Converts different transition files for targeted proteomics and metabolomics analysis.
Can convert multiple formats to and from TraML (standardized transition format). It supports the OpenSWATH TSV format as well as the PQP format for transitions.
The OpenSWATH transition TSV files need to have the following headers, all fields need to be 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 modifications1)
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PrecursorCharge (integer, contains the charge of the precursor)
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PeptideGroupLabel (free text, designates to which peptide label group (as defined in MS:1000893) the peptide belongs to2)
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LabelType (free text, optional description of which label was used, 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)
Remarks:
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1. modifications should be supplied inside the sequence using UniMod identifiers or freetext identifiers that are understood by OpenMS.
example: PEPT(Phosphorylation)IDE(UniMod:27)A )
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2. peptide label groups designate groups of peptides that are isotopically modified forms of the same peptide species. For example, the heavy and light forms of the same peptide will both be assigned the same peptide group label.
example:
PEPTIDEAK -> gets label "PEPTIDEAK_gr1"
PEPTIDEAK[+8] -> gets label "PEPTIDEAK_gr1"
PEPT(Phosphorylation)IDEAK -> gets label "PEPTIDEAK_gr2"
PEPT(Phosphorylation)IDEAK[+8] -> gets label "PEPTIDEAK_gr2"
The command line parameters of this tool are:
INI file documentation of this tool: