Hdx RTC with Pepsin Washes and Clean Blank Does Precondition with Quench for long label times Long label time cutoff is now 50 sec Added MS 1 False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False False |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| 1 Load runtimes for the Analytical Acquisition method file 1 %MLYNXPROJECT%\acqudb\%LCACQMETHOD% -1 -1 Load runtimes for the Clean Blank Acquisition method file True 1 False |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| 1 False c:\masslynx\status.ini
MS_Status
Ready -1 Abort 10 Too 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| 1 False c:\masslynx\status.ini
MS_Status
Ready -1 Abort 10 There 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 DLL 1 1 False HDx %ANALYSIS_METHOD% from meth from meth [ROUND({2:Plugin.AnalyticalRuntime} + {2:Plugin.TrappingRuntime})] %POSTCLEANSOLV1% %POSTCLEANSOLV2% %VALVECLEANSOLV1% %VALVECLEANSOLV2% %PEPSINWASHES% %PEPSINWASHVOL% %PEPSINWASHDELAY% %POSTQUENCHREACTIONTIME% %LCACQMETHOD%
Determines if the MS is Ready False 1 False c:\masslynx\status.ini
MS_Status
Ready 1 Abort 10 The MS System is not ready. Please clear any errors in MassLynx.
Determines if the LC is Ready False 1 False c:\masslynx\status.ini
LC_Status
Ready 1 Abort 10 The 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| 2 False c:\masslynx\status.ini
Queue_Status
Queue Paused 0 Abort 10 The sample queue is paused in MassLynx. Please clear any errors with the LC/MS System.
Clean INJ Syringe with Quench and transfer to waste 22 False PAL %INJTOOL% %QUENCHREAGENTTRAY%:%QUENCHSOURCEVIAL% HDXWaste:1 %QUENCHVOLUME% False 0 mm -3 mm %FILLINGSPEED% 0% %PULLUPDELAY% 0 %INJECTIONSPEED% Put Quench reagent in the reaction wells True 19 False PAL %INJTOOL% %QUENCHREAGENTTRAY%:%QUENCHSOURCEVIAL% %QUENCHREACTIONTRAY%:[%INDEX%+%LABELSTARTVIAL%-1] %QUENCHVOLUME% False 0 µL -3 mm %FILLINGSPEED% 0% %PULLUPDELAY% 0 -3 mm %INJECTIONSPEED% Clean with Solvent 1 52 False PAL %INJTOOL% Fast Wash 1:1 %POSTCLEANSOLV1% %FILLINGSPEED% %PULLUPDELAY% %INJECTIONSPEED% Clean with Solvent 2 True 50 False PAL %INJTOOL% Fast Wash 1:2 %POSTCLEANSOLV2% %FILLINGSPEED% %PULLUPDELAY% %INJECTIONSPEED% Clean with Solvent 1 51 False PAL %INJTOOL% Fast Wash 1:1 %POSTCLEANSOLV1% %FILLINGSPEED% %PULLUPDELAY% %INJECTIONSPEED% Move to Home Position and switch to the PREP Tool %TOOLCHANGETIME% False PAL %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% False PAL %PREPTOOL% Fast Wash 1:1 0 Clean Prep Syringe Solvent 1 True 41 False PAL %PREPTOOL% Fast Wash 1:1 3 %PREPFILLINGSPEED% %PULLUPDELAY% %PREPINJECTIONSPEED% Pick Up Protein True 9 False PAL %PREPTOOL% Picking up Protein %QUENCHSAMPLETRAY%:%PROTEINVIAL% %PROTEINASPVOL% %PREPFILLINGSPEED% %PULLUPDELAY% 41 mm 0 Move to Label Plate True 3 False PAL %PREPTOOL% %LABELREACTIONTRAY%:[%LABELSTARTVIAL%+{JobNo}-1] 41 mm Dispense the Protein True 1 False PAL %PREPTOOL% DispenseSyringe %PROTEINDISPVOL% %PREPINJECTIONSPEED% Depenetrate the Vial 1 False PAL %PREPTOOL% Depenetrate False Move to Waste True 5 False PAL %PREPTOOL% HDXWaste:1 20 mm Empty the Syringe True 1 False PAL %PREPTOOL% EmptySyringe %PREPINJECTIONSPEED% Depenetrate the Waste Position 1 False PAL %PREPTOOL% Depenetrate False Clean Prep Syringe Solvent 2 True 29 False PAL %PREPTOOL% Fast Wash 1:2 %POSTCLEANSOLV2% %PREPFILLPERCENT% % %PREPFILLINGSPEED% %PULLUPDELAY% %PREPINJECTIONSPEED% Clean Prep Syringe Solvent 1 True 28 False PAL %PREPTOOL% Fast Wash 1:1 %POSTCLEANSOLV1% %PREPFILLPERCENT% % %PREPFILLINGSPEED% %PULLUPDELAY% %PREPINJECTIONSPEED% Change to Inj Tool %TOOLCHANGETIME% False PAL %INJTOOL% %LABELREAGENTTRAY%:%D2OPRIMEVIAL% 0 Put Aliquot of Pure D2O in Waste 21 False PAL %INJTOOL% %LABELREAGENTTRAY%:%D2OPRIMEVIAL% HDXWaste:1 %DEUTERIUMVOL% -3 mm %FILLINGSPEED% 10% %PULLUPDELAY% 0 %INJECTIONSPEED% Put Aliquot of Labeling D2O in Waste 22 False PAL %INJTOOL% %LABELREAGENTTRAY%:%D2OLABELVIAL% HDXWaste:1 %DEUTERIUMVOL% -3 mm %FILLINGSPEED% 10% %PULLUPDELAY% 0 %INJECTIONSPEED% Get Labeling D2O True 11 False PAL %INJTOOL% %LABELREAGENTTRAY%:%D2OLABELVIAL% %DEUTERIUMVOL% 5% %FILLINGSPEED% %PULLUPDELAY% -3 mm 0 Move to Reaction Well True 5 False PAL %INJTOOL% %LABELREACTIONTRAY%:[%LABELSTARTVIAL%+{JobNo}-1] -1 mm Dispense the Label True 1 False PAL %INJTOOL% EmptySyringe %MIXDISPENSSPEED% Depenetrate the Vial (timing run only) %TIMINGRUN% 2 True PAL %INJTOOL% Depenetrate False Put Aliquot of equilibrium buffer in Waste 18 False PAL %INJTOOL% %LABELREAGENTTRAY%:%REFLABELVIAL% HDXWaste:1 %DEUTERIUMVOL% -3 mm %FILLINGSPEED% 0 %PULLUPDELAY% 0 %INJECTIONSPEED% Get control 11 False PAL %INJTOOL% %LABELREAGENTTRAY%:%REFLABELVIAL% %DEUTERIUMVOL% 5% %FILLINGSPEED% %PULLUPDELAY% -3 mm 0 Move to Reaction Well 5 False PAL %INJTOOL% %LABELREACTIONTRAY%:[%LABELSTARTVIAL%+{JobNo}-1] -1 mm Dispense the control 2 False PAL %INJTOOL% EmptySyringe %MIXDISPENSSPEED% Mixing Aspirate 1 False PAL %INJTOOL% AspirateSyringe %TRANSFERVOL% %MIXFILLINGSPEED% 0 % %PULLUPDELAY% ms Mixing Dispense 1 False PAL %INJTOOL% EmptySyringe %MIXDISPENSSPEED% HDX Start Label 1 False HDx 3/25/2014 1:05:49 PM Aspirate and Dispense True 2 True PAL Mixing Wait for part of label time |return %LABELTIME% > %MINLABELTIME%| [ %LABELTIME%- %MINLABELTIME%] Pick Up transfer volume 6 PAL Pick up transfer volume Move to Quench Plate 6 False PAL %INJTOOL% %QUENCHREACTIONTRAY%:[%LABELSTARTVIAL%+{JobNo}-1] -1 mm Wait for rest of label time [1] False HDx 3/25/2014 1:06:52 PM True %LABELTIME% Eject sample into Quench Tray 2 True PAL %INJTOOL% EmptySyringe 1 %MIXDISPENSSPEED% for timing runs %TIMINGRUN% 3 False PAL for timing runs %TIMINGRUN% 2 False PAL %LABELREACTIONTRAY%:[%LABELSTARTVIAL%+{JobNo}-1] Mixing Aspirate 1 False PAL AspirateSyringe %TRANSFERVOL% %MIXFILLINGSPEED% 0 % %PULLUPDELAY% ms Mixing Dispense 1 False PAL EmptySyringe %MIXDISPENSSPEED% Depenetrate the Vial 1 False PAL Depenetrate False Clean with Solvent 1 51 False PAL %INJTOOL% Fast Wash 1:1 %POSTCLEANSOLV1% %FILLINGSPEED% %PULLUPDELAY% %INJECTIONSPEED% Put PAL Away 3 False PAL 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 Plate 6 False PAL %INJTOOL% %LABELREACTIONTRAY%:[%LABELSTARTVIAL%+{JobNo}-1] -1 mm Pick up Transfer Volume 4 False PAL %INJTOOL% AspirateSyringe %TRANSFERVOL% %FILLINGSPEED% 5 %PULLUPDELAY% ms Depenetrate the Vial 1 False PAL Depenetrate False Move to Quench Plate 6 False PAL %INJTOOL% %QUENCHREACTIONTRAY%:[%LABELSTARTVIAL%+{JobNo}-1] -1 mm Wait for rest of Label Time [1] False HDx 3/25/2014 1:06:52 PM True %LABELTIME% Eject sample into Quench Tray 1 False PAL %INJTOOL% EmptySyringe 1 %MIXDISPENSSPEED% Aspirate and Dispense 1 False PAL Mixing Quench Hold Time %USEPOSTQUENCHREACTION% [%POSTQUENCHREACTIONTIME%-14] Depenetrate the Vial (timing run only) %TIMINGRUN% 2 True PAL %INJTOOL% Depenetrate False Add Diluent to Quench Vial True 2 False PAL %INJTOOL% %QUENCHREAGENTTRAY%:%POSTQUENCHDILSOURCE% %QUENCHREACTIONTRAY%:[%LABELSTARTVIAL%+{JobNo}-1] %POSTQUENCHDILVOLUME% False 0 mm 0 µL -3 mm %FILLINGSPEED% 0% %PULLUPDELAY% 0 %INJECTIONSPEED% Aspirate and Dispense 2 True PAL Mixing 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| 2 MassLynx False %SAMPTYPE% %MLYNXFILENAME% %SAMPLENAME% 0 %INJECTIONVOL% {JobNo} %LCACQMETHOD% %SAMPLENAME% - TimePoint %LABELTIME% seconds %MLYNXPROJECT% 0 False INLET_FILE=%LCACQMETHOD%;MS_FILE=%MSACQMETHOD%;FILE_TEXT="%SAMPLENAME% - TimePoint %LABELTIME% seconds" Get Sample 2 False PAL %INJTOOL% Loading Sample into Syringe %QUENCHREACTIONTRAY%:[%LABELSTARTVIAL%+{JobNo}-1] %INJECTIONVOL% 5% %FILLINGSPEED% %PULLUPDELAY% -1 mm 0 Moving to the Injection Valve 2 PAL Moving to Injection Valve Waiting for Inlet Start 1 |IF %TIMINGRUN% THEN RETURN 0 ELSE RETURN 1| 2 c:\masslynx\status.ini
MS_Status
Status Waiting for inlet start 1 WaitUntilMatches 5 Waiting for inlet start 1
Inject with constant force True 2 False PAL Injecting %SAMPLENAME% - TimePoint %LABELTIME% seconds Sets Inj Valve State to Hold for next WaitOverlapped |IF %TIMINGRUN% THEN RETURN 0 ELSE RETURN 1| 2 PAL LC Running LC Start %INJ_TO% Sets HDX Injected Flag True 2 False HDx 3/25/2014 1:07:21 PM %SAMPLENAME% [%LABELSTARTVIAL%+{JobNo}-1] %LABELTIME% Start Timer 2 PAL StartTimer 1 Clean Injection Syringe Solvent 1 2 False PAL %INJTOOL% Fast Wash 1:1 %POSTCLEANSOLV1% %FILLINGSPEED% %PULLUPDELAY% Clean Injection Syringe Solvent 2 2 False PAL %INJTOOL% Fast Wash 1:2 %POSTCLEANSOLV2% %FILLINGSPEED% %PULLUPDELAY% Clean Injection Syringe Solvent 1 2 False PAL %INJTOOL% Fast Wash 1:1 %POSTCLEANSOLV1% %FILLINGSPEED% %PULLUPDELAY% Cleaning Injector with Wash Solvent 1 True 2 PAL %INJTOOL% Fast Wash 1:1 %INJ_TO% %VALVECLEANSOLV1% %FILLINGSPEED% %PULLUPDELAY% %INJECTIONSPEED% 0 %INJECTIONSPEED% Cleaning Injector with Wash Solvent 2 True 2 PAL %INJTOOL% Fast Wash 1:2 %INJ_TO% %VALVECLEANSOLV2% %FILLINGSPEED% %PULLUPDELAY% %INJECTIONSPEED% 0 %INJECTIONSPEED% Cleaning Injector with Wash Solvent 1 True 2 PAL %INJTOOL% Fast Wash 1:1 %INJ_TO% %VALVECLEANSOLV1% %FILLINGSPEED% %PULLUPDELAY% %INJECTIONSPEED% 0 %INJECTIONSPEED% Get Pepsin Wash 2 False PAL %INJTOOL% Getting Pepsin Wash Solution %LABELREAGENTTRAY%:%PEPSINWASHVIAL% %PEPSINWASHVOL% 5% %FILLINGSPEED% %PULLUPDELAY% -3 mm 0 Moving to Injection Valve True 2 PAL Moving 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| 2 False PAL Trap Complete Injecting Pepsin Wash 2 False PAL Injecting Pepsin Wash Solution Get Pepsin Wash 2 False PAL %INJTOOL% Getting Pepsin Wash Solution %QUENCHREAGENTTRAY%:%PEPSINWASHVIAL% %PEPSINWASHVOL% 5% %FILLINGSPEED% %PULLUPDELAY% -3 mm 0 Moving to Injection Valve 2 PAL Moving to Injection Valve Delay for Pepsin Washing True [%PEPSINWASHDELAY% - {-1:RunTime} - {-2:RunTime}] Pulse Valve to off 2 False PAL Pepsin Wash 1 1000 ms Injecting Pepsin Wash 2 False PAL Injecting Pepsin Wash Solution Delay for Pepsin Washing True [%PEPSINWASHDELAY% - {-1:RunTime}] Pulse Valve to off 2 False PAL Pepsin Wash 1 1000 ms Cleaning Injector with Wash Solvent 1 True 2 PAL %INJTOOL% Fast Wash 1:1 %INJ_TO% %VALVECLEANSOLV1% False %FILLINGSPEED% %PULLUPDELAY% %INJECTIONSPEED% 0 %INJECTIONSPEED% Move to the Home Position 2 False PAL %INJTOOL% Wait for Remainder of Run True |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| 2 MassLynx False %SAMPTYPE% %MLYNXFILENAME%_CleanBlank %SAMPLENAME%_CleanBlank 0 0 %CBVOL% {JobNo} |IF %USECLEANBLANK% THEN RETURN "%LCCLEANBLANKMETHOD%" ELSE RETURN "%LCACQMETHOD%"| %SAMPLENAME% - TimePoint %LABELTIME% seconds - CleanBlank %MLYNXPROJECT% 0 False INLET_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 Blank 2 False PAL %INJTOOL% Drawing Clean Blank %LABELREAGENTTRAY%:%CLEANBLANKVIAL% %CBVOL% 5% %FILLINGSPEED% %PULLUPDELAY% -3 mm 0 Moving to Injection Valve 2 PAL Moving to Injection Valve Wait for MS to be ready |IF %TIMINGRUN% THEN RETURN 0 ELSE RETURN %USEMASSLYNXSTATUS%| 1 c:\masslynx\status.ini
MS_Status
Status Waiting for Injection WaitUntilMatches 5 Waiting For Injection Ready
Inject with constant force True 2 False PAL Injecting Clean Blank Sample Sets Inj Valve State to Hold for next WaitOverlapped |IF %TIMINGRUN% THEN RETURN 0 ELSE RETURN 1| 2 PAL LC Running LC Start %INJ_TO% Clean Injection Syringe Solvent 2 2 False PAL %INJTOOL% Fast Wash 1:2 %POSTCLEANSOLV2% %FILLINGSPEED% %PULLUPDELAY% Clean Injection Syringe Solvent 1 2 False PAL %INJTOOL% Fast Wash 1:1 %POSTCLEANSOLV1% %FILLINGSPEED% %PULLUPDELAY% Cleaning Injector with Wash Solvent 1 True 2 PAL %INJTOOL% Fast Wash 1:1 %INJ_TO% %VALVECLEANSOLV1% %FILLINGSPEED% %PULLUPDELAY% %INJECTIONSPEED% 0 %INJECTIONSPEED% Moving to Home Position 2 True PAL Wait for the reaminder of the Clean Blank Run True |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}]|
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