This document provides instructions for venting and cleaning a 6400 Series QQQ mass spectrometer. Key steps include: 1. Venting the system and removing covers to access internal components. 2. Removing parts like the source, desolvation assembly, ion optics and ion transfer capillary. 3. Cleaning removable parts using a sonicator bath and preparing them for reinstallation. 4. Replacing any worn components such as canted spring coils. 5. Reinstalling components in reverse order and restoring vacuum to the system.

1. Standard Operating
Procedure
6400 Series QQQ Vent and Clean
Procedure
Revision : 1
Author: Jerry Rattanong Published Date: 11-15-17 Page 1 of 54
6400 SeriesQQQ Vent and CleanProcedure
The instructionsprovidedshouldbe usedtosupplementthe official 6000 SeriesLC/MSSystem
Maintenance Guide.Goto Agilent.com,clickon Resourcesonthe menunearthe top,selectlibraryand
thenusermanuals.Searchfor 6400 SeriesLC/MSSystemMaintenance Guide.
What youwill need:
SonicatorBath
Di H2O
LCMS grade H20
LCMS grade Methanol
Cleanglassbeakers,varioussizesfrom200 to 1000 mL
Cleanglassgraduatedcylinder,100mL
Liquidnox (www.alconox.com)
T8, T20, Torx screwdrivers
1.5mm ball screwdriver
CantedSpringCoils(2)
IonTransferCapillary
*These do notneedto be replacedeveryvent andclean.ConsultyourserviceengineerorAgilentforthe
change intervals.The guide will include instructionsonhow to change the coilsinthe desolvation
assembly andif replacingoutthe iontransfercapillarywithanew one,youobviouslydonotneedto
cleanit.
Ample space infrontof the massspec,behindthe massspecand ample table space tosetparts on.
Ample time toperformthe procedure (2-4hoursto perform, overnighttopumpdown).
Ventthe system
Make sure youare not runningany samplesandthere isno flow intothe massspectrometer. Usingthe
Mass Hunter Data acquisitionprogram,ventthe systembyrightclickingwithinthe QQQSection and
selectingvent.

2. Standard Operating
Procedure
6400 Series QQQ Vent and Clean
Procedure
Revision : 1
Author: Jerry Rattanong Published Date: 11-15-17 Page 2 of 54
Whenselected,adialogbox appears withthe followingmessage:
If you are sure youwant to proceed,clickyes. Whenthe processiscomplete anotherdialogbox
appears:

3. Standard Operating
Procedure
6400 Series QQQ Vent and Clean
Procedure
Revision : 1
Author: Jerry Rattanong Published Date: 11-15-17 Page 3 of 54
It isnow safe completelypoweroff the instrument.Startbyswitchingoff the powerbuttonfrontcover
of the massspec.

4. Standard Operating
Procedure
6400 Series QQQ Vent and Clean
Procedure
Revision : 1
Author: Jerry Rattanong Published Date: 11-15-17 Page 4 of 54
Next,unplugthe mainpowercable.The locationisbehindthe massspecandthe mainpowercable is
the lowerleftone.The cable isremovedhere.

5. Standard Operating
Procedure
6400 Series QQQ Vent and Clean
Procedure
Revision : 1
Author: Jerry Rattanong Published Date: 11-15-17 Page 5 of 54
Locate yourvacuum forelinepump,switchoff the powertothe vacuumand thenunplugit fromthe
back of the Mass Spectrometer.
Next,graspthe handle onthe front coverand pull ittowardsyou.

6. Standard Operating
Procedure
6400 Series QQQ Vent and Clean
Procedure
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Author: Jerry Rattanong Published Date: 11-15-17 Page 6 of 54
Once it isangledtowardyou,pull straightupto remove itfromthe bottom.

7. Standard Operating
Procedure
6400 Series QQQ Vent and Clean
Procedure
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Author: Jerry Rattanong Published Date: 11-15-17 Page 7 of 54
The LED cable is still attachedtothe cover to the backside of the cover.
Release the cable byspreadingtabs apart. The cable isnow loose andcan be removed.

8. Standard Operating
Procedure
6400 Series QQQ Vent and Clean
Procedure
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Author: Jerry Rattanong Published Date: 11-15-17 Page 8 of 54
Place the frontcover somewhereoutof the way.Withthe frontcoverout of the way,the nextstepisto
remove the topcover.

9. Standard Operating
Procedure
6400 Series QQQ Vent and Clean
Procedure
Revision : 1
Author: Jerry Rattanong Published Date: 11-15-17 Page 9 of 54
There are twoscrewsholdingthe topcoverinplace. Go around to the back and remove these screws.

10. Standard Operating
Procedure
6400 Series QQQ Vent and Clean
Procedure
Revision : 1
Author: Jerry Rattanong Published Date: 11-15-17 Page 10 of 54
Liftthe top coverout and place it somewhere outof the way.Next,the leftside covernearthe source
mustbe removed.Toaccomplishthat,we mustremove 4 screws. Use a Torx # 8 screwdrivertoremove
them. Also,remove the solventlinefromthe columncompartmenttothe selectionvalve, if youhaven’t
already.

11. Standard Operating
Procedure
6400 Series QQQ Vent and Clean
Procedure
Revision : 1
Author: Jerry Rattanong Published Date: 11-15-17 Page 11 of 54
Life the coverand place itout of the way.Now,we are leftwithafew cablestodisconnectandremove
fromthe auxiliarymodule.

12. Standard Operating
Procedure
6400 Series QQQ Vent and Clean
Procedure
Revision : 1
Author: Jerry Rattanong Published Date: 11-15-17 Page 12 of 54
Remove the LED Cable fromthe displayboardslot,alsoremove the selectorvalve andleaksensor
cables.
The spray chamberhighvoltage cable onthe leftside canbe removedwhenthe tabispressedin.

13. Standard Operating
Procedure
6400 Series QQQ Vent and Clean
Procedure
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Author: Jerry Rattanong Published Date: 11-15-17 Page 13 of 54
Nextloosenthe retainingscrewonthe bracketof the desolvationchamber.Then removethe nitrogen
dryinggas line and dryinggasheatercable.
The dryinggas heatercable can be removedbytwistingittorelease.

14. Standard Operating
Procedure
6400 Series QQQ Vent and Clean
Procedure
Revision : 1
Author: Jerry Rattanong Published Date: 11-15-17 Page 14 of 54
The dryinggas line isremovedbyadjustable wrench,butthe Source mustbe removedbefore youcan
have enoughclearance toremove the line.Remove the linefromyourselectorvalve to yourESIneedle
firstand thenliftthe source off the twopinson the door hinge.
Setthe Source off to the side.

15. Standard Operating
Procedure
6400 Series QQQ Vent and Clean
Procedure
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Author: Jerry Rattanong Published Date: 11-15-17 Page 15 of 54
Remove the mainboard1 cable fromthe back of the auxillarymodule. Liftthe auxillary module upand
setaside.
Use a flatheadscrewdrivertoloosenthe drainhose tubinghere andremove it.

16. Standard Operating
Procedure
6400 Series QQQ Vent and Clean
Procedure
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Author: Jerry Rattanong Published Date: 11-15-17 Page 16 of 54
Remove the spraysshieldbyturningcounterclockwise andsettothe side onaluminumfoil.Use aTorx
T-10 screwdrivertoremove the twogoldscrewslocatedonthe front. Remove the face plate alongwith
the middle piece and settothe side.Also, remove the capillarycap andsetto the side.

17. Standard Operating
Procedure
6400 Series QQQ Vent and Clean
Procedure
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Author: Jerry Rattanong Published Date: 11-15-17 Page 17 of 54
Replace yourgloveswithfreshcleangloves,graspthe iontransfercapillaryandpull itstraightout.Pull
straightout or riskbreakingitas you remove. Settothe side onto aluminumsheet.

18. Standard Operating
Procedure
6400 Series QQQ Vent and Clean
Procedure
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Author: Jerry Rattanong Published Date: 11-15-17 Page 18 of 54
The desolvation assembly isremovednext. Use aT-20 Torx screwdrivertoremove the retainingscrews
at the upperleftandlowerrightcorner.Slide itoutfromthe supportrods.Place the desolvation
assembly ontoaluminumfoil andprepare tochange outthe two cantedspringcoils.

19. Standard Operating
Procedure
6400 Series QQQ Vent and Clean
Procedure
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Author: Jerry Rattanong Published Date: 11-15-17 Page 19 of 54
Use a needle nose pliertoremove the twocables.Use aT20 Torx screwdrivertoremove the 4 screwson
the front.

20. Standard Operating
Procedure
6400 Series QQQ Vent and Clean
Procedure
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Author: Jerry Rattanong Published Date: 11-15-17 Page 20 of 54
Remove the frontpart of the desolvationassemblyandmake note of the orientationof the brown
spacerscoveringthe opening thatholdsthe firstcantedspringcoil.
Remove andsetto the side.

21. Standard Operating
Procedure
6400 Series QQQ Vent and Clean
Procedure
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Author: Jerry Rattanong Published Date: 11-15-17 Page 21 of 54
Use a fine pointed forcepstoremove the coil fromthe holder.Place anew coil intothe holderby
pushingwithyourfingers intothe channel withinthe holder. Avoidusingtoolstoinsert,asyoumay
damage your newcoil. Insertone side of the coil intothe channel,holditinplace while youpushthe
restintothe channel.Itwill expandandfit.

22. Standard Operating
Procedure
6400 Series QQQ Vent and Clean
Procedure
Revision : 1
Author: Jerry Rattanong Published Date: 11-15-17 Page 22 of 54
Next,goto the back side of the desolvationassembly,removethe fourT-20 screws,pull the coveroff
and disconnectthe twocables.
Remove the 2nd
cantedcoil springusingthe forceps.

23. Standard Operating
Procedure
6400 Series QQQ Vent and Clean
Procedure
Revision : 1
Author: Jerry Rattanong Published Date: 11-15-17 Page 23 of 54
Place the newcantedspringcoil and pushitinto the channel toseatit.
Reconnectthe 2 cablesand place the coverback on the Desolvation Chamber.Tightenthe 4screwsto
secure. Reassemble the frontof the chamber,place the spacersinthe correct orientation secure with
the 4 screwsand install the twocables. Setthe assembledchamberoff tothe side.Prepare toremove
the ionoptics.

24. Standard Operating
Procedure
6400 Series QQQ Vent and Clean
Procedure
Revision : 1
Author: Jerry Rattanong Published Date: 11-15-17 Page 24 of 54
Cleanawayany dustfrom the topof the manifold, loosenthe two retainingscrewson the rightside and
use a Torx-T20 screwdrivertoremove the twoscrewsonthe left.

25. Standard Operating
Procedure
6400 Series QQQ Vent and Clean
Procedure
Revision : 1
Author: Jerry Rattanong Published Date: 11-15-17 Page 25 of 54
Liftthe cover awayand place somewhere safe. Inthe vacuummanifold,take alook atthe cable
connectionarrangementof the ionoptics. The greenwire ispluggedinontopandthe blackisplugged
inthe bottom.The Lenscable isconnectedthrougha plugstyle harness.

26. Standard Operating
Procedure
6400 Series QQQ Vent and Clean
Procedure
Revision : 1
Author: Jerry Rattanong Published Date: 11-15-17 Page 26 of 54
Disconnectall three cables.
The nextstepis to remove the ionoptics. Use your righthand to pushon the back of the skimmer
spacerwhile onthe frontside,use yourlefthandto gentlypull onthe skimmerspacer.There willbe
some resistance until itsuddenly will be looseenoughtoremove.Ensure thatthe ionopticsdoesnot
bang or droponto anything.Place the ionopticsontoaluminumfoilforfurtherdisassembly.

27. Standard Operating
Procedure
6400 Series QQQ Vent and Clean
Procedure
Revision : 1
Author: Jerry Rattanong Published Date: 11-15-17 Page 27 of 54
At thispoint,if youhave an electron multiplierhornandwishtochange it out,now is the time to doso.
If not changingout the electronicmultiplierhorn,place the manifoldcoverbackon to minimizedust.

28. Standard Operating
Procedure
6400 Series QQQ Vent and Clean
Procedure
Revision : 1
Author: Jerry Rattanong Published Date: 11-15-17 Page 28 of 54
Locate the electron multiplierhornonthe rightside of the manifold.

29. Standard Operating
Procedure
6400 Series QQQ Vent and Clean
Procedure
Revision : 1
Author: Jerry Rattanong Published Date: 11-15-17 Page 29 of 54
Disconnectthe signal wire fromthe electronmultiplierhorn.Release the Multiplierfromitscage by
squeezingtogetherthe twohoops onthe retainingclip,pushdowntoclearthe hooksandliftup to
open.

30. Standard Operating
Procedure
6400 Series QQQ Vent and Clean
Procedure
Revision : 1
Author: Jerry Rattanong Published Date: 11-15-17 Page 30 of 54
Remove the electronmultiplierhornandreplace withanew one.Seatin the new multiplier
Secure withthe retailingclipandreconnectthe signal wire.Now let’sgobackto the previouslyremoved
ionopticsassembly.

31. Standard Operating
Procedure
6400 Series QQQ Vent and Clean
Procedure
Revision : 1
Author: Jerry Rattanong Published Date: 11-15-17 Page 31 of 54
Remove the twoscrewsonthe frontof the ion skimmer.
Grasp the edgesof the skimmer withyourleftfingers,holdthe assemblybythe blackspacerwiththe
otherand pull outthe skimmer. Donot dropthe skimmer.

32. Standard Operating
Procedure
6400 Series QQQ Vent and Clean
Procedure
Revision : 1
Author: Jerry Rattanong Published Date: 11-15-17 Page 32 of 54
Setthe skimmeronflatsurface,make sure nothingtouchesthe centercone opening.
Restthe assemblyonthe spacerskimmer suchthat the lens 2 is facingup.Use a 1.5mm ball screwdriver
to remove the twoscrewshere.

33. Standard Operating
Procedure
6400 Series QQQ Vent and Clean
Procedure
Revision : 1
Author: Jerry Rattanong Published Date: 11-15-17 Page 33 of 54
Remove the Lens 2, setto the side. Remove the spacerinsulatordirectly beneath.ThenRemove Lens1.
Remove the lastspacer.Setall to the side.

34. Standard Operating
Procedure
6400 Series QQQ Vent and Clean
Procedure
Revision : 1
Author: Jerry Rattanong Published Date: 11-15-17 Page 34 of 54
Nextremove these twoscrewsthatholdthe octopole tothe skimmerspacer.Holdontothe octopole
tube while doingso,donotdrop it.

35. Standard Operating
Procedure
6400 Series QQQ Vent and Clean
Procedure
Revision : 1
Author: Jerry Rattanong Published Date: 11-15-17 Page 35 of 54
Setthe skimmeroff tothe side,disconnectthe redandwhite wires onthe octopole.Make note of the
orientationbefore youremove.
The skimmerspacerisstill tetheredtothe Octopole bythe blue wire.Remove thatscrew usingatorx
screwdriver,removethe electrical harnessandplace the screw backinand tightendownsoyoudon’t
lose it. Leave the yellowwire connectiontothe skimmerspaceralone.

36. Standard Operating
Procedure
6400 Series QQQ Vent and Clean
Procedure
Revision : 1
Author: Jerry Rattanong Published Date: 11-15-17 Page 36 of 54
Let’sgatherall the parts to gointo the sonicator.Don’tforgetthe sprayshield,face plate andcapillary
cap from before.Ensure thatyoudonot sonicate anyspacersor o-rings.If youdid notreplace the ion
transfercapillarywithanewone,theninclude itforcleaning.

37. Standard Operating
Procedure
6400 Series QQQ Vent and Clean
Procedure
Revision : 1
Author: Jerry Rattanong Published Date: 11-15-17 Page 37 of 54
Place two1mL pipette tipsoneachendof the Iontransfercapillary.Use scissorstocut the endof each
tip.
Place the iontransfercapillaryintoa glass graduatedcylinder.Place the Ionsweepcone,iontransfer
cap, face plate intoa cleanbeaker.Place the Lens1 and Lens2 intoa separate cleanbeaker.Finally,
place the octopole assemblyintoacleanbeaker.

38. Standard Operating
Procedure
6400 Series QQQ Vent and Clean
Procedure
Revision : 1
Author: Jerry Rattanong Published Date: 11-15-17 Page 38 of 54
Cleanandsonicate parts.
(Handle eachcleaningstepwithfreshgloves)
Prepare a solutionof 1%Liquidnox indeionizedwaterorLCMS grade water.Fill eachbeakerto
completelysubmergeall partsandsonicate for10 - 15 mins.Do not sonicate formore longerthanthat.
Discard the solutionineachbeakerandone byone,rinse off the solutionfromthe partswithcopious
amountof tap water. Place all partsintonew cleanbeakersandgraduatedcylinder.Filleachbeaker
withLCMS grade Isopropanol andsonicate for5 mins.Remove the solventsfromthe beakersandfill up
withLCMS grade Methanol.Proceedtosonicate for5 minsagain.Performthe previousstepagainto
remove all tracesof residue fromeachsonicatedpart.

39. Standard Operating
Procedure
6400 Series QQQ Vent and Clean
Procedure
Revision : 1
Author: Jerry Rattanong Published Date: 11-15-17 Page 39 of 54
To dry each part withhouse nitrogengas,keepit submergedinthe methanol until readytocompletely
dry withthe nitrogen.Dryeachpart, one at a time andsetonto cleanaluminumfoil.If house nitrogenis
not available,place all partsontoaluminumfoil andallow toairdry.
Re assemble the IonOptics
Place the octopole ontothe skimmerspacer.Holdinplace andsecure withthe twoscrews.

40. Standard Operating
Procedure
6400 Series QQQ Vent and Clean
Procedure
Revision : 1
Author: Jerry Rattanong Published Date: 11-15-17 Page 40 of 54
Place the spacerback onto the endof the octopole assembly,thenplace lens1intothe assemblyby
locatingthe correct hole thatthe pinwill insertinto.
Place the otherspacer backonto the lens1 theninstall the lens2.Secure withthe twoscrews.

41. Standard Operating
Procedure
6400 Series QQQ Vent and Clean
Procedure
Revision : 1
Author: Jerry Rattanong Published Date: 11-15-17 Page 41 of 54
Reconnectthe white andredwires ontothe octopole assembly. Screw the blue wire backon.
Install the O-ringtothe back of the skimmer.Ensure thatthe skimmerspacerhasitsO-ringinstalledas
well.

42. Standard Operating
Procedure
6400 Series QQQ Vent and Clean
Procedure
Revision : 1
Author: Jerry Rattanong Published Date: 11-15-17 Page 42 of 54
It islikelythatthe O-ringcouldstill be stuckinthe vacuummanifold.Trytokeepitsecure here or on the
skimmerspacerwhile re-installingthe ion opticsassembly.Youmayneedtotry a few timestogetit
seatedandseal properly.

43. Standard Operating
Procedure
6400 Series QQQ Vent and Clean
Procedure
Revision : 1
Author: Jerry Rattanong Published Date: 11-15-17 Page 43 of 54
Slide the ionopticsbackintothe manifold.Re-connectthe blackandgreenwiresasshown.Reconnect
the electrical harness.

44. Standard Operating
Procedure
6400 Series QQQ Vent and Clean
Procedure
Revision : 1
Author: Jerry Rattanong Published Date: 11-15-17 Page 44 of 54
Place the manifoldcoverbackon.Secure withtwoscrewson the leftside andtightendownthe two
screwon the right.

45. Standard Operating
Procedure
6400 Series QQQ Vent and Clean
Procedure
Revision : 1
Author: Jerry Rattanong Published Date: 11-15-17 Page 45 of 54
Next,reassemble the 3piecesthatwill installtothe frontside of the desolvationassembly.

46. Standard Operating
Procedure
6400 Series QQQ Vent and Clean
Procedure
Revision : 1
Author: Jerry Rattanong Published Date: 11-15-17 Page 46 of 54
Alignthe face plate tothe twoholeshere.Screw tosecure but do not tightenall the way.
Instead,screwthe sprayshield inall the way,andonce it isseatedand connectscrew inanymore,align
the hole onthe topof the spray shield tothe 12 o’clock position,holdthatposition andfinally,tighten
the two screws.Remove the sprayshield andre-install sprayshield toensure thatthe hole onthe front
still linesupatthe 12 o’ clock positon. Removethe sprayandsetto the side,fornow.

47. Standard Operating
Procedure
6400 Series QQQ Vent and Clean
Procedure
Revision : 1
Author: Jerry Rattanong Published Date: 11-15-17 Page 47 of 54
Alignthe twoguide postsontothe desolvation assembly.Slide the desolvation assembly tothe endand
secure withthe twoscrews.
Lubricate the iontransfercapillarybysprayingthe sideswithLCMSgrade Isopropanol.Insertintothe
desolvation assembly.Goslowlyandstraightin.Youwill meetresistance ataroundthisposition.

48. Standard Operating
Procedure
6400 Series QQQ Vent and Clean
Procedure
Revision : 1
Author: Jerry Rattanong Published Date: 11-15-17 Page 48 of 54
Pushthe iontransfercapillarybackevenfurther,until youreachthisposition.
Place the iontransfercapillarycapback. Screw in the sprayshield.

49. Standard Operating
Procedure
6400 Series QQQ Vent and Clean
Procedure
Revision : 1
Author: Jerry Rattanong Published Date: 11-15-17 Page 49 of 54
Alignthe auxillarymodule upwiththe slotonthe rightside.Place the auxillarymodule inposition.

50. Standard Operating
Procedure
6400 Series QQQ Vent and Clean
Procedure
Revision : 1
Author: Jerry Rattanong Published Date: 11-15-17 Page 50 of 54
Reconnectthe draintubingonthe bottomof the desolvationassembly,reconnectthe nitrogen drying
gas line and dryinggas heatercable.
Insertcable intothe mainboard,locatedon the back of the auxillarymodule.

51. Standard Operating
Procedure
6400 Series QQQ Vent and Clean
Procedure
Revision : 1
Author: Jerry Rattanong Published Date: 11-15-17 Page 51 of 54
Reconnectthe spraychamberhighvoltage cable,andtightenthe retainingscrew locatedonthe
bracket.
Replace the cover.Secure withthe 4 screws.Reconnect the displayboardLED,selectionvalveandleak
Sensorcables.

52. Standard Operating
Procedure
6400 Series QQQ Vent and Clean
Procedure
Revision : 1
Author: Jerry Rattanong Published Date: 11-15-17 Page 52 of 54
Place the Source back onto the twohingesonthe door. Plugthe line fromselectorvalvebacktothe ESI
probe.Place the line fromthe columncompartmentbackintothe massspec.
Place the lowerendof the mass specfrontcover on.Attach the LED displaycable. Pushthe frontcover
forwardto secure iton the front the instrument.

53. Standard Operating
Procedure
6400 Series QQQ Vent and Clean
Procedure
Revision : 1
Author: Jerry Rattanong Published Date: 11-15-17 Page 53 of 54
Pluginthe mainpowercordand the foreline pumppowercord.Ensure everythingisconnect properly
and correctly.Poweronthe switchonthe back of the vacuum pump.

54. Standard Operating
Procedure
6400 Series QQQ Vent and Clean
Procedure
Revision : 1
Author: Jerry Rattanong Published Date: 11-15-17 Page 54 of 54
FinallyPoweronthe MassSpec.Allowroughlyafull dayto pumpdownthe mass spec.You are finally
finished.