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])  
- 
Collision Energy (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)  
- 
GroupLabel (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 are returned in UniMod annotation.