|Unable to use MSFragger for spectral library||s jager||2023-07-31 06:52|
I have been using MSFragger to analyze my timstof data, and i have been trying to upload the ‘interact.pep.xml’ files as spectral library. I put the '_uncalibrated.mzML' in the parent folder as had been described previously. However, i get the following error message:
"interact.pep.xml: To import an MSFragger search of timsTOF data (with ion_mobility attribute), the corresponding *_uncalibrated.mgf or *_calibrated.mgf file is required"
As of version 3.6, MSFragger does not output these files, and does the mxML counterparts instead (which I have). Can I somehow solve this and import the spectral library.
Or is there a workaround, for example a way i can import a list of peptide sequences with modifications, and that skyline processes this similarly to when I upload the FASTA?
thanks in advance!