Hi, I'm using the 6546-QTOF to analyze some peptide samples using DIA. My workflow is to perform data acquisition using the QTOF, export the data as a .mzml file, then perform analysis using msfragger / fragpipe. Every time I perform analysis with fragpipe, the program crashes with an error "Could not get isolation window info from scan 7557". After consulting with a developer from msfragger, we determined that the root issue is that the datafile is actually missing the isolation window for some scans and not just that fragpipe was failing to read them. I have re-ran this sample on the QTOF a few times, always getting the same isolation window related error, but on different scans. I have also used MSconvert (instead of agilent qualitative analysis program) to generate the .mzml file from the .d file, ultimately producing the same error. When reviewing the TIC data from Agilent qualitative analysis, I can find scan 7557, and see no obvious problems with that scan. The isolation window is reported correctly in the top corner of the mass spectrum for this scan.
How can I fix my export datafile to restore the missing isolation window information?
