Produced mzML files cannot be handled by R's mzR::openMSfile function
See original GitHub issueI produced mzML files from Thermo raw files using the docker version like that:
docker run -v /data:/data -i -t thermorawparser mono /src/bin/x64/Debug/ThermoRawFileParser.exe -d=/data/raw -o=/data/mzml/ -f=1 -m=1 -e -p
The raw files were SPS-MS3 files from an Orbitrap Lumos instrument. It all worked fine, I could run a MSGFplus search and detect TMT quantifications with OpenMS IsobaricAnalyzer.
However, when I wanted to open a spectrum in R with
spectra_list <- mzR::openMSfile(filename = mzml_file)
I got this error:
Error: Can not open file file.mzML! Original error was: Error in pwizModule$open(filename): c++ exception (unknown reason)
I first thought there is something going wrong with Rcpp
, but then I realised that when I convert the files with msconvert
, everything is fine again.
So does ThermoRawFileParser
modify the files in a way that I cannot open them with mzR::openMSfile
any more? I also tried switching on/off the zlib
compression and peak picking, but that didn’t help.
Issue Analytics
- State:
- Created 3 years ago
- Comments:10
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Version 1.3.1 is updated with the fix for the bug, I have mentioned earlier.
So finally, the dataset is out. https://www.ebi.ac.uk/pride/archive/projects/PXD018357. The issue happens basically with all the
20200317_KKL_CoV2_24h_5v5_F*.raw
files.