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mzmine source code repository
https://mzmine.github.io/mzmine_documentation/
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ThermoRawFileImport on MS3 fails #447

Open robinschmid opened 2 years ago

robinschmid commented 2 years ago

The raw data file import generates an mzML with only the last m/z isolation step. Usually mzML has multiple precursor ions sorted by MS level. See the snap below for MS3 from .raw. @tomas-pluskal do you want to reach out about that?

image

tomas-pluskal commented 2 years ago

Could you upload a sample file? I'll write to them.

robinschmid commented 2 years ago

Orbitrap IDX up do MS4 202112_DIMS_MS4_DDA_Orbitrap_IDX.zip

tomas-pluskal commented 2 years ago

Have you tried running the ThermoRawFileParser on this file? I am getting this exception:

C:\ThermoRawFileParser>ThermoRawFileParser.exe -i 202112_DIMS_MS4_DDA_Orbitrap_IDX.raw
2021-12-08 09:47:29 INFO Started parsing 202112_DIMS_MS4_DDA_Orbitrap_IDX.raw
2021-12-08 09:47:30 INFO Processing 1280 MS scans
10% 2021-12-08 09:47:31 ERROR An unexpected error occured while parsing file:202112_DIMS_MS4_DDA_Orbitrap_IDX.raw
2021-12-08 09:47:31 ERROR System.ObjectDisposedException: Cannot access a closed file.
   at System.IO.__Error.FileNotOpen()
   at System.IO.FileStream.Write(Byte[] array, Int32 offset, Int32 count)
   at System.Security.Cryptography.CryptoStream.FlushFinalBlock()
   at System.Security.Cryptography.CryptoStream.Dispose(Boolean disposing)
   at System.IO.Stream.Close()
   at ThermoRawFileParser.Writer.MzMlSpectrumWriter.Write(IRawDataPlus rawFile, Int32 firstScanNumber, Int32 lastScanNumber) in /home/niels/Documents/Development/Projects/ThermoRawFileParser/Writer/MzMlSpectrumWriter.cs:line 577
   at ThermoRawFileParser.RawFileParser.ProcessFile(ParseInput parseInput) in /home/niels/Documents/Development/Projects/ThermoRawFileParser/RawFileParser.cs:line 139
   at ThermoRawFileParser.RawFileParser.TryProcessFile(ParseInput parseInput) in /home/niels/Documents/Development/Projects/ThermoRawFileParser/RawFileParser.cs:line 62

It seems the parsing crashed after ~10% of the file. Not sure if that is also causing your problem with precursors, or if that is a different problem. Will investigate.

tomas-pluskal commented 2 years ago

https://github.com/compomics/ThermoRawFileParser/issues/126

robinschmid commented 2 years ago

Was fixed in the parser so we should update the parser internally

titodamiani commented 1 year ago

@robinschmid @tomas-pluskal has this been fixed? Or it's still an open issue?

tomas-pluskal commented 1 year ago

I think we still have not updated the parser..

SteffenHeu commented 11 months ago

@robinschmid can you comment if this is still an issue?

ansgarkorf commented 11 months ago

Should be fine after Tomas PR: #771