Converts OpenSWATH transition TSV files to TraML files
The OpenSWATH transition TSV files need to have the following headers, all fields need to be separated by tabs:
(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) FullUniModPeptideName (free text, should contain modifications*) PrecursorCharge (integer, contains the charge of the precursor) Labelgroup (free text, e.g. heavy or light) UniprotID (free text) FragmentType (free text, contains the type of the fragment, e.g. "b" or "y") FragmentCharge (integer, contains the fragment charge) FragmentSeriesNumber (integer, e.g. for y7 use "7" here) modifications should be supplied inside the sequence using UniMod identifiers or freetext identifiers that are understood by OpenMS. Please do not use the ambiguous bracket notation (e.g. PEPT[+80]IDE or PEPT[181]IDE) since this is ambiguous and will NOT be interpreted correctly! example: PEPT(Phosphorylation)IDE(UniMod:27)A )