Converts different spectral libraries / transition files for targeted proteomics and metabolomics analysis.
Can convert multiple formats to and from TraML (standardized transition format). The following formats are supported:
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TraML
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OpenSWATH TSV transition lists
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OpenSWATH PQP SQLite files
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SpectraST MRM transition lists
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Skyline transition lists
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Spectronaut transition lists
Transition lists can be either comma- or tab-separated. Modifications should be provided in UniMod format1, but can also be provided in TPP format. The following columns are required:
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PrecursorMz* (float)
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ProductMz* (float; synonyms: FragmentMz)
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LibraryIntensity* (float; synonyms: RelativeFragmentIntensity)
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NormalizedRetentionTime* (float; synonyms: RetentionTime, Tr_recalibrated, iRT, RetentionTimeCalculatorScore) (normalized retention time)
For targeted proteomics files, the following additional columns should be provided:
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ProteinId** (free text; synonyms: ProteinName)
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PeptideSequence** (free text, sequence only (no modifications); synonyms: Sequence, StrippedSequence)
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ModifiedPeptideSequence** (free text, should contain modifications1; synonyms: FullUniModPeptideName, FullPeptideName, ModifiedSequence)
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PrecursorCharge** (integer, contains the charge of the precursorl synonyms: Charge)
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ProductCharge** (integer, contains the fragment charge; synonyms: FragmentCharge)
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FragmentType (free text, contains the type of the fragment, e.g. "b" or "y")
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FragmentSeriesNumber (integer, e.g. for y7 use "7" here; synonyms: FragmentNumber)
OpenSWATH uses grouped transitions to detect candidate analyte signals. These groups are by default generated based on the input, but can also be manually specified:
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TransitionGroupId (free text, designates the transition group [e.g. peptide] to which this transition belongs; synomys: TransitionGroupName, transition_group_id)
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TransitionId (free text, needs to be unique for each transition [in this file]; synonyms: TransitionName, transition_name)
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Decoy (1: decoy, 0: target, i.e. no decoy; determines whether the transition is a decoy transition or not, synomys: decoy, isDecoy)
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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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DetectingTransition (1: use transition to detect peak group, 0: don't use transition for detection; synonyms: detecting_transition)
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IdentifyingTransition (1: use transition for peptidoform inference using IPF, 0: don't use transition for identification; synonyms: identifying_transition)
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QuantifyingTransition (1: use transition to quantify peak group, 0: don't use transition for quantification; synonyms: quantifying_transition)
Optionally, the following columns can be specified but they are not actively used by OpenSWATH:
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CollisionEnergy (float; synonyms: CE)
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Annotation (free text, e.g. y7)
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UniprotId (free text; synonyms: UniprotID)
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LabelType (free text, optional description of which label was used, e.g. heavy or light)
For targeted metabolomics files, the following fields are also supported:
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CompoundName** (synonyms: CompoundId)
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SMILES
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SumFormula
Fields indicated with * are strictly required while fields indicated with ** are only required in the specific context (proteomics or metabolomics).
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: