timsTOF pro data analysis crashed at Dependent peptide search

[animesh]

Any ideas why timsTOF pro data analysis crashed at Dependent peptide search?

id  0
start   17-08-2021 08:34:22
title   Finding_Dependent_Peptides (1/1)
description C:\Users\animeshs\Desktop\Documents\DDA_PASEF\combined\proc Finding_Dependent_Peptides 0 Finding_Dependent_Peptides (1/1)  Process 30 0 0 C:\Users\animeshs\Desktop\Documents\DDA_PASEF\mqpar.xml
error   C:\Users\animeshs\Desktop\Documents\DDA_PASEF\combined\proc Finding_Dependent_Peptides 0 Finding_Dependent_Peptides (1/1)  Process 30 0 0 C:\Users\animeshs\Desktop\Documents\DDA_PASEF\mqpar.xml_Unable to read beyond the end of the stream._   at System.IO.BinaryReader.FillBuffer(Int32 numBytes)__   at System.IO.BinaryReader.ReadInt32()__   at BaseLibS.Util.FileUtils.ReadInt32Array(BinaryReader reader)__   at MaxQuantLibS.Data.IsotopeCluster..ctor(BinaryReader reader)__   at MaxQuantLibS.Domains.Peptides.Data.PlistData.PeakListLayerData.ReadIsotopeClusters()__   at MaxQuantLibS.Domains.Peptides.Data.PlistData.PeakListLayerData.EnsureIsotopeClusters()__   at MaxQuantLibS.Domains.Peptides.Data.PlistData.PeakListLayerData.get_IsotopeClusterCount()__   at MaxQuantLibS.Domains.Peptides.Dependent.DependentSearch.GetIdentifiedPeptideSpectra(Int32 fileIndex, MaxQuantParams mqpar, ProteinSet proteinSet, Boolean decoy, IList`1 scanNumbers, IList`1 fileIndices, IList`1 charges, IList`1 parentMass, IList`1 time, IList`1 massList, IList`1 peakAnnotation, IList`1 sequences, IDictionary`2 cachedAndromedaScoresForMassAnalyzer)__   at MaxQuantLibS.Domains.Peptides.Dependent.DependentSearch.IdentifyDependentPeptides(Int32 fileIndex, String mqparFile)__   at MaxQuantLibS.Domains.Peptides.Dependent.DependentSearch.FindDependentPeptides(Int32 fileIndex, String mqparFile)__   at MaxQuantLibS.Domains.Peptides.Work.DependentPeptide.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 17-08-2021 08:34:52

I am using version 2 series mqpar.xml.txt. The combined folder for this analysis is available at https://drive.google.com/drive/folders/1FaZ1c_WZb3uScnUZPzq5EHVCEZscv-KF?usp=sharing , can share the raw file if the need be?

[kingkong-AI]

Hi Animesh, Did you fins a solution to this issue. I am facing a similar issue wherein I am getting the error, "the profile was last used with a newer version of this application. Please create a new profile." at the dependent peptide stage. It is stuck at that step for more than 10 hours. Thanks in advance!

[animesh]

Had to disable it, apparently MaxQuant doesnt support dependent peptides AFAIK. Latest version just ignored it, so atleast it wont crash but there will be no dependent peptides found as well... Hopefully MaxQuant support for the dependent peptides comes soon 🤞