Produced mzML files cannot be handled by R's mzR::openMSfile function

I 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.

[caetera]

Version 1.3.1 is updated with the fix for the bug, I have mentioned earlier.

[higsch]

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.