MaxQuant v2.4.4 quits at MSMS first search

[Jane Khudyakov]

I just recently updated to MaxQuant v2.4.4 and am using it on a Windows 10 machine with 64 GB RAM with .NET v7.0 installed. It keeps quitting during the MSMS first step with the error message pasted below. Does anyone know how to solve this? The error says " The APL-file does not contain entries in ascending mass order." but we've never had this issue before with MaxQuant 2.4.0.

Thank you!

id 0
start 07/09/2023 19:30:32
title MSMS_first_search (10/63)
description E:\Plasma_NES_Stress_EV\Samples\MQ_Samples_Run_1AB_2_3_4\combined\proc MSMS_first_search 9 MSMS_first_search (10/63)  Process 73 0 E:\Plasma_NES_Stress_EV\Samples\MQ_Samples_Run_1AB_2_3_4\combined\search E:\Plasma_NES_Stress_EV\Samples\MQ_Samples_Run_1AB_2_3_4\combined 9 63 900 True ExternalProcess True False
error E:\Plasma_NES_Stress_EV\Samples\MQ_Samples_Run_1AB_2_3_4\combined\proc MSMS_first_search 9 MSMS_first_search (10/63)  Process 73 0 E:\Plasma_NES_Stress_EV\Samples\MQ_Samples_Run_1AB_2_3_4\combined\search E:\Plasma_NES_Stress_EV\Samples\MQ_Samples_Run_1AB_2_3_4\combined 9 63 900 True ExternalProcess True False_Error: The APL-file does not contain entries in ascending mass order._   at MsLib.Search.AndromedaAnalysis.LoopPpm(RankPredictionModel ipm, ModifiedPeptideSetPredictions pred, AplParser aplParser, PeptideSet peptideSet, String name, Boolean firstSearch, LinkedList`1 modifiedPeptides, ModifiedPeptideSet modifiedPeptideSet, AndromedaParams sp, ProteinSet proteinSet, Modification2[][] lMods, Modification[] vmods, Boolean hasDependentMods, Modification2[][][] dependentMods, Boolean hasAddVmods, Modification[] allVmods, Boolean hasAllDependentMods, Modification2[][][] allDependentMods, ICache`2 peptideCache, ICache`2 massListCache, Char[] fixedMassesAas, Double[] fixedMasses, Modification fixedNtermMod, Modification fixedCtermMod, Int32 nthreads, List`1 buffer, TextWriter writer, Int32 maxLen, Int32[] topIntens, CrossGroupSearchParam crossGroupSearchParam)__   at MsLib.Search.AndromedaAnalysis.SearchAplFile(String name, PeptideSet peptideSet, ModifiedPeptideSet modifiedPeptideSet, String modPepSetPath, AndromedaParams sp, ProteinSet proteinSet, Boolean firstSearch, Int32 nthreads, CrossLinkingType crossLinkingType)__   at MsLib.Search.AndromedaAnalysis.GoProtein(AndromedaParams sp, String aplFileName, PeptideListController plc, Boolean firstSearch, String searchFolder, CalculationType calculationType, Boolean useDotNetCore, Boolean profile, CrossLinkingType crossLinkingType)__   at MsLib.Search.AndromedaAnalysis.SearchFile(String searchFolder, AndromedaParams param, String aplFile, Int32 delay, Boolean firstSearch, CalculationType calculationType, Boolean useDotNetCore, Boolean profile, CrossLinkingType crossLinkingType)__   at MsLib.Search.AndromedaAnalysis.SearchFile(String searchFolder, String parFile, String aplFile, Int32 delay, Boolean firstSearch, CalculationType calculationType, Boolean useDotNetCore, Boolean profilePerformance, CrossLinkingType crossLinkingType, Responder responder)__   at MsLib.Search.AndromedaAnalysis.SearchFile(String searchFolder, String combinedFolder, Int32 jobIndex, Int32 jobCount, Int32 delay, Boolean firstSearch, CalculationType calculationType, Boolean useDotNetCore, Boolean profilePerformance, Responder responder)__   at MaxQuantLibS.Domains.Peptides.Work.CombinedSearcher.Calculation(String[] args, Responder responder)__   at MaxQuantLibS.Domains.Peptides.Work.MaxQuantWorkDispatcherUtil.PerformTask(Int32 taskType, String[] args, Responder responder)__   at MaxQuantLibS.Base.MaxQuantUtils.Run(Int32 softwareId, Int32 taskType, String[] args, Responder responder)__   at MaxQuantTaskCore.Program.Function(String[] args, Responder responder)__   at Utils.Util.ExternalProcess.Run(String[] args, Boolean debug)
end 07/09/2023 20:25:16