Hdx RTC with Pepsin Washes and Clean BlankDoes Precondition with Quench for long label times
Long label time cutoff is now 50 sec
Added MS1FalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalseFalse|if {jit:1:Runtime} >= 1 AND %TIMINGRUN% then
MsgBox("Use Timing Run is True. Set to False in Method after Timing run",vbOKOnly,"Timing Run")
return True
else
return False
end if|1Load runtimes for the Analytical Acquisition method file1%MLYNXPROJECT%\acqudb\%LCACQMETHOD%-1-1Load runtimes for the Clean Blank Acquisition method fileTrue1False|IF %USECLEANBLANK% THEN RETURN "%MLYNXPROJECT%\acqudb\%LCCLEANBLANKMETHOD%" ELSE RETURN "%MLYNXPROJECT%\acqudb\%LCACQMETHOD%"| -1-1 Determies if there are too many jobs submitted to the queue|IF [{JobCount} - 1]>100 THEN RETURN 1 ELSE RETURN 0|1Falsec:\masslynx\status.iniMS_StatusReady-1Abort10Too many samples are submitted for this job. You've submitted {JobCount} experiments. There can be at most 100 experiments performed for a single queue. Determies if there are enough vials availabe for the submitted queue|IF [{JobCount} + %LABELSTARTVIAL% - 1]>100 THEN RETURN 1 ELSE RETURN 0|1Falsec:\masslynx\status.iniMS_StatusReady-1Abort10There are not enough sample vials to complete this queue. You've requested {JobCount} experiments starting with vial %LABELSTARTVIAL%. This exceeds the last vial position of 100. Initializes the HDX Runtime DLL11FalseHDx%ANALYSIS_METHOD%from methfrom meth[ROUND({2:Plugin.AnalyticalRuntime} + {2:Plugin.TrappingRuntime})]%POSTCLEANSOLV1%%POSTCLEANSOLV2%%VALVECLEANSOLV1%%VALVECLEANSOLV2%%PEPSINWASHES%%PEPSINWASHVOL%%PEPSINWASHDELAY%%POSTQUENCHREACTIONTIME%%LCACQMETHOD%Determines if the MS is ReadyFalse1Falsec:\masslynx\status.iniMS_StatusReady1Abort10The MS System is not ready. Please clear any errors in MassLynx.Determines if the LC is ReadyFalse1Falsec:\masslynx\status.iniLC_StatusReady1Abort10The UPLC System is not ready. Please clear any errors in MassLynx.Determines if there is an Issue with the Sample Queue|IF %TIMINGRUN% THEN RETURN 0 ELSE RETURN 1|2Falsec:\masslynx\status.iniQueue_StatusQueue Paused0Abort10The sample queue is paused in MassLynx. Please clear any errors with the LC/MS System. Clean INJ Syringe with Quench and transfer to waste22FalsePAL%INJTOOL%HDXWaste:1%QUENCHVOLUME%False0 mm-3 mm%FILLINGSPEED%0%%PULLUPDELAY%0%INJECTIONSPEED% Put Quench reagent in the reaction wellsTrue19FalsePAL%INJTOOL%%QUENCHREACTIONTRAY%:[%INDEX%+%LABELSTARTVIAL%-1]%QUENCHVOLUME%False0 µL-3 mm%FILLINGSPEED%0%%PULLUPDELAY%0-3 mm%INJECTIONSPEED% Clean with Solvent 152FalsePAL%INJTOOL%Fast Wash 1:1%POSTCLEANSOLV1%%FILLINGSPEED%%PULLUPDELAY%%INJECTIONSPEED% Clean with Solvent 2True50FalsePAL%INJTOOL%Fast Wash 1:2%POSTCLEANSOLV2%%FILLINGSPEED%%PULLUPDELAY%%INJECTIONSPEED% Clean with Solvent 151FalsePAL%INJTOOL%Fast Wash 1:1%POSTCLEANSOLV1%%FILLINGSPEED%%PULLUPDELAY%%INJECTIONSPEED% Move to Home Position and switch to the PREP Tool%TOOLCHANGETIME%FalsePAL%PREPTOOL% Pre Disp Cool Down time|RETURN %PREDISPCOOLTIME% > 0|[ROUND(%PREDISPCOOLTIME%*60) - {-1:RunTime} - %POSTCLEANSOLV1%*({-2:RunTime} + {-4:RunTime}) - %POSTCLEANSOLV2%*({-3:RunTime}) - ({JobCount}*{-5:RunTime})]Change to Prep Tool|if "{JobNo}"="1" And %USEPREDISPENSE% THEN RETURN 0 ELSE RETURN 1|%TOOLCHANGETIME%FalsePAL%PREPTOOL%Fast Wash 1:10Clean Prep Syringe Solvent 1True41FalsePAL%PREPTOOL%Fast Wash 1:13%PREPFILLINGSPEED%%PULLUPDELAY%%PREPINJECTIONSPEED%Pick Up ProteinTrue9FalsePAL%PREPTOOL%Picking up Protein%PROTEINASPVOL%%PREPFILLINGSPEED%%PULLUPDELAY%41 mm0Move to Label PlateTrue3FalsePAL%PREPTOOL%%LABELREACTIONTRAY%:[%LABELSTARTVIAL%+{JobNo}-1]41 mmDispense the ProteinTrue1FalsePAL%PREPTOOL%DispenseSyringe%PROTEINDISPVOL%%PREPINJECTIONSPEED%Depenetrate the Vial1FalsePAL%PREPTOOL%DepenetrateFalseMove to WasteTrue5FalsePAL%PREPTOOL%HDXWaste:120 mmEmpty the SyringeTrue1FalsePAL%PREPTOOL%EmptySyringe%PREPINJECTIONSPEED%Depenetrate the Waste Position1FalsePAL%PREPTOOL%DepenetrateFalseClean Prep Syringe Solvent 2True29FalsePAL%PREPTOOL%Fast Wash 1:2%POSTCLEANSOLV2%%PREPFILLPERCENT% %%PREPFILLINGSPEED%%PULLUPDELAY%%PREPINJECTIONSPEED%Clean Prep Syringe Solvent 1True28FalsePAL%PREPTOOL%Fast Wash 1:1%POSTCLEANSOLV1%%PREPFILLPERCENT% %%PREPFILLINGSPEED%%PULLUPDELAY%%PREPINJECTIONSPEED%Change to Inj Tool%TOOLCHANGETIME%FalsePAL%INJTOOL%%LABELREAGENTTRAY%:%D2OPRIMEVIAL%0 Put Aliquot of Pure D2O in Waste 21FalsePAL%INJTOOL%HDXWaste:1%DEUTERIUMVOL%-3 mm%FILLINGSPEED%10%%PULLUPDELAY%0%INJECTIONSPEED% Put Aliquot of Labeling D2O in Waste 22FalsePAL%INJTOOL%HDXWaste:1%DEUTERIUMVOL%-3 mm%FILLINGSPEED%10%%PULLUPDELAY%0%INJECTIONSPEED% Get Labeling D2OTrue11FalsePAL%INJTOOL%%DEUTERIUMVOL%5%%FILLINGSPEED%%PULLUPDELAY%-3 mm0 Move to Reaction WellTrue5FalsePAL%INJTOOL%%LABELREACTIONTRAY%:[%LABELSTARTVIAL%+{JobNo}-1]-1 mm Dispense the LabelTrue1FalsePAL%INJTOOL%EmptySyringe%MIXDISPENSSPEED% Depenetrate the Vial (timing run only)%TIMINGRUN%2TruePAL%INJTOOL%DepenetrateFalse Put Aliquot of equilibrium buffer in Waste18FalsePAL%INJTOOL%HDXWaste:1%DEUTERIUMVOL%-3 mm%FILLINGSPEED%0%PULLUPDELAY%0%INJECTIONSPEED% Get control 11FalsePAL%INJTOOL%%DEUTERIUMVOL%5%%FILLINGSPEED%%PULLUPDELAY%-3 mm0 Move to Reaction Well5FalsePAL%INJTOOL%%LABELREACTIONTRAY%:[%LABELSTARTVIAL%+{JobNo}-1]-1 mm Dispense the control2FalsePAL%INJTOOL%EmptySyringe%MIXDISPENSSPEED% Mixing Aspirate1FalsePAL%INJTOOL%AspirateSyringe%TRANSFERVOL%%MIXFILLINGSPEED%0 %%PULLUPDELAY% ms Mixing Dispense1FalsePAL%INJTOOL%EmptySyringe%MIXDISPENSSPEED%HDX Start Label1FalseHDx3/25/2014 1:05:49 PM Aspirate and DispenseTrue2TruePALMixing Wait for part of label time|return %LABELTIME% > %MINLABELTIME%|[ %LABELTIME%- %MINLABELTIME%] Pick Up transfer volume6PALPick up transfer volume Move to Quench Plate6FalsePAL%INJTOOL%%QUENCHREACTIONTRAY%:[%LABELSTARTVIAL%+{JobNo}-1]-1 mm Wait for rest of label time[1]FalseHDx3/25/2014 1:06:52 PMTrue%LABELTIME% Eject sample into Quench Tray2TruePAL%INJTOOL%EmptySyringe1%MIXDISPENSSPEED% for timing runs%TIMINGRUN%3FalsePAL for timing runs%TIMINGRUN%2FalsePAL%LABELREACTIONTRAY%:[%LABELSTARTVIAL%+{JobNo}-1] Mixing Aspirate1FalsePALAspirateSyringe%TRANSFERVOL%%MIXFILLINGSPEED%0 %%PULLUPDELAY% ms Mixing Dispense1FalsePALEmptySyringe%MIXDISPENSSPEED% Depenetrate the Vial1FalsePALDepenetrateFalse Clean with Solvent 151FalsePAL%INJTOOL%Fast Wash 1:1%POSTCLEANSOLV1%%FILLINGSPEED%%PULLUPDELAY%%INJECTIONSPEED% Put PAL Away3FalsePAL Wait for the Label Time (Long Times)|RETURN %LABELTIME% >= %SHORTLABELCUTOFF%|[%LABELTIME%-{-1:Runtime}-{-2:Runtime}-{-3:Runtime}-(%MIXINGSTROKES%*({-4:Runtime}+{-5:Runtime}))-30] Move to Label Plate6FalsePAL%INJTOOL%%LABELREACTIONTRAY%:[%LABELSTARTVIAL%+{JobNo}-1]-1 mm Pick up Transfer Volume4FalsePAL%INJTOOL%AspirateSyringe%TRANSFERVOL%%FILLINGSPEED%5%PULLUPDELAY% ms Depenetrate the Vial1FalsePALDepenetrateFalse Move to Quench Plate6FalsePAL%INJTOOL%%QUENCHREACTIONTRAY%:[%LABELSTARTVIAL%+{JobNo}-1]-1 mm Wait for rest of Label Time[1]FalseHDx3/25/2014 1:06:52 PMTrue%LABELTIME% Eject sample into Quench Tray1FalsePAL%INJTOOL%EmptySyringe1%MIXDISPENSSPEED% Aspirate and Dispense1FalsePALMixingQuench Hold Time%USEPOSTQUENCHREACTION%[%POSTQUENCHREACTIONTIME%-14] Depenetrate the Vial (timing run only)%TIMINGRUN%2TruePAL%INJTOOL%DepenetrateFalse Add Diluent to Quench VialTrue2FalsePAL%INJTOOL%%QUENCHREACTIONTRAY%:[%LABELSTARTVIAL%+{JobNo}-1]%POSTQUENCHDILVOLUME%False0 mm0 µL-3 mm%FILLINGSPEED%0%%PULLUPDELAY%0%INJECTIONSPEED% Aspirate and Dispense2TruePALMixing Dilution Hold Time|if %POSTQUENCHDILTIME%>0 then Return 1 else return 0|[%POSTQUENCHDILTIME%-14]Setup MassLynx Acquisition|IF %TIMINGRUN% THEN RETURN 0 ELSE RETURN 1|2MassLynxFalse%SAMPTYPE%%MLYNXFILENAME%%SAMPLENAME%0%INJECTIONVOL%{JobNo}%LCACQMETHOD%%SAMPLENAME% - TimePoint %LABELTIME% seconds%MLYNXPROJECT%0FalseINLET_FILE=%LCACQMETHOD%;MS_FILE=%MSACQMETHOD%;FILE_TEXT="%SAMPLENAME% - TimePoint %LABELTIME% seconds"Get Sample2FalsePAL%INJTOOL%Loading Sample into Syringe%INJECTIONVOL%5%%FILLINGSPEED%%PULLUPDELAY%-1 mm0Moving to the Injection Valve2PALMoving to Injection ValveWaiting for Inlet Start 1|IF %TIMINGRUN% THEN RETURN 0 ELSE RETURN 1|2c:\masslynx\status.iniMS_StatusStatusWaiting for inlet start 1WaitUntilMatches5Waiting for inlet start 1Inject with constant forceTrue2FalsePALInjecting %SAMPLENAME% - TimePoint %LABELTIME% secondsSets Inj Valve State to Hold for next WaitOverlapped|IF %TIMINGRUN% THEN RETURN 0 ELSE RETURN 1|2PALLC RunningLC Start%INJ_TO%Sets HDX Injected FlagTrue2FalseHDx3/25/2014 1:07:21 PM%SAMPLENAME%[%LABELSTARTVIAL%+{JobNo}-1]%LABELTIME%Start Timer2PALStartTimer1Clean Injection Syringe Solvent 12FalsePAL%INJTOOL%Fast Wash 1:1%POSTCLEANSOLV1%%FILLINGSPEED%%PULLUPDELAY%Clean Injection Syringe Solvent 22FalsePAL%INJTOOL%Fast Wash 1:2%POSTCLEANSOLV2%%FILLINGSPEED%%PULLUPDELAY%Clean Injection Syringe Solvent 12FalsePAL%INJTOOL%Fast Wash 1:1%POSTCLEANSOLV1%%FILLINGSPEED%%PULLUPDELAY%Cleaning Injector with Wash Solvent 1True2PAL%INJTOOL%Fast Wash 1:1%INJ_TO%%VALVECLEANSOLV1%%FILLINGSPEED%%PULLUPDELAY%%INJECTIONSPEED%0%INJECTIONSPEED%Cleaning Injector with Wash Solvent 2True2PAL%INJTOOL%Fast Wash 1:2%INJ_TO%%VALVECLEANSOLV2%%FILLINGSPEED%%PULLUPDELAY%%INJECTIONSPEED%0%INJECTIONSPEED%Cleaning Injector with Wash Solvent 1True2PAL%INJTOOL%Fast Wash 1:1%INJ_TO%%VALVECLEANSOLV1%%FILLINGSPEED%%PULLUPDELAY%%INJECTIONSPEED%0%INJECTIONSPEED% Get Pepsin Wash2FalsePAL%INJTOOL%Getting Pepsin Wash Solution%PEPSINWASHVOL%5%%FILLINGSPEED%%PULLUPDELAY%-3 mm0 Moving to Injection ValveTrue2PALMoving to Injection Valve Wait for trapping to complete[ROUND(60*{2:Plugin.TrappingRuntime}) - {-1:Runtime} - {-2:Runtime} - %VALVECLEANSOLV1%*({-3:Runtime} + {-5:Runtime}) - %VALVECLEANSOLV2%*({-4:Runtime}) - %POSTCLEANSOLV1%*({-6:Runtime} + {-8:Runtime}) - %POSTCLEANSOLV2%*({-7:Runtime})] Confirm trapping is complete|IF %TIMINGRUN% THEN RETURN 0 ELSE RETURN 1|2FalsePALTrap Complete Injecting Pepsin Wash2FalsePALInjecting Pepsin Wash Solution Get Pepsin Wash2FalsePAL%INJTOOL%Getting Pepsin Wash Solution%PEPSINWASHVOL%5%%FILLINGSPEED%%PULLUPDELAY%-3 mm0 Moving to Injection Valve2PALMoving to Injection Valve Delay for Pepsin WashingTrue[%PEPSINWASHDELAY% - {-1:RunTime} - {-2:RunTime}] Pulse Valve to off2FalsePALPepsin Wash11000 ms Injecting Pepsin Wash2FalsePALInjecting Pepsin Wash Solution Delay for Pepsin WashingTrue[%PEPSINWASHDELAY% - {-1:RunTime}] Pulse Valve to off2FalsePALPepsin Wash11000 ms Cleaning Injector with Wash Solvent 1True2PAL%INJTOOL%Fast Wash 1:1%INJ_TO%%VALVECLEANSOLV1%False%FILLINGSPEED%%PULLUPDELAY%%INJECTIONSPEED%0%INJECTIONSPEED%Move to the Home Position2FalsePAL%INJTOOL%Wait for Remainder of RunTrue|IF %USEPEPSINCOLWASH% THEN RETURN [ROUND(60*{2:Plugin.AnalyticalRuntime}) + %MSRECOVERY% - {-1:Runtime} - %VALVECLEANSOLV1%*({-2:Runtime}) - %PEPSINWASHES%*%PEPSINWASHDELAY%] ELSE RETURN [ROUND(60*{2:Plugin.AnalyticalRuntime}) + %MSRECOVERY% + ROUND(60*{2:Plugin.TrappingRuntime}) - {-1:Runtime} - %VALVECLEANSOLV1%*({-2:RunTime}+{-4:RunTime}) - %VALVECLEANSOLV2%*({-3:RunTime}) - %POSTCLEANSOLV1%*({-5:RunTime} + {-7:RunTime}) - %POSTCLEANSOLV2%*{-6:RunTime}]| Setup CleanBlank Acquisition|IF %TIMINGRUN% THEN RETURN 0 ELSE RETURN 1|2MassLynxFalse%SAMPTYPE%%MLYNXFILENAME%_CleanBlank%SAMPLENAME%_CleanBlank00%CBVOL%{JobNo}|IF %USECLEANBLANK% THEN RETURN "%LCCLEANBLANKMETHOD%" ELSE RETURN "%LCACQMETHOD%"|%SAMPLENAME% - TimePoint %LABELTIME% seconds - CleanBlank%MLYNXPROJECT%0FalseINLET_FILE=|IF %USECLEANBLANK% THEN RETURN "%LCCLEANBLANKMETHOD%" ELSE RETURN "%LCACQMETHOD%"| ;MS_FILE=|IF %USECLEANBLANK% THEN RETURN "%MSCLEANBLANKMETHOD%" ELSE RETURN "%MSACQMETHOD%"| ;FILE_TEXT="%SAMPLENAME% - TimePoint %LABELTIME% seconds - CleanBlank" Get Clean Blank2FalsePAL%INJTOOL%Drawing Clean Blank%CBVOL%5%%FILLINGSPEED%%PULLUPDELAY%-3 mm0 Moving to Injection Valve2PALMoving to Injection Valve Wait for MS to be ready|IF %TIMINGRUN% THEN RETURN 0 ELSE RETURN %USEMASSLYNXSTATUS%|1c:\masslynx\status.iniMS_StatusStatusWaiting for InjectionWaitUntilMatches5Waiting For Injection Ready Inject with constant forceTrue2FalsePALInjecting Clean Blank Sample Sets Inj Valve State to Hold for next WaitOverlapped|IF %TIMINGRUN% THEN RETURN 0 ELSE RETURN 1|2PALLC RunningLC Start%INJ_TO% Clean Injection Syringe Solvent 22FalsePAL%INJTOOL%Fast Wash 1:2%POSTCLEANSOLV2%%FILLINGSPEED%%PULLUPDELAY% Clean Injection Syringe Solvent 12FalsePAL%INJTOOL%Fast Wash 1:1%POSTCLEANSOLV1%%FILLINGSPEED%%PULLUPDELAY% Cleaning Injector with Wash Solvent 1True2PAL%INJTOOL%Fast Wash 1:1%INJ_TO%%VALVECLEANSOLV1%%FILLINGSPEED%%PULLUPDELAY%%INJECTIONSPEED%0%INJECTIONSPEED% Moving to Home Position2TruePAL Wait for the reaminder of the Clean Blank RunTrue|IF "{3:Plugin.ApplicationMode}" = "ApplicationMode_2" THEN RETURN [ROUND(60*({3:Plugin.AnalyticalRuntime}+{3:Plugin.TrappingRuntime})) + %MSRECOVERY% - {-1:Runtime} - %VALVECLEANSOLV1%*{-2:Runtime} - {-3:Runtime} - {-4:Runtime}] ELSE RETURN [ROUND(60*{3:Plugin.AnalyticalRuntime}) + %MSRECOVERY% - {-1:Runtime} - %VALVECLEANSOLV1%*{-2:Runtime} - {-3:Runtime} - {-4:Runtime}]|1745613204