Hello,
I’m a newbie for metaboanalyst.
I converted MS files with ProteoWizard from .raw file obtained from thermo Orbitrap by following the tutorial.
docker run -it --rm -e WINEDEBUG=-all -v /FILE_PATH/:/data chambm/pwiz-
skyline-i-agree-to-the-vendor-licenses wine msconvert FILENAME -o OUTPUTDIR --mzML --filter
"peakPicking true 1-" --filter "zeroSamples removeExtra" --filter "msLevel 1" --64 –zlib
Next, I converted for “MS2_…” files from .raw file as below,
docker run -it --rm -e WINEDEBUG=-all -v /FILE_PATH/:/data chambm/pwiz-
skyline-i-agree-to-the-vendor-licenses wine msconvert FILENAME -o OUTPUTDIR --mzML --filter
"peakPicking true 2-" --filter "zeroSamples removeExtra" --filter "msLevel 2" --64 –zlib
However, I got an error message,
ERROR:No MS1 spectra in file: MS2_20240626_sample1.mxML
then, ended up as below,
Error in matrix(nrow = nrow(sample_data)) : data is too long
Calls: <Anonymous> -> matrix
Execution halted
srun: error: xiaserver10: task 0: Exited with exit code 1
How should I convert the files for MS2 data including MS1?
I know this is a pretty basic question, but could someone please help…