Converts TraML files to OpenSWATH transition TSV files
The OpenSWATH transition TSV files will have the following headers, all fields are separated by tabs:
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PrecursorMz (float)
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ProductMz (float)
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Tr_recalibrated (float) (normalized retention time)
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transition_name (free text, needs to be unique for each transition [in this file])
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CollisionEnergy (float)
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LibraryIntensity (float)
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transition_group_id (free text, designates the transition group [e.g. peptide] to which this transition belongs)
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decoy (1==decoy, 0== no decoy; determines whether the transition is a decoy transition or not)
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PeptideSequence (free text, sequence only (no modifications) )
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ProteinName (free text)
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Annotation (free text, e.g. y7)
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FullUniModPeptideName (free text, should contain modifications*)
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PrecursorCharge (integer, contains the charge of the precursor)
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GroupLabel (free text, e.g. heavy or light)
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UniprotID (free text)
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FragmentType (free text, contains the type of the fragment, e.g. "b" or "y")
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FragmentCharge (integer, contains the fragment charge)
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FragmentSeriesNumber (integer, e.g. for y7 use "7" here)
modifications are returned in UniMod annotation.