Galaxy's Maxquant problem

Christos-Kotsopoulos · April 30, 2025, 1:15pm

Hello everyone,

I am facing a problem with i am trying to do a mass spec analysis with galaxys Maxquant. I initially used the .raw files from this experiment (PRIDE id:PXD027714) and imported them on galaxy and followed an used pipeline. Then i got this error:

Unhandled Exception:
System.Exception: Exception during execution of external process: 1300689 
Unhandled Exception:
ThermoFisher.CommonCore.Data.Business.NoSelectedDeviceException: RunHeaderEx
  at ThermoFisher.CommonCore.RawFileReader.RawFileAccessBase.RequireDevice (System.String reason) [0x0001c] in <7b20930f488c4a50a6b41afdf3646c13>:0 
  at ThermoFisher.CommonCore.RawFileReader.RawFileAccessBase.get_RunHeaderEx () [0x00000] in <7b20930f488c4a50a6b41afdf3646c13>:0 
  at PluginRawThermo.ThermoRawFile.get_FirstScanNumber () [0x00017] in <63f726adc13d42dab92b89022cfbd864>:0 
  at BaseLibS.Ms.RawFile.InitFromRawFileImpl () [0x00020] in <2a783505a9324377a912fbc866234a84>:0 
  at BaseLibS.Ms.RawFile.InitFromRawFile () [0x00017] in <2a783505a9324377a912fbc866234a84>:0 
  at BaseLibS.Ms.RawFile.Init (System.String path1) [0x00058] in <2a783505a9324377a912fbc866234a84>:0 
  at MsLib.Raw.RawFileUtil.CreateRawFile (System.String path) [0x00047] in <c7996a5d247b4a82ba72a2553c25246f>:0 
  at MaxQuantLibS.Domains.Peptides.Data.GenericRun+<>c__DisplayClass10_0.<.ctor>b__0 () [0x00000] in <6a6754cab5cf48c89c9c64e9dafc7e21>:0 
  at MaxQuantLibS.Domains.Peptides.Data.GenericRun.get_RawFile () [0x0000a] in <6a6754cab5cf48c89c9c64e9dafc7e21>:0 
  at MaxQuantLibS.Domains.Peptides.Data.GenericRunLayer.get_RawFileLayer () [0x00006] in <6a6754cab5cf48c89c9c64e9dafc7e21>:0 
  at

after a quick search i found that a possible solution would be to convert the .raw files to the .mzML format which i did using proteoWizard’s MS converter with the usual parameters and peak picking 1-2

And after i uploaded it and re-run it in Maxquant i got the error message bellow:

Unhandled Exception:
System.Exception: Exception during execution of external process: 829937 
Unhandled Exception:
System.ArgumentException: Could not identify mass analyzer for spectrum 0.
  at PluginRawMzMl.MzMLRawFile.MassAnalyzer (System.Int32 scanNumber, PluginRawMzMl.ScanType scan) [0x00091] in <43a575582d27438f841a4c61dc554bbc>:0 
  at PluginRawMzMl.MzMLRawFile.GetInfoForScanNumber (System.Int32 scanNumber) [0x0009e] in <43a575582d27438f841a4c61dc554bbc>:0 
  at BaseLibS.Ms.RawFile.InitFromRawFileImpl () [0x00048] in <2a783505a9324377a912fbc866234a84>:0 
  at BaseLibS.Ms.RawFile.InitFromRawFile () [0x00017] in <2a783505a9324377a912fbc866234a84>:0 
  at BaseLibS.Ms.RawFile.Init (System.String path1) [0x00058] in <2a783505a9324377a912fbc866234a84>:0 
  at MsLib.Raw.RawFileUtil.CreateRawFile (System.String path) [0x00047] in <c7996a5d247b4a82ba72a2553c25246f>:0 
  at MaxQuantLibS.Domains.Peptides.Data.GenericRun+<>c__DisplayClass10_0.<.ctor>b__0 () [0x00000] in <6a6754cab5cf48c89c9c64e9dafc7e21>:0 
  at MaxQuantLibS.Domains.Peptides.Data.GenericRun.get_RawFile () [0x0000a] in <6a6754cab5cf48c89c9c64e9dafc7e21>:0 
  at MaxQuantLibS.Domains.Peptides.Data.GenericRunLayer.get_RawFileLayer () [0x00006] in <6a6754cab5cf48c89c9c64e9dafc7e21>:0 
  at MaxQuantLibS.Domains.Peptides.Features.FeatureDetectionUtil.AssembleRunInfo (System.String mqparFile, System.Int32 fileIndex) [0x000a4] in <6a6754cab5cf48c89c9c64e9dafc7e21>:0 
  at MaxQuantLibS.Domains.Peptides.Work.AssembleRunInfo.Calculation (System.String[] args, BaseLibS.Util.Responder responder) [0x0000c] in <6a6754cab5cf48c89c9c64e9dafc7e21>:0 
  at MaxQuantLibS.Domains.Peptides.Work.MaxQuantWorkDispatcherUtil.PerformTask (System.Int32 taskType, System.String[] args, BaseLibS.Util.Responder responder) [0x00007] in <6a6754cab5cf48c89c9c64e9dafc7e21>:0 
  at MaxQuantLibS.Base.MaxQuantUtils.Run (System.Int32 softwareId, System.Int32 taskType, System.String[] args, BaseLibS.Util.Responder responder) [0x0002d] in <6a6754cab5cf48c89c9c64e9dafc7e21>:0 
  at MaxQuantTaskCore.Program.Function (System.String[] args, BaseLibS.Util.Responder responder) [0x0001c] in <1c54eed30d1e45488ee6c9e61d204782>:0 
  at Utils.Util.ExternalProcess.Run (System.String[] args, System.Boolean debug) [0x00148] in <94cd7968dc654c259fccb9053e84841e>:0 
  at MaxQuantTaskCore.Program.Main (System.String[] args) [0x00007] in <1c54eed30d1e45488ee6c9e61d204782>:0 
[ERROR] FATAL UNHANDLED EXCEPTION: System.ArgumentException: Could not identify mass analyzer for spectrum 0.
  at PluginRawMzMl.MzMLRawFile.MassAnalyzer (System.Int32 scanNumber, PluginRawMzMl.ScanType scan) [0x00091] in <43a575582d27438f841a4c61dc554bbc>:0 
  at PluginRawMzMl.MzMLRawFile.GetInfoForScanNumber (System.Int32 scanNumber) [0x0009e] in <43a575582d27438f841a4c61dc554bbc>:0 
  at BaseLibS.Ms.RawFile.InitFromRawFileImpl () [0x00048] in <2a783505a9324377a912fbc866234a84>:0 
  at BaseLibS.Ms.RawFile.InitFromRawFile () [0x00017] in <2a783505a9324377a912fbc866234a84>:0 
  at BaseLibS.Ms.RawFile.Init (System.String path1) [0x00058] in <2a783505a9324377a912fbc866234a84>:0 
  at MsLib.Raw.RawFileUtil.CreateRawFile (System.String path) [0x00047] in <c7996a5d247b4a82ba72a2553c25246f>:0 
  at MaxQuantLibS.Domains.Peptides.Data.GenericRun+<>c__DisplayClass10_0.<.ctor>b__0 () [0x00000] in <6a6754cab5cf48c89c9c64e9dafc7e21>:0 
  at MaxQuantLibS.Domains.Peptides.Data.GenericRun.get_RawFile () [0x0000a] in <6a6754cab5cf48c89c9c64e9dafc7e21>:0 
  at MaxQuantLibS.Domains.Peptides.Data.GenericRunLayer.get_RawFileLayer () [0x00006] in <6a6754cab5cf48c89c9c64e9dafc7e21>:0 
  at MaxQuantLibS.Domains.Peptides.Features.FeatureDetectionUtil.AssembleRunInfo (System.String mqparFile, System.Int32 fileIndex) [0x000a4] in <6a6754cab5cf48c89c9c64e9dafc7e21>:0 
  at MaxQuantLibS.Domains.Peptides.Work.AssembleRunInfo.Calculation (System.String[] args, BaseLibS.Util.Responder responder) [0x0000c] in <6a6754cab5cf48c89c9c64e9dafc7e21>:0 
  at MaxQuantLibS.Domains.Peptides.Work.MaxQuantWorkDispatcherUtil.PerformTask (System.Int32 taskType, System.String[] args, BaseLibS.Util.Responder responder) [0x00007] in <6a6754cab5cf48c89c9c64e9dafc7e21>:0 
  at MaxQuantLibS.Base.MaxQuantUtils.Run (System.Int32 softwareId, System.Int32 taskType, System.String[] args, BaseLibS.Util.Responder responder) [0x0002d] in <6a6754cab5cf48c89c9c64e9dafc7e21>:0 
  at MaxQuantTaskCore.Program.Function (System.String[] args, BaseLibS.Util.Responder responder) [0x0001c] in <1c54eed30d1e45488ee6c9e61d204782>:0 
  at Utils.Util.ExternalProcess.Run (System.String[] args, System.Boolean debug) [0x00148] in <94cd7968dc654c259fccb9053e84841e>:0 
  at MaxQuantTaskCore.Program.Main (System.String[] args) [0x00007] in <1c54eed30d1e45488ee6c9e61d204782>:0 

  at QueueingSystem.WorkDispatcher.ProcessSingleRunExternalProcess (System.Int32 taskIndex, System.Int32 threadIndex) [0x0009d] in <9c0f25807e814cdb9d19b5c1d7b1d72f>:0 
  at QueueingSystem.WorkDispatcher.DoWork (System.Int32 taskIndex, System.Int32 threadIndex) [0x0001e] in <9c0f25807e814cdb9d19b5c1d7b1d72f>:0 
  at QueueingSystem.WorkDispatcher.Work (System.Object threadIndex) [0x00054] in <9c0f25807e814cdb9d19b5c1d7b1d72f>:0 
  at System.Threading.ThreadHelper.ThreadStart_Context (System.Object state) [0x00025] in <7cd4deb8302a478d9d393f24754841da>:0 
  at System.Threading.ExecutionContext.RunInternal (System.Threading.ExecutionContext executionContext, System.Threading.ContextCallback callback, System.Object state, System.Boolean preserveSyncCtx) [0x00071] in <7cd4deb8302a478d9d393f24754841da>:0 
  at System.Threading.ExecutionContext.Run (System.Threading.ExecutionContext executionContext, System.Threading.ContextCallback callback, System.Object state, System.Boolean preserveSyncCtx) [0x00000] in <7cd4deb8302a478d9d393f24754841da>:0 
  at System.Threading.ExecutionContext.Run (System.Threading.ExecutionContext executionContext, System.Threading.ContextCallback callback, System.Object state) [0x0002b] in <7cd4deb8302a478d9d393f24754841da>:0 
  at System.Threading.ThreadHelper.ThreadStart (System.Object obj) [0x0000f] in <7cd4deb8302a478d9d393f24754841da>:0 
[ERROR] FATAL UNHANDLED EXCEPTION: System.Exception: Exception during execution of external process: 829937 
Unhandled Exception:
System.ArgumentException: Could not identify mass analyzer for spectrum 0.
  at PluginRawMzMl.MzMLRawFile.MassAnalyzer (System.Int32 scanNumber, PluginRawMzMl.ScanType scan) [0x00091] in <43a575582d27438f841a4c61dc554bbc>:0 
  at PluginRawMzMl.MzMLRawFile.GetInfoForScanNumber (System.Int32 scanNumber) [0x0009e] in <43a575582d27438f841a4c61dc554bbc>:0 
  at BaseLibS.Ms.RawFile.InitFromRawFileImpl () [0x00048] in <2a783505a9324377a912fbc866234a84>:0 
  at BaseLibS.Ms.RawFile.InitFromRawFile () [0x00017] in <2a783505a9324377a912fbc866234a84>:0 
  at BaseLibS.Ms.RawFile.Init (System.String path1) [0x00058] in <2a783505a9324377a912fbc866234a84>:0 
  at MsLib.Raw.RawFileUtil.CreateRawFile (System.String path) [0x00047] in <c7996a5d247b4a82ba72a2553c25246f>:0 
  at MaxQuantLibS.Domains.Peptides.Data.GenericRun+<>c__DisplayClass10_0.<.ctor>b__0 () [0x00000] in <6a6754cab5cf48c89c9c64e9dafc7e21>:0 
  at MaxQuantLibS.Domains.Peptides.Data.GenericRun.get_RawFile () [0x0000a] in <6a6754cab5cf48c89c9c64e9dafc7e21>:0 
  at MaxQuantLibS.Domains.Peptides.Data.GenericRunLayer.get_RawFileLayer () [0x00006] in <6a6754cab5cf48c89c9c64e9dafc7e21>:0 
  at MaxQuantLibS.Domains.Peptides.Features.FeatureDetectionUtil.AssembleRunInfo (System.String mqparFile, System.Int32 fileIndex) [0x000a4] in <6a6754cab5cf48c89c9c64e9dafc7e21>:0 
  at MaxQuantLibS.Domains.Peptides.Work.AssembleRunInfo.Calculation (System.String[] args, BaseLibS.Util.Responder responder) [0x0000c] in <6a6754cab5cf48c89c9c64e9dafc7e21>:0 
  at MaxQuantLibS.Domains.Peptides.Work.MaxQuantWorkDispatcherUtil.PerformTask (System.Int32 taskType, System.String[] args, BaseLibS.Util.Responder responder) [0x00007] in <6a6754cab5cf48c89c9c64e9dafc7e21>:0 
  at MaxQuantLibS.Base.MaxQuantUtils.Run (System.Int32 softwareId, System.Int32 taskType, System.String[] args, BaseLibS.Util.Responder responder) [0x0002d] in <6a6754cab5cf48c89c9c64e9dafc7e21>:0 
  at MaxQuantTaskCore.Program.Function (System.String[] args, BaseLibS.Util.Responder responder) [0x0001c] in <1c54eed30d1e45488ee6c9e61d204782>:0 
  at Utils.Util.ExternalProcess.Run (System.String[] args, System.Boolean debug) [0x00148] in <94cd7968dc654c259fccb9053e84841e>:0 
  at MaxQuantTaskCore.Program.Main (System.String[] args) [0x00007] in <1c54eed30d1e45488ee6c9e61d204782>:0 
[ERROR] FATAL UNHANDLED EXCEPTION: System.ArgumentException: Could not identify mass analyzer for spectrum 0.
  at PluginRawMzMl.MzMLRawFile.MassAnalyzer (System.Int32 scanNumber, PluginRawMzMl.ScanType scan) [0x00091] in <43a575582d27438f841a4c61dc554bbc>:0 
  at PluginRawMzMl.MzMLRawFile.GetInfoForScanNumber (System.Int32 scanNumber) [0x0009e] in <43a575582d27438f841a4c61dc554bbc>:0 
  at BaseLibS.Ms.RawFile.InitFromRawFileImpl () [0x00048] in <2a783505a9324377a912fbc866234a84>:0 
  at BaseLibS.Ms.RawFile.InitFromRawFile () [0x00017] in <2a783505a9324377a912fbc866234a84>:0 
  at BaseLibS.Ms.RawFile.Init (System.String path1) [0x00058] in <2a783505a9324377a912fbc866234a84>:0 
  at MsLib.Raw.RawFileUtil.CreateRawFile (System.String path) [0x00047] in <c7996a5d247b4a82ba72a2553c25246f>:0 
  at MaxQuantLibS.Domains.Peptides.Data.GenericRun+<>c__DisplayClass10_0.<.ctor>b__0 () [0x00000] in <6a6754cab5cf48c89c9c64e9dafc7e21>:0 
  at MaxQuantLibS.Domains.Peptides.Data.GenericRun.get_RawFile () [0x0000a] in <6a6754cab5cf48c89c9c64e9dafc7e21>:0 
  at MaxQuantLibS.Domains.Peptides.Data.GenericRunLayer.get_RawFileLayer () [0x00006] in <6a6754cab5cf48c89c9c64e9dafc7e21>:0 
  at MaxQuantLibS.Domains.Peptides.Features.FeatureDetectionUtil.AssembleRunInfo (System.String mqparFile, System.Int32 fileIndex) [0x000a4] in <6a6754cab5cf48c89c9c64e9dafc7e21>:0 
  at MaxQuantLibS.Domains.Peptides.Work.AssembleRunInfo.Calculation (System.String[] args, BaseLibS.Util.Responder responder) [0x0000c] in <6a6754cab5cf48c89c9c64e9dafc7e21>:0 
  at MaxQuantLibS.Domains.Peptides.Work.MaxQuantWorkDispatcherUtil.PerformTask (System.Int32 taskType, System.String[] args, BaseLibS.Util.Responder responder) [0x00007] in <6a6754cab5cf48c89c9c64e9dafc7e21>:0 
  at MaxQuantLibS.Base.MaxQuantUtils.Run (System.Int32 softwareId, System.Int32 taskType, System.String[] args, BaseLibS.Util.Responder responder) [0x0002d] in <6a6754cab5cf48c89c9c64e9dafc7e21>:0 
  at MaxQuantTaskCore.Program.Function (System.String[] args, BaseLibS.Util.Responder responder) [0x0001c] in <1c54eed30d1e45488ee6c9e61d204782>:0 
  at Utils.Util.ExternalProcess.Run (System.String[] args, System.Boolean debug) [0x00148] in <94cd7968dc654c259fccb9053e84841e>:0 
  at MaxQuantTaskCore.Program.Main (System.String[] args) [0x00007] in <1c54eed30d1e45488ee6c9e61d204782>:0 

  at QueueingSystem.WorkDispatcher.ProcessSingleRunExternalProcess (System.Int32 taskIndex, System.Int32 threadIndex) [0x0009d] in <9c0f25807e814cdb9d19b5c1d7b1d72f>:0 
  at QueueingSystem.WorkDispatcher.DoWork (System.Int32 taskIndex, System.Int32 threadIndex) [0x0001e] in <9c0f25807e814cdb9d19b5c1d7b1d72f>:0 
  at QueueingSystem.WorkDispatcher.Work (System.Object threadIndex) [0x00054] in <9c0f25807e814cdb9d19b5c1d7b1d72f>:0 
  at System.Threading.ThreadHelper.ThreadStart_Context (System.Object state) [0x00025] in <7cd4deb8302a478d9d393f24754841da>:0 
  at System.Threading.ExecutionContext.RunInternal (System.Threading.ExecutionContext executionContext, System.Threading.ContextCallback callback, System.Object state, System.Boolean preserveSyncCtx) [0x00071] in <7cd4deb8302a478d9d393f24754841da>:0 
  at System.Threading.ExecutionContext.Run (System.Threading.ExecutionContext executionContext, System.Threading.ContextCallback callback, System.Object state, System.Boolean preserveSyncCtx) [0x00000] in <7cd4deb8302a478d9d393f24754841da>:0 
  at System.Threading.ExecutionContext.Run (System.Threading.ExecutionContext executionContext, System.Threading.ContextCallback callback, System.Object state) [0x0002b] in <7cd4deb8302a478d9d393f24754841da>:0 
  at System.Threading.ThreadHelper.ThreadStart (System.Object obj) [0x0000f] in <7cd4deb8302a478d9d393f24754841da>:0

igor · April 30, 2025, 10:52pm

Hi @Christos-Kotsopoulos

This part of the error message points on the issue:

It looks like data issue potentially related to the conversion:

github.com/cox-labs/CoxLab_Bug_Reporting

Different versions of MaxQuant analyze mzML files and Thermo RAW files

opened 11:50AM - 23 Apr 25 UTC

Yin-HJ

MaxQuant

**Describe the bug** I want to use MaxQuant to analyze mzML files converted from… Thermo RAW files in linux (I know MQ supports RAW files; in my case, I want to edit RAW files). I did some tests, here are the details 1. Initially, I used an earlier version of MQ (v.2.0.2.0) for analysis, and the raw format file analysis was smooth(because of the special database, I got about 1040 ms2 records in msms.txt). 2. However, when using converted mzML files (conversion made by msconvert in Windows and ThermoRawFileParser in Linux, the two converted mzML files are similar), MaxQuant reported an error at the Assemble step, and the error content is "**Could not Identify mass analyzer for spectrum 0._** _see Fig 1_". 3. Then, I tried to analyze using the latest version of MaxQuant (v2.6.7.0), and the process ended successfully, but I only got 11 ms2 records in msms.txt (mzML files converted from different methods got similar results). [ √ ] 4. After thatI tried to use MaxQuant (v2.6.7.0) to test the RAW format files, but an error occurred again. In the MSMS_preparation step, the error content was as follows: “**Arithmetic operation resulted in an overflow._ at MaxQuantLibS.Domains.Peptides.Data.PlistData.GenericPeakListLayerData.ReadCalibration()**... _see Fig 2_” ![Image](https://github.com/user-attachments/assets/dd814421-1066-47ef-9791-ccd78f4d30d5) **Attached files** For the configuration files, in addition to the basic experimental design, I checked GroupParameter-LFQ, Global Parameter-Label-free quantification - iBAQ, and Global Parameter - Identification - Match between runs, all using default parameters; The following are the mqpar.xmls for analysis [mqpar_v2.0.2.0.txt](https://github.com/user-attachments/files/19865801/mqpar_v2.0.2.0.txt) [mqpar_v2.6.7.0.txt](https://github.com/user-attachments/files/19865803/mqpar_v2.6.7.0.txt) Tested data are from [PRIDE-PXD006512](https://www.ebi.ac.uk/pride/archive/projects/PXD006512) - mzML converted by ThermoRawFileParse.exe in shell by: `mono ThermoRawFileParser.exe -i 20151115_liver_XL20_P_01.raw -b 20151115_liver_XL20_P_01.mzML -f 2` - mzML converted by msconvert in windows as follow Fig: ![Image](https://github.com/user-attachments/assets/c60033aa-b48d-4a3c-b7e6-dd1be7f46c4d) **Desktop** - OS: [Centos - 7.9.2009 ] - OS: [Windows11 - 23H2 ] **What I want to do** 1. I want to analyze the edited mass spectrum files in mzML format based on MaxQuant. 2. In addition, **why are the results of MaxQuant v2.6.7.0 analyzing mzML format files (about 1120 records in msms.txt) far different from analyzing RAW format files (about 11 records in msms.txt)?** **Additional context** 1. In fact, I suspected that there was a problem with the converted mzML format files; during the msconver conversion, I filtered the spectrum by "Vendor msLevel=1-2". The file size is close to that converted by ThermoRawFileParser.exe. Considering the successful execution of MaxQuant v2.6.7.0, it should not be the mzML file problem, I think。 2. By the way, if I do not use the "Vendor msLevel=1-2" filter, an error will be reported at the MSMS_preparation step analyzed by v2.0.2.0: ”Unable to read beyond the end of steam._ at System.IO.Stream.READAtLeastCore...“ (Yeah, error from assemble to MSMS_preparation). The same data analyzed by v2.6.7.0, pipeline ended successfully, I got the txt folder, but most files include msms.txt are empty, mzRange.txt contains many records. I am very confused and can provide the test RAW and mzML test data if needed. I'm not sure if there was a bug, or maybe I did something wrong that caused the error. Hope to get some help！ **I would be grateful for any suggestions or recommendations！** Yin HJ 2025/04/23 **Update 2025/04/24:** 1. I know why v2.6.7.0 could not analyze RAW files: because MaxQuant does not overwrite existing files, such as the index files, some files generated by v2.0.2.0 are used for analysis in V2.6.7.0. 2. Yestoday and today, I tried use MaxQuant v 2.6.7.0 with the same mzML format data, 1 success, 1 failure； On the other two computers, both v2.6.7.0 and v2.6.3.0 versions of MaxQuant failed, and the same error was reported for the three failures: "**Index was outside the bounds of the array._** " ![Image](https://github.com/user-attachments/assets/666bab1b-15bb-4f0d-ac23-0af75c34e390) 3. **There should be a bug for MaxQuant when analyzing mzML format files.**

Maybe try msconvert and other output formats, for example .mxXML.

Hope that helps.

Kind regards,
Igor

Christos-Kotsopoulos · April 30, 2025, 11:10pm

Hello @igor

First of all thank you for your response!
Several things happened since i posted that question.
I re-converted the .raw → mzML and still got the error i provided above (System.ArgumentException: Could not identify mass analyzer for spectrum 0) and re-tried to run the .raw file and got the same respective error (ThermoFisher.CommonCore.Data.Business.NoSelectedDeviceException: RunHeaderEx). Had the same luck with mzXML.
However, i run now some other .raw files (from another PRIDE repo) and seem to work fine for now at least -when i run the files i mentioned in the post i had an error in the first 5 mins. I’ll have to wait for the analysis to be completed.

So i think, there might be something wrong with the metadata of the original raw file and that it doesn’t matter the format that i will use. However i will check also the link you provided. Once again thank you very much!

With best regards,
Chris

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