Ive been able to obtain data by inputting either raw files or mzml files but both have failed in being able to output a mgf file from alignment results. Ive been able to only obtain csv or txt files as the export and was wondering how I could troubleshoot this. I've tried looking online if anyone has gone through similar issues but could not find a solution to this issue. Appreciate any help and your suggestions.
Do you get blank file or don't get any file at all? I have had similar issue before and I only got a blank export for mgf, 0KB.