Here is what I did. I generate a mzXML from Thermo RAW data using ReAdW. Then I ran msconvert to try to get a mgf file from that mzXML generated from RAW data (The command was: msconvert --.mzXML --.mgf; also tried other ways like: msconvert --.mgf --.mzXML etc). But the software always generate a mzML file instead of a mgf file. I don't what's wrong with my conversion. Anyone has ideas? Thx!
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