ConvertTraMLToTSV

Converts TraML files to OpenSWATH transition TSV files

The OpenSWATH transition TSV files will have the following headers, all fields are separated by tabs:

PrecursorMz (float) ProductMz (float) Tr_calibrated (float) transition_name (free text, needs to be unique for each transition [in this file]) CE (float) LibraryIntensity (float) transition_group_id (free text, designates the transition group [e.g. peptide] to which this transition belongs) decoy (1==decoy, 0== no decoy; determines whether the transition is a decoy transition or not) PeptideSequence (free text, sequence only (no modifications) ) ProteinName (free text) Annotation (free text, e.g. y7) FullPeptideName (free text, should contain modifications*) MissedCleavages Replicates NrModifications Charge (integer) Labelgroup (free text, e.g. heavy or light)

modifications are returned in UniMod annotation.