not place reservoir bottles on top of the instrument or on its front ledge unless in the bottle tray provided Warning To prevent ignition of flammable solvent vapors in...

Page 7: ...exposure to toxic or biohazardous substances never place containers on top of the instrument or on its front covers Warning To avoid burn injuries ensure the source heater is turned off and the ion bl...

Page 8: ...of decontamination to be used and the appropriate protection for personnel undertaking the decontamination process You must handle items such as syringes fused silica lines and borosilicate tips used...

Page 9: ...ice may not cause harmful interference and 2 this device must accept any interference received including interference that may cause undesired operation Electrical power safety notice Do not position...

Page 10: ...Symbol Definition Manufacturer Date of manufacture Part number catalog number Serial number Supply ratings Authorized representative of the European Community Confirms that a manufactured product com...

Page 11: ...pment with this symbol may contain hazardous substances and should not be disposed of as general waste For compliance with the Waste Electrical and Electronic Equipment Directive WEEE 2012 19 EU conta...

Page 12: ...follow acceptable calibration methods using at least five standards to generate a standard curve The concentration range for standards should include the entire range of QC samples typical specimens a...

Page 13: ...1 ISM Classification ISM Group 1 Class A This classification has been assigned in accordance with CISPR 11 Industrial Scientific and Medical ISM instrument requirements Group 1 products apply to inten...

Page 14: ...h 14 2014 715004387 Rev B EC authorized representative Waters Corporation Stamford Avenue Altrincham Road Wilmslow SK9 4AX United Kingdom Telephone 44 161 946 2400 Fax 44 161 946 2480 Contact Quality...

Page 15: ...ty advisories ix Operating this instrument x Applicable symbols x Audience and purpose xii Intended use of the Xevo TQD xii Calibrating xii Quality control xii EMC considerations xiii Canada spectrum...

Page 16: ...System operation 35 Ion optics 36 MS operating modes 37 MS MS operating modes 38 Product daughter ion mode 39 Precursor parent ion mode 40 Multiple reaction monitoring mode 40 Constant neutral loss m...

Page 17: ...62 APCI mode 62 Installing the IonSABRE II probe 63 Removing the IonSABRE II probe 65 Combined APPI APCI source 66 APPI operation 66 APCI operation 67 Dual mode operation 68 The combined APPI APCI so...

Page 18: ...n from the source 95 Operating the source isolation valve 96 Removing O rings and seals 99 Cleaning the instrument case 100 Emptying the exhaust trap bottle 100 Gas ballasting the roughing pump 102 Ga...

Page 19: ...bly 137 Cleaning the ion guide assembly 140 Removing the differential aperture from the ion guide 142 Fitting the differential aperture to the ion guide assembly 144 Fitting the ion guide assembly to...

Page 20: ...189 APPI APCI source replacing the APPI lamp drive seals 191 Removing the APPI lamp drive assembly seals 191 Fitting the new APPI lamp drive assembly O rings 197 Replacing the instrument s fuses 199...

Page 21: ...g the liquid waste line 233 Connecting the workstation 235 Connecting Ethernet cables 236 I O signal connectors 237 Signal connections 238 Connecting to the power supply 241 C Materials of Constructio...

Page 22: ...xxii March 14 2014 715004387 Rev B...

Page 23: ...uding its controls and connections for gas and plumbing Contents Topic Page Uses and compatibility 24 Ionization techniques and source probes 31 IntelliStart Fluidics system 34 Ion optics 36 MS operat...

Page 24: ...ation ESI APCI ESCi source Requirement Dedicated APCI operation requires an additional probe IonSABRE II Optional dual mode APPI APCI source Optional NanoFlow ESI source Optional TRIZAIC UPLC source O...

Page 25: ...tart technology monitors LC MS MS performance and reports when the instrument is ready for use The software automatically tunes and mass calibrates the instrument displays performance readbacks and en...

Page 26: ...e ACQUITY Xevo TQD UPLC MS system includes an ACQUITY UPLC ACQUITY UPLC H Class or ACQUITY UPLC I Class system and the Waters Xevo TQD fitted with the ESI APCI ESCi source The nanoACQUITY Xevo TQD UPL...

Page 27: ...ocuments on http www waters com click Services and Support Support Library System Core components ACQUITY UPLC Binary solvent manager Sample manager Column heater UPLC detectors Solvent tray ACQUITY U...

Page 28: ...tween 0 20 and 5 00 L min With open loop control and nanoACQUITY UPLC columns of internal diameters ranging from 75 m to 1 mm the flow rates can extend to 100 L min The column hardware and the matched...

Page 29: ...2777 autosampler Spark Holland Symbiosis system Software and data system MassLynx v4 1 or UNIFI software can control the mass spectrometer See page 30 for more information about those applications Bot...

Page 30: ...rmation about using MassLynx software You configure settings monitor performance run diagnostic tests and maintain the system and its modules via the MassLynx Instrument Console application The Instru...

Page 31: ...accommodates eluent flow rates as high as 2 mL min making it suitable for LC applications in the range 100 L min to 2 mL min See page 58 for further details Combined ESI and APCI ESCi Combined electr...

Page 32: ...e concentration the ion currents observed approximate those seen in normal flow rate electrospray However for similar experiments NanoFlow s significant reduction in sample consumption accompanies sig...

Page 33: ...hromatography APGC The Waters APGC couples an Agilent GC with the Xevo TQD making it possible to perform LC and GC analyses in the same system without compromising performance The APGC provides comple...

Page 34: ...se smaller volumes see page 52 The reservoirs can also deliver sample through direct or combined infusion to enable optimization at analytical flow rates From a wash reservoir that contains solvent fo...

Page 35: ...tions between the fluidics components to carry out the operations processed by the software You can set IntelliStart fluidics configuration requirements in the system console You can edit the paramete...

Page 36: ...an be filtered according to their mass to charge ratios 4 The mass separated ions pass into the T Wave collision cell where they either undergo collision induced dissociation CID or pass to the second...

Page 37: ...ed ion recording SIR mode for quantitation when you cannot find a suitable fragment ion to perform a more specific multiple reaction monitoring MRM analysis see page 38 In SIR and MRM modes neither qu...

Page 38: ...tatic at precursor mass Fragment precursor ions and pass all masses Scanning Precursor parent ion spectrum Scanning Static at product mass MRM Static at precursor mass Static at product mass PICS Prod...

Page 39: ...t ion mode Typical applications Product ion mode is typically used for the following applications Method development for MRM screening studies Identifying product ions for use in MRM transitions Optim...

Page 40: ...MS MS equivalent of SIR Because both MS1 and MS2 are static greater dwell time on the ions of interest is possible so the sensitivity achieved is better compared with scanning mode MS MS This mode is...

Page 41: ...de the background for all other components This enables fast characterization of potential matrix effects providing a platform for more robust method development Typical application You typically use...

Page 42: ...s If it does the loss registers at the detector In constant neutral loss mode the spectrum shows the masses of all precursors that actually lost a fragment of a certain mass Constant neutral loss mode...

Page 43: ...he ACQUITY UPLC Console or UNIFI software displays an error message alerting you that a leak has developed See Waters ACQUITY UPLC Leak Sensor Maintenance Instructions for complete details Vacuum syst...

Page 44: ...following figure shows the rear panel locations of the connectors used to operate the instrument with external devices Instrument rear panel Power Source vent Turbo vacuum Nitrogen inlet Collision cel...

Page 45: ...ration This chapter describes how to start and shut down the instrument Contents Topic Page Starting the mass spectrometer 46 Preparing the IntelliStart Fluidics system 52 Rebooting the instrument 54...

Page 46: ...e rear panel ensure the nitrogen supply is connected to the instrument s nitrogen inlet connection see the figure on page 44 Requirement The nitrogen must be dry and oil free with a purity of at least...

Page 47: ...to initialize and to sound an alert indicating that the PC is ready Tip The power and status LEDs change as follows Each system instrument s power LED shows green During initialization the binary or...

Page 48: ...which the turbopump is starting the roughing pump starts IntelliStart displays Instrument in standby and the Operate LED remains off c Wait a minimum of 2 hours for the instrument to be fully pumped d...

Page 49: ...mode and the Operate LED remains off c Wait a minimum of 2 hours for the instrument to be fully pumped down evacuated Tip In the Instrument Summary pane the Status indicator shows green when the instr...

Page 50: ...tatus Power LED The power LED to the top right hand side of the mass spectrometer s front panel indicates when the instrument is powered on or powered off Operate LED The Operate LED on the right hand...

Page 51: ...e according to the following table If you are using an APCI interface IntelliStart software automatically sets the parameters according to the following table Flow rate versus temperature and gas flow...

Page 52: ...ndard reservoir bottles 15 mL for instrument setup and calibration Use the Low volume Adaptor Kit sold separately to infuse smaller volumes The low volume vials have a volume of 1 5 mL Required materi...

Page 53: ...o the manifold and tighten it 3 Screw the low volume vial into the adaptor 4 For each low volume vial ensure that the end of the solvent delivery tube is positioned so that it is close to but does not...

Page 54: ...strument s solvent delivery system can require more than one purge cycle to minimize carryover Rebooting the instrument The reset button causes the mass spectrometer to reboot Reboot the instrument wh...

Page 55: ...ource When leaving the mass spectrometer unused for a long period In these instances put the mass spectrometer in Standby mode See the online Help for details Emergency shutdown of the mass spectromet...

Page 56: ...2 Preparing for Operation 56 March 14 2014 715004387 Rev B...

Page 57: ...chemical ionization Combined Atmospheric Pressure Photoionization APPI APCI NanoFlow For details about other Waters and third party source options refer to the documentation supplied with the source...

Page 58: ...inside its source 2 Remove the protective sleeve if fitted from the ESI probe tip Warning To avoid personal contamination with biohazards or toxic materials and to avoid spreading contamination to unc...

Page 59: ...assembly 4 Tighten the probe locking ring to secure the probe in place Requirement Fully tighten the probe locking ring Doing so ensures a successful result on the automatic pressure test which runs...

Page 60: ...low rates 1 2 mL min Requirements If you are replacing the tubing between the selector valve and the probe minimize the length to reduce peak broadening When cutting the tubing to length cut it square...

Page 61: ...probe from the probe adjuster assembly 6 If available fit the protective sleeve to the ESI probe tip Warning To avoid personal contamination with biohazards or toxic materials and to avoid spreading c...

Page 62: ...mode an option for the mass spectrometer produces singly charged protonated or deprotonated molecules for a broad range of nonvolatile analytes The APCI interface consists of the ESI APCI ESCi enclos...

Page 63: ...instrument for working on the source see page 88 2 With the probe label facing toward you carefully slide the IonSABRE II probe into the hole in the probe adjuster assembly ensuring that the probe loc...

Page 64: ...flow rates 1 2 mL min use 0 005 inch ID tubing for sample flow rates 1 2 mL min Requirements If you are replacing the tubing between the selector valve and the probe minimize the length to reduce peak...

Page 65: ...g ring 5 Carefully remove the probe from the probe adjuster assembly Warning To avoid personal contamination with biohazards or toxic materials and to avoid spreading contamination to uncontaminated s...

Page 66: ...advanced into the source APPI mode The IonSABRE II probe introduces vaporized sample into the source where photons generated by an ultraviolet UV lamp mounted in the APPI lamp drive assembly produce s...

Page 67: ...introduces vaporized sample into the source The sample passes between the sample cone and the corona pin which typically operates with a discharge current of 5 A The corona discharge generates ions th...

Page 68: ...for dual operation When the source is configured for dual operation in APCI mode current is applied to the corona pin but the repeller electrode is inactive Dual operation in APCI mode When the source...

Page 69: ...comprises the standard IonSABRE II probe and a source enclosure with an APPI lamp drive incorporated The combined APPI APCI source enclosure Notice To prevent damage to the corona pin and lamp assemb...

Page 70: ...ne window provides a constant photon output You vary the intensity of incident radiation upon the sample molecules by adjusting the distance between the UV lamp and probe tip APPI lamp drive assembly...

Page 71: ...ce enclosure see page 92 5 Install the corona pin see page 93 6 Connect the APPI drive cable to the instrument s front panel connector Warning To avoid personal contamination with biohazards or toxic...

Page 72: ...front panel 4 Disconnect the APPI drive cable from the instrument s front panel 5 Remove the source enclosure see page 90 Notice To prevent damage to the corona pin and lamp assembly ensure that the l...

Page 73: ...comprises the NanoFlow stage for x axis y axis and z axis adjustment the sprayer enclosure and a microscope camera NanoFlow source stage and microscope camera A sprayer is mounted on an X Y Z stage th...

Page 74: ...e page 61 If you are removing an IonSABRE II probe see page 65 3 Remove the existing source enclosure see page 90 Warning To avoid personal contamination with biohazards or toxic materials and to avoi...

Page 75: ...unted beneath the stage on the front of the NanoFlow source and your sprayer Tip For details regarding how to fit each sprayer see the corresponding reference Waters Universal NanoFlow Sprayer Install...

Page 76: ...age cable to the instrument s HV connection Tip The NanoFlow stage contains a high voltage interlock so the capillary voltage the voltage applied to the sprayer assembly and the sampling cone voltage...

Page 77: ...tage out of the NanoFlow source enclosure and remove the magnetic cover 4 Unscrew the retaining screw and lift the sprayer from the stage Warning To avoid lacerations puncture injuries and possible co...

Page 78: ...capillary from the sprayer 7 Carefully remove the new borosilicate glass capillary from its case by lifting vertically while pressing on the foam with two fingers 8 Load sample into the capillary usin...

Page 79: ...the capillary 10 Fit the capillary into the holder probe 11 Finger tighten the nut so that 5 mm of glass capillary protrude from its end Tip Measure the protrusion from the end of the nut to the shoul...

Page 80: ...n For tuning instructions see the instrument s online help Restarting a stalled borosilicate glass capillary electrospray Should the spray stop you can restart it To do so in the MassLynx Tune window...

Page 81: ...n or inside its source 88 Removing and refitting the source enclosure 90 Installing and removing the corona pin 93 Operating the source isolation valve 96 Removing O rings and seals 99 Cleaning the in...

Page 82: ...e heater 167 Replacing the ion block source heater 170 Replacing the source assembly seals 174 Replacing the air filter 178 Replacing the roughing pump oil 180 Replacing the roughing pump s oil demist...

Page 83: ...equired See page 100 Replace the oil free scroll pump s seals Annually See Edwards document XDS35i Instruction Manual A730 01 880 Gas ballast the roughing pump ESI weekly See page 102 Inspect and adju...

Page 84: ...ona pin APCI and ESCi modes When the corona pin is corroded or black or the sensitivity decreases to unacceptable levels See page 166 Replace the IonSABRE II probe heater Options using the IonSABRE II...

Page 85: ...Annually Tip Applications that contaminate the roughing pump oil reduce this period which must be determined from experience See page 183 Clean the APPI APCI source UV lamp window When the window bec...

Page 86: ...collaboration option that controls the two way connection with the ACQUITY UPLC system by enabling the Connections INSIGHT iAssist service level Consult these sources for more information about Connec...

Page 87: ...ging tubing or operating the instrument Know the physical and chemical properties of the solvents used see the Material Safety Data Sheets for the solvents in use Warning To avoid electric shock do no...

Page 88: ...ent for operations on or inside its source 1 In the Instrument Console click Stop Flow to stop the LC flow or if column flow is required divert the LC flow to waste as follows a In the Instrument Cons...

Page 89: ...C flow to waste as follows a On the Setup pane click Fluidics b On the Sample Fluidics page from the Flow Path menu select Waste 2 Click Instrument Standby Mode and confirm that the Operate indicator...

Page 90: ...the source If you are removing an ESI probe see page 61 If you are removing an IonSABRE II probe see page 65 3 Disconnect the probe adjuster and options cables from the instrument s connectors 4 Pull...

Page 91: ...ands grasp the source enclosure and lift it vertically off the two supporting studs on the source adaptor housing 6 Store the cables neatly by plugging them into the cable storage positions on the rea...

Page 92: ...nt s connectors Warning To avoid personal contamination with biologically hazardous or toxic materials and to avoid spreading contamination to uncontaminated surfaces wear clean chemical resistant pow...

Page 93: ...re Warning To avoid personal contamination with biologically hazardous or toxic materials and to avoid spreading contamination to uncontaminated surfaces wear clean chemical resistant powder free glov...

Page 94: ...Store the blanking plug in a safe location Corona pin mounting contact 4 Fit the corona pin to the mounting contact ensuring that the corona pin is securely mounted Corona pin Warning To avoid punctur...

Page 95: ...page 95 Tip Store the corona pin in a safe location 4 Fit the blanking plug to the corona pin mounting contact see the figure on page 94 5 Close the source enclosure Warning To avoid personal contamin...

Page 96: ...he enclosure Warning To avoid personal contamination with biohazards or toxic materials and to avoid spreading contamination to uncontaminated surfaces wear clean chemical resistant powder free gloves...

Page 97: ...horizontal position Warning To avoid personal contamination with biohazards or toxic materials and to avoid spreading contamination to uncontaminated surfaces wear clean chemical resistant powder fre...

Page 98: ...4 Maintenance Procedures 98 March 14 2014 715004387 Rev B 2 Close the source enclosure TP03130 Isolation valve handle in open position...

Page 99: ...O ring 1 Use the forked end of tool 1 to impale the O ring or seal 2 Pull the O ring or seal from its groove if necessary use tool 2 as an aid 3 Dispose of the O ring or seal in accordance with local...

Page 100: ...Emptying the exhaust trap bottle Inspect the exhaust trap bottle in the instrument s exhaust line daily and empty it before it is more than 10 full Nitrogen exhaust trap bottle Notice To avoid damagin...

Page 101: ...rap bottle to the cap 6 Secure the nitrogen exhaust trap bottle in the upright position 7 Close the source enclosure Tip A leak test runs automatically If the test results in a failure ensure that the...

Page 102: ...ors tend to condense in the pump oil diminishing pumping efficiency Gas ballasting purges condensed contaminants from the oil Note This procedure is not required for an oil free roughing pump Roughing...

Page 103: ...103 A handle operated gas ballast valve See page 105 Gas ballasting a pump fitted with a screwdriver operated gas ballast valve Required material Flat blade screwdriver Notice To avoid shortening the...

Page 104: ...er turn to the open position 2 Run the pump for 30 to 60 minutes Tip It is normal for the roughing pump temperature to increase during ballasting To maintain an ambient temperature of less than 40 C i...

Page 105: ...To maintain an ambient temperature of less than 40 C in the space where the pump is located ensure the space is adequately ventilated 3 Move the gas ballast valve handle on the pump clockwise from th...

Page 106: ...the oil level in the sight glass is lower when the pump is running than when it is stopped When the pump is running the oil level is typically at 30 to 60 of the maximum level Adding oil to the rough...

Page 107: ...r plug is tightened the plug seals by means of an O ring Compression is controlled by the O ring groove depth in the plug Overtightening does not improve the plug seal it merely makes the plug difficu...

Page 108: ...related causes for decreased signal intensity See page 109 If cleaning the sample cone and cone gas nozzles fails to increase signal sensitivity also clean the extraction cone See page 119 If cleanin...

Page 109: ...nation to uncontaminated surfaces wear clean chemical resistant powder free gloves when working with the source components Warning To avoid electric shock before beginning this procedure prepare the i...

Page 110: ...sampling cone assembly 90 degrees moving the handle from the vertical to the horizontal position 3 Slide the sampling cone assembly out of the ion block assembly Notice To avoid damaging the instrume...

Page 111: ...nd cone extraction tool To disassemble the sampling cone assembly 1 Slide the collar to the end of the combined 2 5 mm Allen wrench and cone extraction tool Warning To avoid personal contamination wit...

Page 112: ...ert the collar in the sample cone 3 Rotate the tool and collar counter clockwise and then lift them to remove the sample cone from the cone gas nozzle Notice To avoid damaging the fragile sample cone...

Page 113: ...of deterioration or damage dispose of it in accordance with local environmental regulations 6 Unscrew and remove the PEEK cone gas nozzle handle from the cone gas nozzle Warning To avoid spreading co...

Page 114: ...1 If the sample cone contains debris place a drop of formic acid on its aperture 2 Immerse the sample cone cone gas nozzle and cone gas nozzle handle in separate glass vessels containing 1 1 methanol...

Page 115: ...in the ultrasonic bath for 10 minutes 5 Carefully remove the components from the vessels and blow dry them with inert oil free gas 6 Inspect each component for persisting contamination If contaminatio...

Page 116: ...2 Carefully fit the sample cone into the cone gas nozzle 3 Fit the O ring into the groove created between the sample cone and cone gas nozzle Fit a new O ring if the old one has been disposed of Notic...

Page 117: ...aminated surfaces wear clean chemical resistant powder free gloves when working with the source components Warning To avoid puncture wounds take great care while working with the source enclosure open...

Page 118: ...the cone gas nozzle handle is oriented horizontally and at the top and then slide the sampling cone assembly into the ion block assembly 3 Grasp the cone gas nozzle handle and use it to rotate the sam...

Page 119: ...Vent and shut down the mass spectrometer see the mass spectrometer s online Help for details 2 Close the source isolation valve see page 96 Warning To avoid personal contamination with biohazards or...

Page 120: ...mbined 2 5 mm Allen wrench and cone extraction tool to unscrew the 4 captive screws that secure the ion block assembly 4 Remove the ion block assembly from the PEEK ion block support TP03130 Screws se...

Page 121: ...llen wrench and cone extraction tool to loosen the captive screws securing the 2 PEEK extraction cone retainer clips and then rotate the retainer clips clear of the extraction cone Warning To avoid pe...

Page 122: ...ve the extraction cone handle insulator from the extraction cone handle Notice To avoid damaging the extraction cone aperture take great care when removing it from the ion block To avoid damaging the...

Page 123: ...gas for example nitrogen for drying air drying optional Wash bottle containing HPLC grade or better 1 1 methanol water Large beaker Warning To avoid personal contamination with biohazards or toxic mat...

Page 124: ...nd then placing the vessels in the ultrasonic bath for 10 minutes 4 Carefully remove the extraction cone from the vessel and blow dry it using inert oil free gas 5 Inspect the extraction cone for pers...

Page 125: ...to the source assembly Required materials Chemical resistant powder free gloves Combined 2 5 mm Allen wrench and cone extraction tool Warning To avoid personal contamination with biohazards or toxic...

Page 126: ...nozzle and extraction cone fails to increase signal sensitivity Disassembling the source ion block assembly Required materials Chemical resistant powder free gloves Combined 2 5 mm Allen wrench and co...

Page 127: ...s 4 Slide the sampling cone assembly out of the ion block assembly Notice To ensure correct operation of the ion block assembly after reassembly follow these guidelines Do not remove the sampling cone...

Page 128: ...mm Allen wrench and cone extraction tool to loosen the 2 ion block cover plate captive securing screws 6 Remove the ion block cover plate 7 Grasp the isolation valve and pull it out of the ion block...

Page 129: ...d 2 5 mm Allen wrench and cone extraction tool to loosen the captive PEEK terminal block securing screw 11 Use the needle nose pliers to grasp the PEEK terminal block and partially lift it out of the...

Page 130: ...ly grasp the heat shrink tubing on the heater cartridge assembly and carefully slide it and the PEEK terminal block out of the ion block 13 Use the O ring removal kit to carefully remove the cover sea...

Page 131: ...hole in the ion block blanking plug and then unscrew and remove the ion block blanking plug and associated seal 17 If the blanking plug seal shows signs of deterioration or damage dispose of it in ac...

Page 132: ...ction cone retainer clips 19 Remove the extraction cone from the ion block Notice To avoid damaging the extraction cone aperture take great care when removing the extraction cone from the ion block To...

Page 133: ...Chemical resistant powder free gloves Appropriately sized glass vessels in which to completely immerse components when cleaning Use only glassware not previously cleaned with surfactants HPLC grade o...

Page 134: ...ltrasonic bath for 10 minutes 4 Carefully remove the components from the vessels and blow dry them using inert oil free gas Inspect each component for persisting contamination Requirement If contamina...

Page 135: ...extraction cone seal to the ion block 2 Fit the extraction cone handle s insulator onto the extraction cone handle 3 Fit the extraction cone onto the ion block 4 Fit the 2 PEEK extraction cone retaine...

Page 136: ...extraction tool to tighten the captive PEEK terminal block securing screw 11 Ensure that the grooves for the cover seal cone gas O ring and isolation valve O ring are free of dirt and debris Tip If c...

Page 137: ...and use it to rotate the sampling cone assembly through 90 degrees 21 Fit the ion block assembly to the source assembly see page 125 Cleaning the ion guide assembly Clean the ion guide assembly if cle...

Page 138: ...the adaptor housing and remove the ion block support 4 If any of the O rings show signs of deterioration or damage dispose of them in accordance with local environmental regulations Warning To avoid s...

Page 139: ...of the ion guide and remove the guide from the adaptor housing Notice To avoid damaging the ion guide assembly when removing it from the source assembly do not grasp the ion guide by its metal lens p...

Page 140: ...inert gas for example nitrogen for drying air drying optional HPLC grade or better 1 1 methanol water Wash bottle containing HPLC grade or better 1 1 methanol water Large beaker To clean the ion guide...

Page 141: ...ow dry it using inert oil free gas 7 Inspect the ion guide assembly for persisting contamination Requirement If contamination is present do as follows a Use the wash bottle containing methanol to rins...

Page 142: ...secure the differential aperture to the 3 supporting rods 2 Remove the differential aperture from the ion guide Notice To avoid a reduction in sensitivity remove and clean the differential aperture on...

Page 143: ...ol water formic acid 4 Place the vessel in the ultrasonic bath for 30 minutes 5 If you used formic acid in the cleaning solution rinse the differential aperture by immersing it in a glass vessel conta...

Page 144: ...ligns correctly with the ion guide assembly sight along the central axis of the ion guide from the ion entry side and confirm that the hole at the centre of the differential aperture is concentric wit...

Page 145: ...n block support onto the source 1 Ensure that the grooves for the PEEK ion block support O rings are free from dirt and debris Warning To avoid personal contamination with biohazards or toxic material...

Page 146: ...p To fit an O ring in its groove start fitting the O ring at the notch in the groove and then progressively work the ring into the groove in either direction from the notch 3 Fit the PEEK ion block su...

Page 147: ...e gloves 7 mm wrench 10 mm wrench To remove the ESI probe tip and gasket 1 Remove the ESI probe from the source see page 61 Warning To avoid personal contamination with biohazards or toxic materials a...

Page 148: ...ch 14 2014 715004387 Rev B 2 Use the 10 mm wrench to remove the probe tip Tip If the probe tip is difficult to remove use the 7 mm wrench in conjunction with the 10 mm wrench Probe tip 10 mm wrench Pr...

Page 149: ...accordance with local environmental regulations 5 If the probe tip is damaged dispose of it in accordance with local environmental regulations Warning To avoid spreading contamination dispose of the...

Page 150: ...mm wrench to tighten the probe tip 4 Use the nebulizer adjuster knob to adjust the capillary so that it protrudes by approximately 0 5 mm from the end of the probe 5 Fit the ESI probe onto the source...

Page 151: ...ose pliers To remove the existing capillary 1 Remove the probe from the source see page 61 2 Retrieve the combined 2 5 mm Allen wrench and cone extraction tool from its storage location on the source...

Page 152: ...ined 2 5 mm Allen wrench and cone extraction tool to remove the 3 screws retaining probe end cover 4 Remove the end cover and gasket from the probe assembly 5 Unscrew and remove the nebulizer adjuster...

Page 153: ...March 14 2014 715004387 Rev B 153 6 Use the 10 mm wrench to remove the probe tip Tip If the probe tip is difficult to remove use the 7 mm wrench in conjunction with the 10 mm wrench Probe tip 10 mm w...

Page 154: ...e 9 Unscrew and remove the knurled collar from the UNF coupling 10 Remove the knurled collar and conductive sleeve from the capillary 11 Use the 7 mm wrench to loosen the locknut Tip Use the 8 mm wren...

Page 155: ...uired materials Chemical resistant powder free gloves Combined 2 5 mm Allen wrench and cone extraction tool 10 mm wrench Needle nose pliers LC pump HPLC grade or better 1 1 acetonitrile water Ferrule...

Page 156: ...screw the connector into the PEEK union so that it is finger tight Rationale Doing so ensures a minimum dead volume when fitting the capillary 3 Fit the UNF coupling to the new capillary Warning To a...

Page 157: ...e capillary 10 Tighten the knurled collar onto the UNF coupling 11 Perform a leak test by attaching the free end of the PEEK tubing to an LC pump and pumping 50 50 acetonitrile water through it at 1 m...

Page 158: ...m Allen wrench and cone extraction tool to fit and tighten the 3 screws retaining the probe end cover 20 Return the combined 2 5 mm Allen wrench and cone extraction tool to its storage location on the...

Page 159: ...further details To clean the IonSABRE II probe tip 1 On the Instrument Console system tree click Xevo TQD Manual optimization 2 On the Manual Optimization page click to stop the liquid flow 3 Click G...

Page 160: ...ve the probe from the source see page 65 2 Retrieve the combined 2 5 mm Allen wrench and cone extraction tool from its storage location on the source adaptor housing 3 Use the combined 2 5 mm Allen wr...

Page 161: ...e PEEK union UNF coupling assembly and capillary from the probe Tip The PEEK union used with the IonSABRE II probe is notched on one of its flats a feature that distinguishes it from the PEEK union us...

Page 162: ...l regulations Installing the new capillary Required materials Chemical resistant powder free gloves Needle nose pliers 7 mm wrench Combined 2 5 mm Allen wrench and cone extraction tool Red PEEK tubing...

Page 163: ...t connector and screw the connector finger tight into the PEEK union Rationale Doing so ensures a minimum dead volume when fitting the capillary 3 Fit the UNF coupling to the new capillary Requirement...

Page 164: ...50 acetonitrile water through it at 1 mL min If leakage occurs disassemble and remake the connection and repeat the leak test If the backpressure on the LC pump is high replace the capillary and repea...

Page 165: ...ch and cone extraction tool to fit and tighten the 3 screws retaining the probe end cover 20 Return the combined 2 5 mm Allen wrench and cone extraction tool in its storage location on the source adap...

Page 166: ...g film and a methanol saturated tissue 3 Install the corona pin in the source see page 93 Warning To avoid personal contamination with biohazards or toxic materials and to avoid spreading contaminatio...

Page 167: ...robe heater Required material Chemical resistant powder free gloves To remove the IonSABRE II probe heater 1 Remove the probe from the source see page 65 Warning To avoid personal contamination with b...

Page 168: ...ce with local environmental regulations Notice To avoid damaging the probe heater s electrical connections do not twist the heater when removing it from the probe assembly Warning To avoid spreading c...

Page 169: ...llary sleeve on the probe assembly 3 Fit the probe heater to the probe assembly ensuring that the heater is fully seated on the probe assembly 4 Fit the probe to the instrument see page 63 5 In the In...

Page 170: ...5 mm Allen wrench and cone extraction tool Ion block source heater To replace the ion block source heater 1 Remove the ion block assembly from the instrument see page 119 2 Ensure that the isolation v...

Page 171: ...014 715004387 Rev B 171 3 Use the combined 2 5 mm Allen wrench and cone extraction tool to loosen the 2 captive screws securing the ion block cover plate 4 Remove the ion block cover plate Ion block c...

Page 172: ...llen wrench and cone extraction tool to remove the 2 screws securing the heater wires to the PEEK terminal block 6 Use the needle nose pliers to carefully swing the ring terminal tags out of the termi...

Page 173: ...he combined 2 5 mm Allen wrench and cone extraction tool to fit and tighten the 2 screws securing the heater wires to the PEEK terminal block 12 Fit the ion block cover plate onto the ion block assemb...

Page 174: ...nclosure seal Nebulizer gas seal Desolvation gas seal Removing the probe adjuster assembly probe and source enclosure seals Required materials Chemical resistant powder free gloves O ring removal kit...

Page 175: ...mbly see page 99 Probe seal Nebulizer gas seal 3 Use the O ring removal kit to carefully remove the following seals from the source enclosure Source enclosure seal Nebulizer gas seal Desolvation gas s...

Page 176: ...embly seals Required materials Chemical resistant powder free gloves Wash bottle containing HPLC grade or better 1 1 methanol water New seals Warning To avoid spreading contamination dispose of the se...

Page 177: ...nclosure Tip Start by feeding the seal into the groove at the bottom right hand corner and then working around the seal in a counterclockwise direction 3 Fit the following new seals to the source encl...

Page 178: ...material New air filter To replace the air filter 1 Lift the instrument s visor so that the source probe is fully exposed 2 Fully open the source enclosure 3 Disconnect the probe cable from the high...

Page 179: ...rd you 5 Remove and dispose of the old filter 6 Place the new filter flat on the inside part of the grill with its edges beneath the metal lip 7 Close the air filter grill 8 Connect the probe cable to...

Page 180: ...le Gas ballasting helps to circulate and mix the oil through the pump before draining 2 Vent and shut down the instrument see the mass spectrometer s online Help for details 3 Allow the roughing pump...

Page 181: ...drain plug is clean and properly seated 10 Use the 8 mm Allen wrench to fit and tighten the roughing pump s oil drain plug Warning To avoid spreading contamination dispose of the roughing pump oil in...

Page 182: ...se the 8 mm Allen wrench to refit the oil filler plug 15 Gas ballast the roughing pump see page 102 Tip After you add oil to the pump the following situations can occur The oil level drops slightly du...

Page 183: ...e mass spectrometer s online Help for details 2 Allow the roughing pump to cool 3 Use the 6 mm Allen wrench to remove the 4 bolts securing the exhaust flange to the roughing pump Warning To avoid pers...

Page 184: ...7 Rev B 4 Carefully remove the exhaust flange and oil demister element from the roughing pump 5 Use the 10 mm wrench to remove the nut that secures the oil demister element to the exhaust flange TP026...

Page 185: ...lange from the oil demister element 7 Remove the spring from the oil demister element 8 Dispose of the oil demister element in accordance with local environmental regulations Warning To avoid spreadin...

Page 186: ...of the spring fit the exhaust flange to the oil demister element Warning To avoid personal contamination with biohazards or toxic materials and to avoid spreading contamination to uncontaminated surf...

Page 187: ...st flange to the roughing pump Requirement The bolts securing the source exhaust flange to the roughing pump must each be sequentially and incrementally tightened until they are all fully tight 5 Use...

Page 188: ...om its storage location on the source adaptor housing 4 Hook the short end of the Allen wrench through the ring on the back of the bulb extraction plug and tug to remove it Warning To avoid personal c...

Page 189: ...urce enclosure 11 Slide closed the instrument s source interface door APPI APCI source cleaning the lamp window The transmission of the high energy photons responsible for APPI relies on the cleanline...

Page 190: ...on the source see page 88 2 Pull the source enclosure release located at the bottom right hand side outward and swing open the enclosure 3 Use methanol or isopropyl alcohol applied to the lint free cl...

Page 191: ...ly seals Required materials Chemical resistant powder free gloves Combined 2 5 mm Allen wrench and cone extraction tool 3 mm Allen wrench Small Phillips cross head screwdriver Small Pozidriv screwdriv...

Page 192: ...bulb extraction plug aperture 5 Clear an area lay out the soft cloth or mat and lay the source enclosure on its face Warning To avoid personal contamination with biohazards or toxic materials and to a...

Page 193: ...action tool to remove the remaining 2 lamp drive cover screws which were hidden by the release handle 8 Slide the cover off the lamp drive 9 Use the 3 mm Allen wrench to remove the 4 source enclosure...

Page 194: ...2 Slide the lamp assembly shaft and flange out of the APPI source enclosure Tip The cables remain attached to the shaft which you fully withdraw and lay on the bench beside the source enclosure TP0320...

Page 195: ...r screws 15 Remove the PEEK insulator from the end of the mounting shaft 16 Slide the shaft mounting flange off the shaft and note the correct orientation for its reassembly 17 Use the O ring removal...

Page 196: ...g from the APPI source enclosure side 20 Dispose of the O rings in accordance with local environmental regulations Warning To avoid spreading contamination dispose of the O rings in accordance with lo...

Page 197: ...ring in the small radius at the bottom of the groove Then use a suitable tool one with a circular cross section to roll the remainder of the O ring into the groove 2 Fit the lamp bulb sealing O ring...

Page 198: ...nge is uniformly seated on the APPI source enclosure side plate 8 Use the combined 2 5 mm Allen wrench and cone extraction tool to tighten the four mounting flange securing screws 9 Remove the mountin...

Page 199: ...e enclosure to the machine refit the corona pin and probe Refer to page 71 for instructions Replacing the instrument s fuses If one or both of the mass spectrometer s fuses blow the instrument will sh...

Page 200: ...4 Maintenance Procedures 200 March 14 2014 715004387 Rev B...

Page 201: ...uct manuals where they accompany statements describing the hazards and advising how to avoid them This appendix presents the safety symbols and statements that apply to all of the products that Waters...

Page 202: ...r a component of an instrument or device When one of these symbols appear in a manual s narrative sections or procedures an accompanying statement identifies the applicable risk and explains how to av...

Page 203: ...rning Risk of tipping Warning Risk of explosion Warning Risk of eye injury Warning To avoid injury from bursting nonmetallic tubing heed these precautions when working in the vicinity of such tubing w...

Page 204: ...tective panels The components they cover are not user serviceable Warning To avoid nonlethal electric shock ensure the mass spectrometer is in Standby mode before you touch any of its external surface...

Page 205: ...es of Health NIH publication Biosafety in Microbiological and Biomedical Laboratories BMBL Observe Good Laboratory Practice GLP at all times particularly when working with hazardous materials and cons...

Page 206: ...Bottles Prohibited symbol The Bottles Prohibited symbol alerts you to the risk of instrument damage caused by solvent spills Notice To avoid damaging the instrument s case do not clean it with abrasi...

Page 207: ...la conformit la r glementation peut annuler le droit de l utilisateur exploiter l quipement Achtung Jedwede nderungen oder Modifikationen an dem Ger t ohne die ausdr ckliche Genehmigung der f r die o...

Page 208: ...se trouvant proximit de l instrument Evitez d utiliser des tubes s v rement d form s ou endommag s Evitez d utiliser des tubes non m talliques avec du t trahydrofurane THF ou de l acide sulfurique ou...

Page 209: ...dimetilsolfossido provocano rigonfiamenti nei tubi non metallici riducendo notevolmente la pressione di rottura dei tubi stessi Advertencia se recomienda precauci n cuando se trabaje con tubos de pol...

Page 210: ...A Safety Advisories 210 March 14 2014 715004387 Rev B Nonmetallic Tetrahydrofuran THF Methylene chloride Dimethyl sulfoxide THF...

Page 211: ...par le mat riel risque d tre d fectueuses Vorsicht Der Benutzer wird darauf aufmerksam gemacht dass bei unsachgem er Verwenddung des Ger tes die eingebauten Sicherheitseinrichtungen unter Umst nden n...

Page 212: ...type et de la puissance indiqu s sur le panneau proximit du couvercle de la boite fusible de l instrument Vorsicht Zum Schutz gegen Feuer die Sicherungen nur mit Sicherungen ersetzen deren Typ und Ne...

Page 213: ...la rubrique Remplacement des fusibles du chapitre traitant des proc dures de maintenance Vorsicht Zum Schutz gegen Feuer die Sicherungen nur mit Sicherungen ersetzen deren Typ und Nennwert im Abschni...

Page 214: ...symbols The following electrical symbols and their associated statements can appear in instrument manuals and on an instrument s front or rear panels Electrical power on Electrical power off Standby...

Page 215: ...5004387 Rev B 215 Handling symbols The following handling symbols and their associated statements can appear on labels affixed to the packaging in which instruments devices and component parts are shi...

Page 216: ...A Safety Advisories 216 March 14 2014 715004387 Rev B...

Page 217: ...nt or remove it from service contact Waters Technical Service for recommended cleaning flushing and packaging procedures See page 87 Contents Topic Page External wiring and vacuum connections 218 Conn...

Page 218: ...panel connections appear in the figure below Note that the connectors and controls not identified are for use by Waters engineers only Rear panel Power Source vent Turbo vacuum Nitrogen inlet Collisio...

Page 219: ...tallation kit NW25 center rings included in the installation kit NW25 clamps included in the installation kit 10 mm reducer fitting included in the installation kit 10 mm ID nylon tube included in the...

Page 220: ...ct the roughing pump 1 Place the PTFE drip tray on the floor within 5 feet of the instrument 2 Place the pump on the PTFE drip tray Warning To avoid personal contamination with biohazards or toxic mat...

Page 221: ...osite end of the 10 mm nylon tube to the 10 mm source vent port on the instrument s rear panel 7 Using 1 hose clamp connect a length of 12 7 mm clear PVC exhaust tubing to the roughing pump exhaust po...

Page 222: ...ck the oil level in the pump see Checking the roughing pump oil level on page 106 and if needed Adding oil to the roughing pump on page 106 Requirement To ensure correct operation of the roughing pump...

Page 223: ...rical connections To make the electrical connections to the roughing pump 1 Connect the relay cable from the roughing pump d c connector to the pump connector on the instrument s rear panel 2 Connect...

Page 224: ...fe NW25 tee included in the installation kit NW25 center rings included in the installation kit NW25 clamps included in the installation kit NW40 center rings included in the installation kit Warning...

Page 225: ...ed in the Waters Rotary Pump Kit Bear in mind these requirements when connecting the roughing pump The pump must be horizontal or within one degree of horizontal The ambient temperature of area in whi...

Page 226: ...1 inch vacuum hose in step 4 to the 1 inch OD straight vacuum port on the instrument s rear panel 6 Connect the opposite end of the 10 mm nylon tube to the 10 mm source vent port on the instrument s...

Page 227: ...9 Connect electric cables to the roughing pump see page 227 Connecting electric cables to the Edwards oil free roughing pump Roughing pump connections To connect cables 1 Connect the relay cable from...

Page 228: ...as supply 1 Use the sharp knife to cut a 3 8 cm to 5 0 cm 1 5 inch to 2 inch length of 6 mm PTFE tubing Requirement Cut the tubing squarely that is perpendicularly to its horizontal axis 2 Connect one...

Page 229: ...ust connections 5 Attach the nitrogen regulator to the nitrogen supply 6 Install the 6 mm stud into the regulator outlet 7 Connect the free end of the long piece of 6 mm PTFE tubing to the 6 mm stud S...

Page 230: ...e 1 8 inch Swagelok nut and ferrule to connect the 1 8 inch stainless steel tube to the collision cell gas inlet on the rear of the instrument see the figure on page 229 2 Use the wrench to tighten th...

Page 231: ...nitrogen exhaust ensure that the nitrogen exhaust is vented via the nitrogen exhaust trap bottle and laboratory exhaust system The laboratory exhaust system must provide a minimum vacuum of 0 20 kPa...

Page 232: ...in the source exhaust system confirm the integrity of the system by performing the following leak test Leaks can result in the release of biohazardous or toxic materials Notice To avoid damage to the...

Page 233: ...ver the barbed fitting of the drain located at the bottom of the instrument Warning To prevent personal contamination with biohazards or toxic materials always wear chemical resistant powder free glov...

Page 234: ...t its end is above the surface of the waste solvent Positioning of drain tube Warning To prevent leakage of biohazards or toxic materials ensure that the drain line does not crimp or bend impeding flo...

Page 235: ...ort on the rear panel of the instrument 3 Connect the other end of the shielded network cable to the port labeled Instrument LAN on the workstation rear panel To connect the instrument to the power so...

Page 236: ...net connections 1 Connect one end of one shielded Ethernet cable to the network switch and then connect the other end to the Ethernet card on the preconfigured ACQUITY workstation Tip On preconfigured...

Page 237: ...are typically SELV include contact closure inputs and outputs for autosamplers and UV RI and fluorescence detector signal outputs for LC MS systems The electrical connections on the rear panel of this...

Page 238: ...ctions Description Analog Out Used for analog chart output functionality The output voltage range is 0 to 1 V The resolution of the voltage output is 12 bits Stop Flow Out Used to stop the solvent flo...

Page 239: ...tive leads of the signal cable to the connector 3 Slide the clamp with the bend facing down into the protective shield 4 Insert the clamp and shield with the bend facing down into the connection cover...

Page 240: ...signal cable into the connection cover and position the clamp over the cable leads Tighten the clamp into place with the second self tapping screw 6 Place the second connection cover over the first c...

Page 241: ...panel of the instrument 2 Connect the male end of the instrument power cord to the 200 to 240 V AC wall outlet prepared as described in the instrument Site Preparation Guide 3 Connect the power cord...

Page 242: ...B External Connections 242 March 14 2014 715004387 Rev B...

Page 243: ...aused by personal exposure to biohazards or toxic materials you must confirm the integrity of the source exhaust system and address any safety issues raised by the contents of this Appendix Contents T...

Page 244: ...r details about the most common ingredients used to prepare mobile phases Items exposed to solvent Item Material Autotune reservoirs High density polyethylene Corona discharge pin mounting contact PEE...

Page 245: ...er Methanol Acetonitrile Formic acid 0 1 Acetic acid 0 1 Trifluoroacetic acid 0 1 Ammonium acetate 10 mM Ammonium formate 10 mM These solvents are not expected to cause any problems with the materials...

Page 246: ...C Materials of Construction and Compliant Solvents 246 March 14 2014 715004387 Rev B...

Page 247: ...tubing or stainless steel finger tight screws to connect the selector valve to the source probes use the PEEK tubing and natural beige colored PEEK finger tight screws specified on page 250 Warning To...

Page 248: ...nt behind the visor The letters etched on the front of the valve represent the components to which the associated port is connected Etched letters with a light background indicate inputs while letters...

Page 249: ...15004387 Rev B 249 Plumbing schematic Requirement Ensure that the end of the tubing is fully submerged in the solvent in the wash reservoir P W R B A S LC LC column Xevo TQD probe Pump Reservoir A Res...

Page 250: ...visit Notice To avoid leaks when plumbing the IntelliStart Fluidics system use only the tubes nuts and ferrules shown in the following tables to ensure over pressure protection The use of parts not re...

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