Dear Group Members, I am new to OMSSA. I had an mzXML which i converted to mgf (using mzXML2search.exe).When I exported OMSSA results as CSV files for target - decoy searches, i was puzzled to see same scan ID repeated multiple times (without any rank). I also observed that OMSSA assigned same peptide to precursor where charge was assumed as +2 once and +3(this i assume from the scan ID (file column) names which end in *.2 and *.3). If my assumption is correct, there is something wrong with the way i handled OMSSA. Can someone help me rectify the problem. The duplicates have same scores, e-values etc. Of 1183 rows(assuming it reports 1 PSM per row), 85 are duplicates based on scan number & or file name/ id. Has anyone else faced such a problem before? or any ideas what i may be doing wrongly?
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