cox-labs / coxlab_bug_reporting Goto Github PK

Describe the bug
It takes 120 to 150 hours per file to finish the deisotoping step. Is this normal? I will also post this in the gmail group.
Also another post here might be of similar problem? (#21)

MQ ver. 2.4
Raw data: Bruker Tims-tof DDA .d folder (size approx. 6 GB)

Settings:

• Group parameters:
  Type-TIMS-DDA; Instrument-BRUKER TIM; Lable free quantification tab-LFQ
• Global parameters:
  Reference Sequence-UP000005640_9606.fasta and UP000005640_9606_additional.fasta;
  Protein Quantification tab, Peptides for Quantification - Unique+razor;
  Identification - Match between runs

The CPU has 24 cores and I put all of them in the Threads.

Expected behavior
Shorter time since if it crashes in the process then it's another 5 days to wait.

Desktop (please complete the following information):

• OS: Windows 10 Pro for Workstations 64-bit
• Version 22H2
• RAM 128GB

Additional context
I doubled checked the changes from MQ ver. 2.2 to 2.4. Something changed that might be of interest for this problem:

• Goup Parameters:
  LFQ tab: LFQ min ratio count changed from 1->2 in Ver. 2.4
  Instrument tab: Bruker Tims, Isotope time correlation 0.6->0.3
• Global Parameters:
  Match between runs: Match time window changed from 0.7->0.4

Thanks in advance for looking into this. Looking forward to hearing from you.

Describe the bug
MaxQuantGui.exe throws an error:

Unhandled exception. System.IO.FileNotFoundException: Could not load file or assembly 'mscorlib, Version=4.0.0.0, Culture=neutral, PublicKeyToken=b77a5c561934e089'. The system cannot find the file specified.

File name: 'mscorlib, Version=4.0.0.0, Culture=neutral, PublicKeyToken=b77a5c561934e089'

To Reproduce
Steps to reproduce the behavior:

1. We installed dotnet-sdk 3.1.426 (verified with dotnet --list-sdks) and MaxQuant 2.4.2.0
2. As an additional setup, we had to link certain files in dotnet to MaxQuant's bin directory: ln -s /path/to/dotnet/shared/Microsoft.NETCore.App/3.1.32/* /path/to/maxquant/bin. Otherwise it will complain about not being able to find those files.
3. Run dotnet /path/to/MaxQuantGui.exe

Expected behavior
The GUI is expected to work.

Desktop (please complete the following information):

• OS: CentOS
• Version: 7.9.2009

Describe the bug
I am using Perseus software (the latest version) to analyze my proteomics data, unfortunately I am running
into an error in the "match rows by name" function. The error occurs when I try to use the
function on an exported matrix (a matrix obtained after performing export row clusters
from a Hierarchical clustering)

The message I am receiving is:
************** Exception Text **************
System.NullReferenceException: Object
reference not set to an instance of an object.
at
PerseusPluginLib.Join.MatchingRowsByName.
GetParameters(IMatrixData[] inputData,
String& errString)
at
PerseusLibS.Data.Matrix.MatrixData.GetMultiP
rocessingParameters(InternalData[] inputData,
IMultiProcessing processing, String&
errorString)
at
PerseusLib.Forms.PerseusMainControl.GetPar
ameters(IMultiProcessing processing,
InternalData[] mdata)
at
PerseusLib.Forms.PerseusMainControl.Contin
ueMultiProcessing(IMultiProcessing
multiProcessing, String[] names, DataType
type)
at
PerseusLib.Forms.MultiProcessingInputForm.
OkButtonClick(Object sender, EventArgs e)
at
System.Windows.Forms.Control.OnClick(Event
Args e)
at
System.Windows.Forms.Button.OnClick(Event
Args e)
at
System.Windows.Forms.Button.OnMouseUp(
MouseEventArgs mevent)
at
System.Windows.Forms.Control.WmMouseUp(
Message& m, MouseButtons button, Int32
clicks)
at
System.Windows.Forms.Control.WndProc(Mes
sage& m)
at
System.Windows.Forms.ButtonBase.WndProc(
Message& m)
at
System.Windows.Forms.Button.WndProc(Mes
sage& m)
at
System.Windows.Forms.NativeWindow.Callba
ck(IntPtr hWnd, Int32 msg, IntPtr wparam,
IntPtr lparam)

************** Loaded Assemblies **************
mscorlib
Assembly Version: 4.0.0.0
Win32 Version: 4.8.4515.0 built by:
NET48REL1LAST_C
CodeBase:
file:///C:/Windows/Microsoft.NET/Framework64
/v4.0.30319/mscorlib.dll

PerseusGui
Assembly Version: 1.6.13.0
Win32 Version: 1.6.13.0
CodeBase:
file:///C:/Users/Rami/Desktop/Perseus_2.0.6.0/
Perseus_2.0.6.0/bin/PerseusGui.exe

CefSharp.Core
Assembly Version: 63.0.3.0
Win32 Version:
CodeBase:
file:///C:/Users/Rami/Desktop/Perseus_2.0.6.0/
Perseus_2.0.6.0/bin/CefSharp.Core.DLL

PerseusLib
Assembly Version: 2.0.6.0
Win32 Version: 2.0.6.0
CodeBase:
file:///C:/Users/Rami/Desktop/Perseus_2.0.6.0/
Perseus_2.0.6.0/bin/PerseusLib.DLL

System.Windows.Forms
Assembly Version: 4.0.0.0
Win32 Version: 4.8.4515.0 built by:
NET48REL1LAST_C
CodeBase:
file:///C:/Windows/Microsoft.Net/assembly/GAC
MSIL/System.Windows.Forms/v4.0_4.0.0.0_
b77a5c561934e089/System.Windows.Forms.d
ll

System
Assembly Version: 4.0.0.0
Win32 Version: 4.8.4488.0 built by:
NET48REL1LAST_C
CodeBase:
file:///C:/Windows/Microsoft.Net/assembly/GAC
_MSIL/System/v4.0_4.0.0.0__b77a5c561934e
089/System.dll

System.Drawing
Assembly Version: 4.0.0.0
Win32 Version: 4.8.4390.0 built by:
NET48REL1LAST_C
CodeBase:
file:///C:/Windows/Microsoft.Net/assembly/GAC
_MSIL/System.Drawing/v4.0_4.0.0.0__b03f5f7
f11d50a3a/System.Drawing.dll

BaseLibS
Assembly Version: 1.0.0.0
Win32 Version: 1.0.0.0
CodeBase:
file:///C:/Users/Rami/Desktop/Perseus_2.0.6.0/
Perseus_2.0.6.0/bin/BaseLibS.DLL

netstandard
Assembly Version: 2.0.0.0
Win32 Version: 4.8.4084.0
CodeBase:
file:///C:/Windows/Microsoft.Net/assembly/GAC
_MSIL/netstandard/v4.0_2.0.0.0__cc7b13ffcd2
ddd51/netstandard.dll

CefSharp
Assembly Version: 63.0.3.0
Win32 Version: 63.0.3.0
CodeBase:
file:///C:/Users/Rami/Desktop/Perseus_2.0.6.0/
Perseus_2.0.6.0/bin/CefSharp.DLL

PerseusLibS
Assembly Version: 2.1.2.0
Win32 Version: 2.1.2.0
CodeBase:
file:///C:/Users/Rami/Desktop/Perseus_2.0.6.0/
Perseus_2.0.6.0/bin/PerseusLibS.DLL

PerseusApi
Assembly Version: 1.0.0.0
Win32 Version: 1.0.0.0
CodeBase:
file:///C:/Users/Rami/Desktop/Perseus_2.0.6.0/
Perseus_2.0.6.0/bin/PerseusApi.DLL

System.Core
Assembly Version: 4.0.0.0
Win32 Version: 4.8.4515.0 built by:
NET48REL1LAST_C
CodeBase:
file:///C:/Windows/Microsoft.Net/assembly/GAC
_MSIL/System.Core/v4.0_4.0.0.0__b77a5c561
934e089/System.Core.dll

System.Configuration
Assembly Version: 4.0.0.0
Win32 Version: 4.8.4190.0 built by:
NET48REL1LAST_B
CodeBase:
file:///C:/Windows/Microsoft.Net/assembly/GAC
_MSIL/System.Configuration/v4.0_4.0.0.0__b0
3f5f7f11d50a3a/System.Configuration.dll

System.Xml
Assembly Version: 4.0.0.0
Win32 Version: 4.8.4084.0 built by:
NET48REL1
CodeBase:
file:///C:/Windows/Microsoft.Net/assembly/GAC
_MSIL/System.Xml/v4.0_4.0.0.0__b77a5c5619
34e089/System.Xml.dll

FloatingTabs
Assembly Version: 1.0.0.0
Win32 Version: 1.0.0.0
CodeBase:
file:///C:/Users/Rami/Desktop/Perseus_2.0.6.0/
Perseus_2.0.6.0/bin/FloatingTabs.DLL

BaseLib
Assembly Version: 1.0.0.0
Win32 Version: 1.0.0.0
CodeBase:
file:///C:/Users/Rami/Desktop/Perseus_2.0.6.0/
Perseus_2.0.6.0/bin/BaseLib.DLL

System.ValueTuple
Assembly Version: 4.0.0.0
Win32 Version: 4.8.4084.0
CodeBase:
file:///C:/Windows/Microsoft.Net/assembly/GAC
_MSIL/System.ValueTuple/v4.0_4.0.0.0__cc7b
13ffcd2ddd51/System.ValueTuple.dll

PluginBase
Assembly Version: 1.6.2.2
Win32 Version: 1.6.2.2
CodeBase:
file:///C:/Users/Rami/Desktop/Perseus_2.0.6.0/
Perseus_2.0.6.0/bin/PluginBase.DLL

Utils
Assembly Version: 1.5.8.0
Win32 Version: 1.5.8.0
CodeBase:
file:///C:/Users/Rami/Desktop/Perseus_2.0.6.0/
Perseus_2.0.6.0/bin/Utils.DLL

PluginInterop
Assembly Version: 1.0.0.0
Win32 Version: 1.0.0.0
CodeBase:
file:///C:/Users/Rami/Desktop/Perseus_2.0.6.0/
Perseus_2.0.6.0/bin/PluginInterop.DLL

PerseusPluginLib
Assembly Version: 1.0.0.0
Win32 Version: 1.0.0.0
CodeBase:
file:///C:/Users/Rami/Desktop/Perseus_2.0.6.0/
Perseus_2.0.6.0/bin/PerseusPluginLib.DLL

PluginBase2
Assembly Version: 1.6.1.3
Win32 Version: 1.6.1.3
CodeBase:
file:///C:/Users/Rami/Desktop/Perseus_2.0.6.0/
Perseus_2.0.6.0/bin/PluginBase2.DLL

PluginBasic3
Assembly Version: 1.6.10.50
Win32 Version: 1.6.10.50
CodeBase:
file:///C:/Users/Rami/Desktop/Perseus_2.0.6.0/
Perseus_2.0.6.0/bin/PluginBasic3.DLL

PluginCoexpression
Assembly Version: 1.0.0.0
Win32 Version: 1.0.0.0
CodeBase:
file:///C:/Users/Rami/Desktop/Perseus_2.0.6.0/
Perseus_2.0.6.0/bin/PluginCoexpression.DLL

PluginCyTOF
Assembly Version: 1.0.0.0
Win32 Version: 1.0.0.0
CodeBase:
file:///C:/Users/Rami/Desktop/Perseus_2.0.6.0/
Perseus_2.0.6.0/bin/PluginCyTOF.DLL

PluginDEanalysis
Assembly Version: 1.0.0.0
Win32 Version: 1.0.0.0
CodeBase:
file:///C:/Users/Rami/Desktop/Perseus_2.0.6.0/
Perseus_2.0.6.0/bin/PluginDEanalysis.DLL

PluginIsobaricLabeling
Assembly Version: 1.0.0.0
Win32 Version: 1.0.0.0
CodeBase:
file:///C:/Users/Rami/Desktop/Perseus_2.0.6.0/
Perseus_2.0.6.0/bin/PluginIsobaricLabeling.DL
L

PluginLearning
Assembly Version: 1.6.10.50
Win32 Version: 1.6.10.50
CodeBase:
file:///C:/Users/Rami/Desktop/Perseus_2.0.6.0/
Perseus_2.0.6.0/bin/PluginLearning.DLL

PluginMetis
Assembly Version: 1.0.0.0
Win32 Version: 1.0.0.0
CodeBase:
file:///C:/Users/Rami/Desktop/Perseus_2.0.6.0/
Perseus_2.0.6.0/bin/PluginMetis.DLL

PluginMultiVolcano
Assembly Version: 1.0.0.0
Win32 Version: 1.0.0.0
CodeBase:
file:///C:/Users/Rami/Desktop/Perseus_2.0.6.0/
Perseus_2.0.6.0/bin/PluginMultiVolcano.DLL

PluginNetwork
Assembly Version: 1.6.10.43
Win32 Version: 1.6.10.43
CodeBase:
file:///C:/Users/Rami/Desktop/Perseus_2.0.6.0/
Perseus_2.0.6.0/bin/PluginNetwork.DLL

PluginPHOTON
Assembly Version: 1.0.0.0
Win32 Version: 1.0.0.0
CodeBase:
file:///C:/Users/Rami/Desktop/Perseus_2.0.6.0/
Perseus_2.0.6.0/bin/PluginPHOTON.DLL

PluginProteomicRuler
Assembly Version: 1.0.0.0
Win32 Version: 1.0.0.0
CodeBase:
file:///C:/Users/Rami/Desktop/Perseus_2.0.6.0/
Perseus_2.0.6.0/bin/PluginProteomicRuler.DLL

PluginTimeSeries
Assembly Version: 1.6.10.0
Win32 Version: 1.6.10.0
CodeBase:
file:///C:/Users/Rami/Desktop/Perseus_2.0.6.0/
Perseus_2.0.6.0/bin/PluginTimeSeries.DLL

NumPluginBase
Assembly Version: 1.0.0.0
Win32 Version: 1.0.0.0
CodeBase:
file:///C:/Users/Rami/Desktop/Perseus_2.0.6.0/
Perseus_2.0.6.0/bin/NumPluginBase.DLL

UtilsWf
Assembly Version: 1.0.0.0
Win32 Version: 1.0.0.0
CodeBase:
file:///C:/Users/Rami/Desktop/Perseus_2.0.6.0/
Perseus_2.0.6.0/bin/UtilsWf.DLL

System.Runtime.InteropServices.RuntimeInfor
mation
Assembly Version: 4.0.0.0
Win32 Version: 4.8.4084.0
CodeBase:
file:///C:/Windows/Microsoft.Net/assembly/GAC
_MSIL/System.Runtime.InteropServices.Runti
meInformation/v4.0_4.0.0.0__b03f5f7f11d50a3
a/System.Runtime.InteropServices.RuntimeInf
ormation.dll

************** JIT Debugging **************
To enable just-in-time (JIT) debugging, the
.config file for this
application or computer (machine.config) must
have the
jitDebugging value set in the
system.windows.forms section.
The application must also be compiled with
debugging
enabled.

For example:

When JIT debugging is enabled, any
unhandled exception
will be sent to the JIT debugger registered on
the computer
rather than be handled by this dialog box."

To Reproduce
Steps to reproduce the behavior:

1. After performing two sample t-test/ANOVA filter the only significant proteins then obtain Hierarchical cluster
2. Export row clusters (after defining row clusters)
3. match rows by name and select the base and the other matrixes

Expected behavior
to merge the other matrix with the base one.

Describe the bug
When I used the "msms.txt" and "evidence.txt" from MaxQuant v2.4.0.0 to generate DIA libraries for MAXDIA(MaxQuant v2.4.0.0), an error occured: Input string was not in a correct format.

The error information was attached.

When I used the "msms.txt" and "evidence.txt" from old version MaxQuant 2.0.3 to generate DIA libraries for MAXDIA(MaxQuant v2.4.0.0), the procedure "generate libraries" was passed.

Were there any ways to solve this problem?

Generate_libraries 11.error.txt

To Reproduce
I have several DDA data form Tims-tof pro, and they were analyzed by MaxQuant v2.4.0.0.
Then I get the "msms.txt" and "evidence.txt"from MaxQuant v2.4.0.0.
Next, I used the "msms.txt" and "evidence.txt" to generate DIA libraries for MAXDIA(MaxQuant v2.4.0.0), the error occured.
So, I reanalyzed the DDA data using old version MaxQuant 2.0.3.
When I used the "msms.txt" and "evidence.txt" from old version MaxQuant 2.0.3 to generate DIA libraries for MAXDIA(MaxQuant v2.4.0.0), the procedure "generate libraries" was passed.

Describe the bug
MaxQuant (Version 2.4.2.0) throws an error while assembling proteins for DDA FAIMS data labeled at MS1-level with “Re-quantify” option enabled.

Here are the contents of the “Assembling_proteins XXX.error.txt” and “Assembling_proteins XXX.comment.txt” files generated in the “proc” directory for two separate runs.

[Case 1]

Assembling_proteins 0180.error.txt

id	0
start	21/05/2023 05:21:30
title	Assembling_proteins (01/80)
description	H:\combined\proc Assembling_proteins 0 Assembling_proteins (01/80)  Process 46 0 H:\combined H:\mqpar.xml 0
error	H:\combined\proc Assemblissembling_proteins (01/80)  Process 46 0 H:\combined H:\mqpar.xml 0_Object reference not set to an instance of an object._   at MaxQuantLibS.Domains.Peptides.Features.ReQuantResult.ContainsIsotopeIndex(Int32 id)__   at MaxQuantLibS.Domains.Peptides.Search.Identifications.AddSearchEngineHit(ModificationSpecificPeptide msp, MsmsHit msmsHit, GroupParams param, IList`1 p, Int32 fileIndex, Int32 faimsIndex, QueryType type, Int32 multipletId, Int32 isotopeId, Multiplet m, IsotopeCluster isotopeCluster, Double retentionTime, GenericPeakListLayerData peakList, Double mz, ReQuantResult reQuantResult, NeucodeQuantResult ncQuantResult, Dictionary`2 addtlResults, Boolean isMs3, Boolean isIsobaric, Boolean isTims, Int32 imsMean, Double imsDip, Int32 imsMin, Int32 imsMax, Double ccsMean, Double ccsMin, Double ccsMax)__   at MaxQuantLibS.Domains.Peptides.Search.Identifications.AddSearchEngineHit(IdentifiedPeptide ip, MsmsHit msmsHit, GroupParams param, IList`1 p, Int32 fileIndex, Int32 faimsIndex, QueryType type, Int32 multipletId, Int32 isotopeId, Multiplet multiplet, IsotopeCluster isotopeCluster, Double retentionTime, GenericPeakListLayerData peakList, Double mz, ReQuantResult reQuantificationResult, NeucodeQuantResult ncQuantResult, Dictionary`2 addtlResults, Boolean isMs3, Boolean isIsobaric, Boolean isTims, Int32 imsMean, Double imsDip, Int32 imsMin, Int32 imsMax, Double ccsMean, Double ccsMin, Double ccsMax)__   at MaxQuantLibS.Domains.Peptides.Search.Identifications.ProcessPeptides(RankPredictionModel ipm, MaxQuantParams mqpar, Int32 fileIndex, Int32 faimsIndex, Dictionary`2 proteinIdToGroupIndex, GenericPeakListLayerData peakList, RawFileLayer rf, MsmsData msmsData, IdentifiedPeptide[] identifiedPeptides, String[] peptideSequences, ReQuantResult reQuantResult, NeucodeQuantResult ncQuantResult, ProteinSet proteinSet, String basePath, Int32[] topIntens, IDictionary`2 cachedAndromedaScoresForMassAnalyzer)__   at MaxQuantLibS.Domains.Peptides.Data.GenericRunLayer.ProcessSearchEnginePeptides(RankPredictionModel ipm, Int32 fileIndex, Int32 faimsIndex, Dictionary`2 proteinIdToGroupIndex, IdentifiedPeptide[] peptides, String[] peptideSequences, ProteinSet proteinSet, GroupParams gp, MaxQuantParams mqpar, Int32[] topIntens, IDictionary`2 cachedAndomedaForMassAnalyzer)__   at MaxQuantLibS.Domains.Peptides.ProteinTasks.ProteinAssembly.ProcessSearchEnginePeptides(Dictionary`2 proteinIdToGroupIndex, IdentifiedPeptide[] peptides, ProteinSet proteinSet, MaxQuantParams mqpar, IDictionary`2 andromedaScorePositioningCache, Responder responder, Int32 f1)__   at MaxQuantLibS.Domains.Peptides.ProteinTasks.ProteinAssembly.ProcessPeptides(String combinedFolder, MaxQuantParams mqpar, Int32 fileIndex, IDictionary`2 andromedaScorePositioningCache, Responder responder)__   at MaxQuantLibS.Domains.Peptides.ProteinTasks.ProteinAssembly.ProcessPeptidesX(String combinedFolder, String mqparFile, Int32 jobIndex, Responder responder)__   at MaxQuantLibS.Domains.Peptides.Work.ProteinAssembler.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	21/05/2023 05:21:42

Assembling_proteins 0180.comment.txt

0 006

[Case 2]

Assembling_proteins 0116.error.txt

id	0
start	21/05/2023 08:21:12
title	Assembling_proteins (01/16)
description	H:\combined\proc Assembling_proteins 0 Assembling_proteins (01/16)  Process 46 0 H:\combined H:\mqpar.xml 0
error	H:\combined\proc Assembling_proteins 0 Assembling_proteins (01/16)  Process 46 0 H:\combined H:\mqpar.xml 0_Object reference not set to an instance of an object._   at MaxQuantLibS.Domains.Peptides.Features.ReQuantResult.ContainsIsotopeIndex(Int32 id)__   at MaxQuantLibS.Domains.Peptides.Search.Identifications.AddSearchEngineHit(ModificationSpecificPeptide msp, MsmsHit msmsHit, GroupParams param, IList`1 p, Int32 fileIndex, Int32 faimsIndex, QueryType type, Int32 multipletId, Int32 isotopeId, Multiplet m, IsotopeCluster isotopeCluster, Double retentionTime, GenericPeakListLayerData peakList, Double mz, ReQuantResult reQuantResult, NeucodeQuantResult ncQuantResult, Dictionary`2 addtlResults, Boolean isMs3, Boolean isIsobaric, Boolean isTims, Int32 imsMean, Double imsDip, Int32 imsMin, Int32 imsMax, Double ccsMean, Double ccsMin, Double ccsMax)__   at MaxQuantLibS.Domains.Peptides.Search.Identifications.AddSearchEngineHit(IdentifiedPeptide ip, MsmsHit msmsHit, GroupParams param, IList`1 p, Int32 fileIndex, Int32 faimsIndex, QueryType type, Int32 multipletId, Int32 isotopeId, Multiplet multiplet, IsotopeCluster isotopeCluster, Double retentionTime, GenericPeakListLayerData peakList, Double mz, ReQuantResult reQuantificationResult, NeucodeQuantResult ncQuantResult, Dictionary`2 addtlResults, Boolean isMs3, Boolean isIsobaric, Boolean isTims, Int32 imsMean, Double imsDip, Int32 imsMin, Int32 imsMax, Double ccsMean, Double ccsMin, Double ccsMax)__   at MaxQuantLibS.Domains.Peptides.Search.Identifications.ProcessPeptides(RankPredictionModel ipm, MaxQuantParams mqpar, Int32 fileIndex, Int32 faimsIndex, Dictionary`2 proteinIdToGroupIndex, GenericPeakListLayerData peakList, RawFileLayer rf, MsmsData msmsData, IdentifiedPeptide[] identifiedPeptides, String[] peptideSequences, ReQuantResult reQuantResult, NeucodeQuantResult ncQuantResult, ProteinSet proteinSet, String basePath, Int32[] topIntens, IDictionary`2 cachedAndromedaScoresForMassAnalyzer)__   at MaxQuantLibS.Domains.Peptides.Data.GenericRunLayer.ProcessSearchEnginePeptides(RankPredictionModel ipm, Int32 fileIndex, Int32 faimsIndex, Dictionary`2 proteinIdToGroupIndex, IdentifiedPeptide[] peptides, String[] peptideSequences, ProteinSet proteinSet, GroupParams gp, MaxQuantParams mqpar, Int32[] topIntens, IDictionary`2 cachedAndomedaForMassAnalyzer)__   at MaxQuantLibS.Domains.Peptides.ProteinTasks.ProteinAssembly.ProcessSearchEnginePeptides(Dictionary`2 proteinIdToGroupIndex, IdentifiedPeptide[] peptides, ProteinSet proteinSet, MaxQuantParams mqpar, IDictionary`2 andromedaScorePositioningCache, Responder responder, Int32 f1)__   at MaxQuantLibS.Domains.Peptides.ProteinTasks.ProteinAssembly.ProcessPeptides(String combinedFolder, MaxQuantParams mqpar, Int32 fileIndex, IDictionary`2 andromedaScorePositioningCache, Responder responder)__   at MaxQuantLibS.Domains.Peptides.ProteinTasks.ProteinAssembly.ProcessPeptidesX(String combinedFolder, String mqparFile, Int32 jobIndex, Responder responder)__   at MaxQuantLibS.Domains.Peptides.Work.ProteinAssembler.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	21/05/2023 08:21:24

Assembling_proteins 0116.comment.txt

0 006

Desktop (please complete the following information):

• OS: Windows
• Version: 10

Additional context
An error occurred during the same process when “Match between runs” was enabled instead of “Re-quantify” as well.
If you need more details, I would be pleased to share them.

Sincerely,
Fumiko

Describe the bug
The cut-off line calculated by the FDR and s0 changed from one volcano plot to an other, without any changes to the two dataset or the FDR or s0. I compared the two groups N_Delta and N_Omicron yesterday and the cut-off line with an FDR 0.05 and s0 0.1 was lower than in a volcano plot created with the same two groups N_Delta Vs N_Omicron and the same FDR 0.05 and s0 0.1 today. I can change the FDR parameter in both plots and it changes accordingly but the lines are never the same, for the same FDR and s0 values.
I will attach two screenshots showing this strange behaviour. I can also only reproduce the FDR*s0 line from today by repeating the volcano plot analysis in the same and different matrixes, not the one created yesterday.
Perseus Version 2.07.0

To Reproduce
Steps to reproduce the behavior:
Sadly i cant reproduce the first volcano with the different FDRs0 line. but for the recreation of the new FDRs0 line i just have to create a new volcano plot comparing the group N_Delta and N_Omicron.

Expected behavior
No change in the FDRs0 line while doing the exact same analysis but just on a different day.

Screenshots

Desktop (please complete the following information):

• OS: [Windows 11 Home]
• Version [Perseus Version 2.07.0]

Additional context
I am new to Perseus so maybe the bug resulted from me miss handeling the product, but i checked all settings for both analysis twice and to me they are not different.

Describe the bug
In the Perseus version 2.0.11.0
Only the "8" is appearing and not the "_" with "Filter rows based on text column"

To Reproduce
Steps to reproduce the behavior:

1. Go to 'Filter rows based on text column'
2. Click in the space "Search string"
3. try to digit "_" (important to select significant pairs produced by a Post Hoc test as Perseus by default create a text column with "sample1_sample2").
4. With or withour the shift key, it is always "8" that is written, not "_"

Expected behavior
I want to be able to type the character "_"

Desktop (please complete the following information):

• OS: Windows 10 Professional
• Version 22H2

Describe the bug
At the moment this is disabled. Before enabling, check carefully that the spectra are properly exported, including all annotation is properly displayed and subscript numbers and superscript symbols are properly transfered to PDF.

To Reproduce
Steps to reproduce the behavior:

1. Go to '...'
2. Click on '....'
3. Scroll down to '....'
4. See error

Expected behavior
A clear and concise description of what you expected to happen.

Screenshots
If applicable, add screenshots to help explain your problem.

Desktop (please complete the following information):

• OS: [e.g. iOS]
• Version [e.g. 22]

Additional context
Add any other context about the problem here.

Hi,

I believe there is a bug in the pipeline you used to generate the discovery libraries (https://datashare.biochem.mpg.de/s/qe1IqcKbz2j2Ruf?path=%2FDiscoveryLibraries).
I can see what follows in the human and mouse files, probably is also in the other ones.

If you look at the msms.txt file, the Intensities and Masses columns looks suspiciously identical (well, Intensities are just rounded-up Masses)

See the attached examples, first 5 rows of the mouse msms.txt
msms_mouse.txt

Also, it looks like the is no correspondence between the Masses and Matches

y1 is definitely not 1566.62789

Dear All,

I tried to run LFQ for 12 thermo raw files (3 conditions × 4 replicates) on MQ. The software crushed with a label free normalization error no matter the normalization step was applied or not. I also downloaded the newest version of MQ, i.e. 2.3.1.0. It ended up with the same error. I tried with other data and got the same error. It seems that there are a number of reports on this issue. I am wondering if anyone has some idea to fix it. Thank you.

Desktop (please complete the following information):

• OS: Windows 10 Enterprise 22H2
• MQ: 2.2.0.0

Label-free_normalization 11.error.txt

This is not a bug,
but I would like to ask if I need to set "PTM" to "True" in the “Raw files tab” in addition to setting "Variable modifications" in "Modifications" when I run the PTMs data in MaxQuant. If it is not necessary to set "PTM" to Ture, what is the meaning of "PTM" here?

Thank you for the hard work you are putting into Perseus and Maxquant. We appreciate the software, however I am struggling with using the PerseusR interloper that we would really like to use in our lab in the future.

Bug descripiton
I would like to use PerseusR, however running custom scripts always reports "Output Error" (screenshot) without generating anything in Perseus. In the "pipeline viewer" a green box saying "External" quickly appears before the error message, the green box disappears with the error box when "OK" is clicked.

It seems the script is not parsed in Perseus since even faulty scripts will produce the same error as files that only contain commented lines or supposedly functional scripts (i.e., example script from Github). The error also appears very quickly so that I think R was not actually launched (It's a slow language after all...).

Perseus itself and PerseusR were installed successfully and correctly, I believe. I followed this tutorial ) and all the prompts from R during the installation of additional packages as well as PerseusR were identical. As test I tried using "Clustering" > "Umap" on a random matrix and it works fine. I receive an output and no error.
Only custom scripts seem to be not accepted.

Screenshots and other data
I added the "parameters.xml" as a zip file (upload restrictions) parameters.zip that can be generated when clicking the "Download Parameter for preview" button in the "External" > "Matrix => R" menu. This xml file is always the same, independent on the input.

The error I receive regardless of input script is shown here (it is not very explanatory):

System:

• OS: Windows 10 enterprise
• R's sessionInfo output:
  • R version 4.3.1 (2023-06-16 ucrt)
  • Platform: x86_64-w64-mingw32/x64 (64-bit)
  • Running under: Windows 10 x64 (build 19044)
• Perseus 2.0.11

Thank you for reading, I welcome all comments! If I failed to add some crucial information, please let me know.
Thank you again,
Florian

Describe the bug

Maxquant analysis takes more than 128 hours at "second peptide search" step.
This has happened twice (repeated the same analysis from the start of analysis, but it is still the same)

I am comparing the steps according to the publication on the Maxquant's expected run time:

My first search, main search and MS/MS preparation took only 45min to a few hours as per below:

Desktop (please complete the following information):

• OS: Windows 10 Pro for Workstations
• Version: 22H2

Appreciate your feedback on this issue. Thank you.

Here is just a test

Dear Maxquan Team
I tried to analyze an O480 raw file of a TMT18plex-labeled sample. Maxquant V2.1.4.0 crashed at MSMS_preparation . The message
displayed is the following "

File 1/1_Illegal isobaric labels._ at MaxQuantLibS.Domains.Peptides.Basic.GroupParams.GetIsobaricLabels(Double[]& allMasses, String[]& allSpecificities, Modification[][]& representativeMods, Double[,]& correction, Modification[] isoLabels, Dictionary`2"
Thank you very much for your help

Fernando

To Reproduce
Steps to reproduce the behavior:

1. MaxQuant.exe Load raw file
2. Click on 'Group specific Parameters.' Type -> Reporter ion MS2 -> 18 plex.
3. Select Mouse Uniprot database
4. Star Run MaxQuant
   Screenshots
   

If applicable, add screenshots to help explain your problem.

Desktop (please complete the following information):

• OS: WINDOWS10
• Version [e.g. 22]

Additional context
#runningTimes.txt

Add any other context about the problem here.
MSMS_preparation 11.comment.txt
MSMS_preparation 11.error.txt
mqpar.zip

Hello all.
I am running MQ 2.4 on Windows 11, with a single TMT-11plex acquired on a Bruker TIMS-TOF HT in DDA-PASEF mode.
The run keeps crashing during the 'Writing Tables' step giving below error message (from proc folder).
I already tried running the search from scratch, but the same error occurs.
II see a few other users have similar problems using different MQ versions and MS-platforms, but no solution yet.

Is there anyone here who had similar issue or can provide a solution/workaround?

Your help is greatly appreciated.
Best,
G

id 0
start 25/04/2023 09:42:58
title Writing_tables (09/23)
description C:\Users\xyz.d\combined\proc Writing_tables 8 Writing_tables (09/23) Process 23 0 C:\Users\xyz.d\combined C:\Users\xyz.d\mqpar.xml True 8
error C:\Users\xyz.d\combined\proc Writing_tables 8 Writing_tables (09/23) Process 23 0 C:\Users\xyz.d\combined C:\Users\xyz.d\mqpar.xml True 8_Object reference not set to an instance of an object._ at MaxQuantLibS.Domains.Peptides.Table.MsmsTable.FillReporterRatios(MsmsHit hit, DataRow2 row)__ at MaxQuantLibS.Domains.Peptides.Table.MsmsTable.FillReporters(MsmsHit hit, MaxQuantParams mqpar, DataRow2 row)__ at MaxQuantLibS.Domains.Peptides.Table.MsmsTable.Fill(IDataTable table, CombinedData combinedData, MaxQuantParams mqpar)__ at MaxQuantLibS.Domains.Peptides.Table.TableUtilsP.WriteTablesMsms(String mqparFile, String combinedFolder, String txtFolder, String serFolder)__ at MaxQuantLibS.Domains.Peptides.Table.TableUtilsP.WriteTablesTimsImpl(String combinedFolder, String txtFolder, String serFolder, String mqparFile, Int32 taskIndex)__ at MaxQuantLibS.Domains.Peptides.Table.TableUtilsP.WriteTablesTims(String combinedFolder, String mqparFile, Int32 taskIndex)__ at MaxQuantLibS.Domains.Peptides.Work.WriteTable.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 25/04/2023 09:42:58

Describe the bug
A clear and concise description of what the bug is.

Using PerseusR in Perseus and R to apply Limma correction in DE analysis (which works great and I have a nice adj p value column!) I can not save the session in an sps file.

• Windows10

Hello, is maxquant have manual decoy db search mode? Thanks. And why maxquant do not allow mgf as input file format?

Describe the bug
Adding Isotopic Label Corrections is not possible for 18plex

To Reproduce
In v2.2.0.0
Go to: "Group Specific Parameters" -> "Type" = Reporter Ion MS2.
Select any TMT plex (e.g. 18plex)
Then press Edit for any label
Then for any correction factor (e.g. -2[%]) press [+] and enter values for -2x 13C and -13C-15N (e.g. select 1% and 2% respectively)
These values are not saved into the main Table upon closing the Define Isobaric Label window.

It is therefore only possible to specify a single value for each correction, not two as given by the Thermo Product Data Sheet for the TMT kit.

Expected behavior

1. In the "Define Isobaric Label" pop-up window, Define "Internal Label" and "Terminal Label" as "TMTpro 18plex-Lys134C" and "TMTpro 18plex-Lys135N" respectively.
2. This populates the Isobaric Labels table (previous window) correctly, as it should, after you press OK.
3. Entering any values for Correction Factor (in the "Define Isobaric Label" pop-up window) will also work, but NOT if you use the [+] button to enter 2 values per isotope. In this case the Isobaric Labels table (previous window) stays blank.

Screenshots

Desktop (please complete the following information):

• OS: Windows 10 Enterprise 21H2
• Version e.g. 2.2.0.0

Additional context
I have contacted another lab [email protected] as I know they also use 18plex. They report the same issue.
Happy new Year!

[email protected]

Would it be possible to provide download links for older versions of MQ? At the moment I'm particularly interested in version 2.0.3.0.

Dear MaxQuant team,

Would it be possible to define new one-letter symbols for unnatural amino acids in MaxQuant? That would be very helpful.

Describe the bug
Thermo Ascend files throw errors (likely from them changing the file in some way and MQ using Thermo's rawfilereader

To Reproduce
Steps to reproduce the behavior:

1. Go to '...'
2. Click on '....'
3. Scroll down to '....'
4. See error

Expected behavior
A clear and concise description of what you expected to happen.

Screenshots
If applicable, add screenshots to help explain your problem.

Desktop (please complete the following information):

• OS: [e.g. iOS]
• Version [e.g. 22]

Additional context
Add any other context about the problem here.

Describe the bug
MQ 2.4.2.0 did not finish "Finish_protein_assembly" - step; no error message thrown; I abrogated the MQ analysis after > 90hrs;
2 DIA-PASEF files obtained on a timsTOF pro were subjected to MQ analysis using both the canonical and the additional mouse fasta discovery libraries

To Reproduce
mqpar.xml file attached

Screenshots

Desktop (please complete the following information):

• OS: Windows 10 Pro for Workstations
• 384 GB RAM, 40 cores

Additional context
Neither DIA-NN 1.8.1 nor Spectronaut did have problems with the two DIA-PASEF files
mqpar.zip

The community page says:

If you have questions you can't find the answer to in the documentation, try asking in the Google group with the topic closest to your problem:

Unfortunately, the archive seems to be non-public. Accessing https://groups.google.com/g/maxquant-list?pli=1 I get:

Sie sind nicht berechtigt, auf diese Inhalte zuzugreifen

I do not want to use a Google account. Is it possible to access the archive?

Describe the bug
Dear All,

we noticed a bug in Perseus 1.6.14.0 (checked in the latest available version but already present in older ones) in the two-sample test configuration frame.

The two-sample test works well, all comparisons requested are well done but what is reported in the workflow is not exactly what has been defined.

To illustrate this, please find the settings of a two-sample test with multiple conditions (2 screenshots needed to capture all conditions - "...conf_begin" and "...conf_end") and what is reported at the end in the workflow "2sampletest_WF.png".
In summary, it seems that repetitions are not well processed: only the first occurrence is kept in the workflow display as shown in "2sampletest_summary.png". In yellow, the conditions kept in the workflow compared to the initial settings of the two-sample test.
A related problem appears if you try to reorder a condition in the field if already one occurrence exists. For example with [J3, J2, J4, J2], if you select the last J2 to push it up for one place, it's in fact the first J2 that is selected and moved one place up ("moveUp_lastCTRLJ2" and "firstCTRLJ2_hasMoved").
The main thing is that the test is done as expected but the workflow is really helpful to check what has been set, especially for tricky tests.

To Reproduce
Steps to reproduce the behavior:

1. Go to '...'
2. Click on '....'
3. Scroll down to '....'
4. See error

Expected behavior
A clear and concise description of what you expected to happen.

Screenshots
If applicable, add screenshots to help explain your problem.

Desktop (please complete the following information):

• OS: [e.g. iOS]
• Browser [e.g. chrome, safari]
• Version [e.g. 22]

Additional context
Add any other context about the problem here.

id 0
start 04/08/2023 10:38:43
title Configuring (1/1)
description C:\07212023A\combined\proc Configuring 0 Configuring (1/1) Process 53 0 C:\07212023A\combined C:\07212023A\mqpar.xml
error C:\07212023A\combined\proc Configuring 0 Configuring (1/1) Process 53 0 C:\07212023A\combined C:\07212023A\mqpar.xml_An error occurred while parsing EntityName. Line 146, position 30._ at System.Xml.XmlTextReaderImpl.Throw(Exception e)__ at System.Xml.XmlTextReaderImpl.Throw(String res, String arg)__ at System.Xml.XmlTextReaderImpl.Throw(String res)__ at System.Xml.XmlTextReaderImpl.ParseEntityName()__ at System.Xml.XmlTextReaderImpl.ParseEntityReference()__ at System.Xml.XmlTextReaderImpl.Read()__ at System.Xml.XmlTextReader.Read()__ at MaxQuantLibS.Domains.Peptides.Basic.MaxQuantParamsReaderV000.Read(String filePath)__ at MaxQuantLibS.Domains.Peptides.Basic.MaxQuantParams..ctor(String filePath)__ at MaxQuantLibS.Domains.Peptides.Basic.MaxQuantParams.Read(String filename)__ at MaxQuantLibS.Domains.Peptides.Basic.MaxQuantTasks.InitWorkflow(String combinedFolder, String mqparFile)__ at MaxQuantLibS.Domains.Peptides.Work.InitializeWorkflow.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 04/08/2023 10:38:43

Describe the bug
Dear,

When running MaxDIA with a DDA generated library in MaxQuant using the MQ version 2.2.0.0, the error "Unable to load DLL 'xgboost' appears at the Peptide FDR1 step. This is on OS Win10, running .Net framework 4.8.4084.0
Do I need to install something extra here?

Thank you for your answer.

Kind regards,
An

To Reproduce
Steps to reproduce the behavior:

1. Go to '...'
2. Click on '....'
3. Scroll down to '....'
4. See error

Expected behavior
A clear and concise description of what you expected to happen.

Screenshots
If applicable, add screenshots to help explain your problem.

Desktop (please complete the following information):

• OS: Windows
• Version 10

Additional context
Add any other context about the problem here.

I found some interesting placements of pyro-Glu in a dataset we ran with MaxNovo. The settings inside MaxNovo for the placement specify any N terminal as position and the correct single aminoacid as specificity. I also do not think we can change these settings as they are built in defaults.
4 example sequences from msmsScans.txt column DN sequence

{D(Glu->pyro-Glu)|N(Gln->pyro-Glu)}QVYR
{D(Glu->pyro-Glu)|N(Gln->pyro-Glu)}{L|I}QGDD[EP]AAE{L|I}ARNPVT
{N(Glu->pyro-Glu)|L(Gln->pyro-Glu)|I(Gln->pyro-Glu)}PASHTMPGTTEVGARVP[{L|I}T]NN
{E|F(Glu->pyro-Glu)}TYHNH{L|I}{[W(Oxidation_W)M]|[W{M(Oxidation (M))|F}]}[{M(Oxidation (M))|F}T]Q

Additionally I found an interesting placement of these pyro glu modifications in the Sequence column. In the other column (DN sequence) this modification is defined as a sidechain modification while here it is listed as a N terminal modification ( I assume based on the location and pro forma like syntax).
All 3 sequences in the Sequence column starting with a modification

_(Gln->pyro-Glu)QPRDERSRRRSAQVKRNAQKIRVPTDGQLL_
_(Gln->pyro-Glu)QPRDERSRRRSAQVKRNAQKIRVPTDGQLL_
_(Glu->pyro-Glu)ESAESEQSLKYESM(Oxidation (M))ETKIIVPGRR_

One last small question: is it indeed the case that MaxNovo does not output the fixed modifications as they are assumed to be in place at all possible locations? Now using the output of MaxNovo I add every fixed modification to every possible location, could this lead to problems in my output?
An example sequence with a Cys, we have Cys carboymethylation turned on as a fixed modification, and it is not in this sequence.

{L|I}{M(Oxidation (M))|F}VSGNCCPN{L|I}SVM{L|I}{M(Oxidation (M))|F}P

I hope you can help me shine a light on this behaviour. I love the fact that MaxNovo is giving these results with explicit ambiguity!

Maxquant 2.1.4 is shutting down during MaxDIA run (discovery mode libraries) without reporting any error in the proc folder.
I have 330 files in total from which 5 different samples with 66 SEC fractions each. I need to run them all at once to get the LFQ values and compare them. I am assigning the experiments as follows:

File Experiment Fraction
Sample_t0_fraction_01.raw t0 1
Sample_t0_fraction_02.raw t0 2
. . .
. . .
Sample_t1_fraction_01.raw t1 1
Sample_t2_fraction_01.raw t2 1

(All in the same parameter group)
I use the default settings with LFQ and iBAQ on, plus "Separate LFQ in parameter groups" on.

That's the last file generated in proc:

System

• Microsoft Windows Server 2019 Standard, Version 10.017763
• MaxQuant Version: 2.1.4 (30 threads)

I have also tried to run only one samples (with 66 Fractions) and it still crashes, so I'm not sure if it's a sample size issue.

Cheers!

Describe the bug
When running MQ using the MaxDIA setting, the program runs smoothly until it reaches the DIA Preparation2 stage, where the error:

0_49.517894803001546% of library protein identifiers do not exist in the fasta file._

at MaxQuantLibS.Domains.Peptides.Dia.Activities.DiaPreparation.CheckProteinIdentifiers(DiaLibrary[] libs, MaxQuantParams mqpar)__ at MaxQuantLibS.Domains.Peptides.Dia.Activities.DiaPreparation.GetLibs(MaxQuantParams mqpar, GroupParams gp)__ at MaxQuantLibS.Domains.Peptides.Dia.Activities.DiaPreparation.GenerateLibraries(String mqparFile, Int32 groupIndex, Responder responder)__ at MaxQuantLibS.Domains.Peptides.Work.DiaPrep2.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)

appears. I have seen multiple other people on the google group get this error with no resolution as of yet. The library I am using has been produced using the DIA-NN programme, producing a tsv spectral library file compatible with MQ. The library was generated via in silico digest of the HSV-1 and Human proteomes from Uniprot, and the same fasta files are used when running MQ in DIA.

To Reproduce
Steps to reproduce the behavior:
Run MaxQuant in MaxDIA using a library generated elsewhere.

Desktop (please complete the following information):

• OS: Windows 10 Education
• Version: 21H2
• MaxQuant is updated to the latest version

Describe the bug
Running any MaxDIA pipeline using .wiff as input fails on Feature detection step:

Configuring
Assemble run info
Finish run info
Testing fasta files
Preparing searches
Generate libraries
Feature detection

Unhandled Exception: System.Exception: Exception during execution of external process: 12508 Unhandled exception. System.IO.FileNotFoundException: Could not find file 'C:\Users\slavat.WISMAIN\Dow       nloads\T8_kin_1_\p0\T8_kin_1_.bg.dia0'.
File name: 'C:\Users\slavat.WISMAIN\Downloads\T8_kin_1_\p0\T8_kin_1_.bg.dia0'
   at System.IO.FileStream.ValidateFileHandle(SafeFileHandle fileHandle)
   at System.IO.FileStream.CreateFileOpenHandle(FileMode mode, FileShare share, FileOptions options)
   at System.IO.FileStream..ctor(String path, FileMode mode, FileAccess access, FileShare share, Int32 bufferSize, FileOptions options)
   at System.IO.FileStream..ctor(String path, FileMode mode, FileAccess access, FileShare share)
   at BaseLibS.Util.FileUtils.GetBinaryReader(String path)
   at MaxQuantLibS.Domains.Peptides.Features.FeatureDetectionUtil.DetectFeatures(MaxQuantParams mqpar, Int32 taskIndex, Boolean positiveMode, Responder responder, Int32 batchBegin, Int32 batchEnd       )
   at MaxQuantLibS.Domains.Peptides.Features.FeatureDetectionUtil.DetectFeatures(String mqparFile, Int32 taskIndex, Boolean positiveMode, Responder responder, Int32 batchBegin, Int32 batchEnd)
   at MaxQuantLibS.Domains.Peptides.Work.FeatureDetection.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)
   at MaxQuantTaskCore.Program.Main(String[] args)

   at QueueingSystem.WorkDispatcher.ProcessSingleRunExternalProcess(Int32 taskIndex, Int32 threadIndex)
   at QueueingSystem.WorkDispatcher.DoWork(Int32 taskIndex, Int32 threadIndex)
   at QueueingSystem.WorkDispatcher.Work(Object threadIndex)
   at System.Threading.ExecutionContext.RunInternal(ExecutionContext executionContext, ContextCallback callback, Object state, Boolean preserveSyncCtx)
   at System.Threading.ExecutionContext.Run(ExecutionContext executionContext, ContextCallback callback, Object state, Boolean preserveSyncCtx)
   at System.Threading.ExecutionContext.Run(ExecutionContext executionContext, ContextCallback callback, Object state)
   at System.Threading.ThreadHelper.ThreadStart(Object obj)

Same error happens in GUI

To Reproduce
Steps to reproduce the behavior:

1. Go to 'any DIA dataset in .wiff format https://www.ebi.ac.uk/pride/archive/projects/PXD036444'
2. Click on 'run MaxDIA in discovery mode with fasta/evidence/msms files from MQ web'
3. See error

Expected behavior
Not crashing, this does not happen when .raw files are used as input

Screenshots
If applicable, add screenshots to help explain your problem.

Desktop (please complete the following information):

• OS: Windows
• Version 10

Additional context
Add any other context about the problem here.

Dear MaxQuant team,
Thanks for your ongoing support.
We run BRUKER TimsTOF files with MQ2.2.2.0 (TimsMaxDIA, FASTA files, peptides, msms, evidence from MPI homepage). MQ is stuck in the "DIA_library_search3" processing step.
With different sample files we got the same issue.

Happy to share files if needed.
Thanks very much in advance.

I've been doing analyses of SILAC labeled experiments (Arg10 + Lys8). When analyzing the RAW files over time in different versions, I have noticed that in MQ version 2.1, the evidence table still shows unique intensity numbers for the L and the H as it should. However, in the versions thereafter show exactly half of the total in L and H for the MULTI-MSMS and MULTI-SECPEP type peptides. I am afraid this influences the final output for the intensity in the proteingroups table too and would thus lead to a wrong conclusion of the experiment. I've looked at the L and H intensities of individual proteins in the ProteinGroup table and they are indeed a sum of the L or H intensities in the peptides associated to the same proteingroup id in the evidence table, thus this means that when a peptide is detected both H and L, they now always contribute equally, which kind of nullifies the whole set up of doing a SILAC experiment. I know most people look at the H/L ratio, but since I am not sure whether the ratio is eventually also depending on the intensity, I hope this can be corrected soon :)

I only discovered this recently as I used to only look at the proteingroups table, but I wanted to check some findings in the evidence table and then I noticed this.

another minor error in version 2.4 is that when you open the txt files in Excel to have a quick look, it does not automatically make columns anymore (did with txt files of older version).

on a positive note though: version 2.4 is the first one that does not lag at certain steps in a run (like not going any further in 1 file of a prep_for_first_search orso: sometimes it was stuck on 1 file in 1 step for 10 hours or more, like it lost to code to move to the next step) :) So I am very happy to see that improvement!

Thanks for looking into this!

To Reproduce
Steps to reproduce the behavior:
have a SILAC experiment dataset
run the analysis in MQ 2.1 and 2.4 (apart from selecting the correct labels, do not change any other settings)
compare evidence tables in L and H intensities when "MULTI-" as the 'type'

Expected behavior
this was the evidence table in version 2.1:

and this is the evidence table of version 2.4 (same RAW files):

(don't worry about missing columns, I had to delete some to get it all visible in 1 screen)

The H/L ratio's in the evidence table of individual peptides actually seems to be the same still, but the intensity signals have changed.

Desktop:

• OS: Windows 10 (not have other specifics available now)

Describe the bug
This log2LFQ distribution is looking like following

Attached proteinGroups.txt

To Reproduce
Attached parameters used for the search
mqpar..xml.txt

Expected behavior
Not sure what to expect but the DIA-NN search (some details of the search shared at vdemichev/DiaNN#682)

and DDA search for the plasma-sample distribution looks like

So i think these low values is something maxLFQ-DIA is introducing?

Desktop (please complete the following information):

• OS: Windows
• Version 11

Describe the bug
A clear and concise description of what the bug is.

To Reproduce
Steps to reproduce the behavior:

1. Go to '...'
2. Click on '....'
3. Scroll down to '....'
4. See error

Expected behavior
A clear and concise description of what you expected to happen.

Screenshots
If applicable, add screenshots to help explain your problem.

Desktop (please complete the following information):

• OS: [e.g. iOS]
• Version [e.g. 22]

Additional context
Add any other context about the problem here.

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?

Describe the bug
Upon using MaxQuant version 2.4.2.0 for peptide identification with the digestion parameter set as Unspecific and other parameters set to default, the resulting PSMs in the output file are labeled as CID instead of HCD, which is the expected fragmentation method.

To Reproduce
Steps to reproduce the behavior:

1. Use MaxQuant version 2.4.2.0 for peptide identification.
2. Set the digestion parameter to Unspecific.
3. Keep other parameters as default.
4. Analyze the output file and observe that the reported fragmentation method is CID instead of HCD

Expected behavior
The expected behavior is that the resulting PSMs in the output file should be labeled as HCD, which corresponds to the fragmentation method used in the spectra acquisition.

Desktop (please complete the following information):

• OS: Windows 10
• Version: 2.4.2.0

Additional context
I have thoroughly reviewed the MaxQuant documentation and ensured that the appropriate settings were selected for HCD fragmentation. However, the obtained results indicate that the fragmentation method is being incorrectly reported as CID. I kindly request your assistance in understanding the possible causes of this issue and identifying any misconfigurations or overlooked steps. If additional information or data files are required for further investigation, please let me know, and I will promptly provide them. Your support is highly appreciated in resolving this matter and ensuring the accuracy of the peptide identification results.

Thank you for your attention to this matter, and I look forward to your response.

Best regards,
Baron

We get the error from GUI and CLI:
.NET Core 2.1 needs to be installed

Command line:
Maxquant_2.0.1.0\bin\MaxQuantCmd.exe mqpar.xml

dotnet --list-sdks
2.1.526 [C:\Program Files\dotnet\sdk]
7.0.201 [C:\Program Files\dotnet\sdk]

Maybe you do not find it because the name changed from dotnetcore to dotnet?

Describe the bug
A clear and concise description of what the bug is.

To Reproduce
Steps to reproduce the behavior:

1. Go to '...'
2. Click on '....'
3. Scroll down to '....'
4. See error

Expected behavior
A clear and concise description of what you expected to happen.

Screenshots
If applicable, add screenshots to help explain your problem.

Desktop (please complete the following information):

• OS: [e.g. iOS]
• Version [e.g. 22]

Additional context
Add any other context about the problem here.

Describe the bug
Hi MaxQuant team,

I'm trying to analyze the raw files a18182 to a18190 from this publication:
https://pubs.acs.org/doi/10.1021/jasms.0c00299
by using the following files to enable TMTpro16 quantification on the newest MaxQuant version (v2.0.3.1):
http://proteomicsnews.blogspot.com/2020/11/process-tmtpro16-plex-reagents-in.html
Weirdly enough, all MS2-based quant files (e.g. a18182) are perfectly quantified (cross-compared to other TMT quant tools), whereas the reporter ion columns in msms.txt for MS3-based files (e.g. a18183) are empty, and the ones in msmsScans.txt have quants that are all over the place.

Desktop (please complete the following information):

• OS: Windows
• Version MaxQuant

Additional context
Add any other context about the problem here.

Describe the bug
I'm using for the first time FAIMS data, with 2 or 3 CV. I divided in 2-3 raw files so there is one CV for raw file. The run stop during the protein assembling step and MQ closes. I just downloaded the last version, but it gives exactly the same error, that I can't understand how to solve. it seems a file missing. All reposrts are attached
Assembling_proteins 0116.comment.txt
Assembling_proteins 0116.error.txt
#runningTimes.txt
mqpar_FAIMS-DDA.txt

To Reproduce
Steps to reproduce the behavior:

1. Go to '...'
2. Click on '....'
3. Scroll down to '....'
4. See error

Expected behavior
A clear and concise description of what you expected to happen.

Screenshots
If applicable, add screenshots to help explain your problem.

Desktop (please complete the following information):

• OS: [e.g. iOS]
• Version [e.g. 22]

Additional context
Add any other context about the problem here.

Describe the bug
When submitting a search with two parameter groups, and LFQ was selected in both groups, but the "Separate LFQ in Parameter Groups" is checked...MaxQuant shuts down on that step, and the following error was reported:

id 0
start 06/06/2023 12:07:00
title Label-free_normalization (1/1)
description Z:\RawData\QExactivePlus\Research\LB\052523\combined\proc Label-free_normalization 0 Label-free_normalization (1/1) Process 57 0 Z:\RawData\QExactivePlus\Research\LB\052523\mqpar.xml Z:\RawData\QExactivePlus\Research\LB\052523\combined 10 1
error Z:\RawData\QExactivePlus\Research\LB\052523\combined\proc Label-free_normalization 0 Label-free_normalization (1/1) Process 57 0 Z:\RawData\QExactivePlus\Research\LB\052523\mqpar.xml Z:\RawData\QExactivePlus\Research\LB\052523\combined 10 1_Index was outside the bounds of the array._ at MsLib.Data.Protein.MaxLfqNorm.CalcNormCoefficientsMedianImpl(IProteinQuantData pqd, Int32[] fileInds, Int32 nfiles, String[] exps, Func2 getFileIndices)__ at MsLib.Data.Protein.MaxLfqNorm.CalcNormCoefficientsClassicImpl(IProteinQuantData pqd, Int32[] fileInds, Int32 nthreads, Boolean prefracMaxIntensity, Int32 maxFeatures, Boolean restrictFeatures, Int32 minEdgesPerNode, Int32 avEdgesPerNode, Boolean fastLfq, Int32 nfiles, String[] exps, Func2 getFraction, Func2 getExperiment, Func2 getFileIndices, Func2 getFileName, Boolean median)__ at MsLib.Data.Protein.MaxLfqNorm.CalcNormCoefficientsClassic(IProteinQuantData pqd, Int32[] fileInds, Int32 nthreads, Boolean prefracMaxIntensity, Int32 maxFeatures, Boolean restrictFeatures, Int32 minEdgesPerNode, Int32 avEdgesPerNode, Boolean fastLfq, Int32 nfiles, String[] exps, Func2 getFraction, Func2 getExperiment, Func2 getFileIndices, Func2 getFileName, Boolean median)__ at MsLib.Data.Protein.MaxLfqNorm.CalcNormCoefficients(IProteinQuantData pqd, Int32[] fileInds, Int32 nthreads, Boolean prefracMaxIntensity, Int32 maxFeatures, Boolean restrictFeatures, LfqNormType lfqNormType, Int32 minEdgesPerNode, Int32 avEdgesPerNode, Boolean fastLfq, Int32 nfiles, String[] exps, Func2 getFraction, Func2 getExperiment, Func2 getFileIndices, Func2 getFileName, Int32 lfqNormClusterSize, Boolean classicLfqForSingleShots, Boolean isSingleShot)__ at MsLib.Data.Protein.MaxLfqNorm.CalcNormCoeffs(IProteinQuantData pqd, String combinedFolder, Int32 nthreads, Int32 lfqInd, Int32 maxFeatures, Boolean restrictFeatures, LfqNormType lfqNormType, Int32 minEdgesPerNode, Int32 avEdgesPerNode, Boolean fastLfq, Int32 nfiles, String[] exps, Func2 getFraction, Func2 getExperiment, Func2 getFileIndices, Func`2 getFileName, Int32[] fileInds, Int32 lfqNormClusterSize, Boolean classicLfqForSingleShots, Boolean isSingleShot)__ at MaxQuantLibS.Domains.Peptides.ProteinTasks.ProteinAssembly.CalcNormCoeffsLfq(String mqparFile, String combinedFolder, Int32 nthreads, Int32 lfqInd)__ at MaxQuantLibS.Domains.Peptides.Work.LfqNorm.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 06/06/2023 12:08:15

If I uncheck "Separate LFQ in Parameter Groups", and resubmit partial processing at the "Label Free Collect" Step, the search completed successfully

Desktop (please complete the following information):

• OS: Win10
• MaxQuant Version [2.4.2.0]

Describe the bug
DIA and LFQ. error in proc: Label-free_quantification_modpep_33.error

Label-free_quantification__modpep_ 33.error.txt

To Reproduce

Part 1: Running MaxDIA with label-free data
Assignment_MaxQuant_DIA.pdf

Expected behavior
Code runs normally

Screenshots
If applicable, add screenshots to help explain your problem.

Desktop (please complete the following information):

• OS: [e.g. windows]
• Version [e.g. 10]

Additional context

At the MPI for Molecular Genetics a lot of users use GNU/Linux for bioinformatic work, and also the servers run with it.

As I understand it, there is a GUI for Microsoft Windows but not GNU/Linux.

If that is correct, are you planning on porting the GUI to GNU/Linux too in the future?

The entered correction factors for the differenct N and C channels in TMTpro16plex are not saved after pressing OK button

To Reproduce
In MaxQuant, under Group-specific parameters in "Type" choose Reporter ion MS2
Select "16plex"
Mark one row and select "Edit"
Press "+" next to the correction factor labels and enter the factors for 13C and 15N
Press "OK"
The entered factor do not appear in the table
When selecting again "Edit", the previous entered factors are not present

Windows 10
MaxQuant 2.1.4.0

will this comes to slack

MQ crashed after finish with calculations (done) . Using the latest version of MQ. Tried on different computers and same issue.
Also cannot change any settings in any instrument parameters field.
I have installed the latest version of net core 3.1.426

Desktop (please complete the following information):

• OS: [e.g. iOS] wind 10 enterprise 21 H2
• Version [e.g. 22]

Describe the bug
A clear and concise description of what the bug is.

To Reproduce
Steps to reproduce the behavior:

1. Go to '...'
2. Click on '....'
3. Scroll down to '....'
4. See error

Expected behavior
A clear and concise description of what you expected to happen.

Screenshots
If applicable, add screenshots to help explain your problem.

Desktop (please complete the following information):

• OS: [e.g. iOS]
• Version [e.g. 22]

Additional context
Add any other context about the problem here.

Dear MQ team,

The De-isotoping IMS step takes at least two days to finish. Other search software seems to take only seconds to isotope. Does it really take 40 hours to deisotope IMS or could it be a bug?

Thanks
Maithy

Describe the bug
A session save error (failed to write session") appears after data processing using R plugin (such as quantile normalization)

This bug has also been reported by others in YouTrack and in the Google group.

To Reproduce
Steps to reproduce the behavior, I reduced the steps to the minimum to reproduce the error:

1. Open Perseus 2.0.7.0
2. Click on 'Create a random matrix', a matrix is generated
3. Click on Normalization, then select "Quantile normalization", another matrix is generated, which indicated that the R script ran and generated results without issues.
   A screenshot of the steps
   
4. Click on "File-Save", see error
   
5. After clicking "Ok", a second window showed up
   

Expected behavior
I expect the session to be saved and reloaded just like ones where R plugins are not involved.

Screenshots
See above

Desktop (please complete the following information):

• OS: Windows 10 Pro, version 20H2
• Perseus Version 2.0.7.0 (same error was seen in previous versions as well, as reported by others)
• R Version: 4.2.1

Additional context
All necessary R packages, such as PerseusR, BioBase, devtools have been installed properly.