Generic Transition Lists

Overview

OpenSWATH [1] supports generic transition lists in tab- or comma-separated value (TSV/CSV) formats. TargetedFileConverter is part of OpenMS [2] and is available for Windows, macOS and Linux.

Transitions lists from Trans-Proteomic Pipeline and Skyline can be directly converted. Alternatively, it is possible to use the generic transition list format, described below.

Contact and Support

We provide support for TargetedFileConverter using the OpenMS support channels. Please address general questions to the open-ms-general mailing list.

Format

The input to TargetedFileConverter can come either directly from Trans-Proteomic Pipeline or Skyline or the generic transition list format. The columns should be separated either by comma or tab and the files should be saved with Windows or Unix line endings.

Required Columns

The following columns are required:

  • PrecursorMz * (float)
  • ProductMz * (float; synonyms: FragmentMz)
  • LibraryIntensity * (float; synonyms: RelativeFragmentIntensity)
  • NormalizedRetentionTime * (float; synonyms: RetentionTime, Tr_recalibrated, iRT, RetentionTimeCalculatorScore) (normalized retention time)

Targeted Proteomics Columns

For targeted proteomics, the following additional columns should be provided:

  • ProteinId ** (free text; synonyms: ProteinName)
  • PeptideSequence ** (free text, sequence only (no modifications); synonyms: Sequence, StrippedSequence)
  • ModifiedPeptideSequence ** (free text, should contain modifications; synonyms: FullUniModPeptideName, FullPeptideName, ModifiedSequence)
  • PrecursorCharge ** (integer, contains the charge of the precursorl synonyms: Charge)
  • ProductCharge ** (integer, contains the fragment charge; synonyms: FragmentCharge)
  • FragmentType (free text, contains the type of the fragment, e.g. “b” or “y”)
  • FragmentSeriesNumber (integer, e.g. for y7 use “7” here; synonyms: FragmentNumber)

Warning

ModifiedPeptideSequence should contain modifications in UniMod (preferred) (.(UniMod:1)PEPC(UniMod:4)PEPM(UniMod:35)PEPR.(UniMod:2)) or TPP (n[43]PEPC[160]PEPM[147]PEPRc[16]) formats. N- and C-terminal modifications are indicated after a pre- or suffix ..

Targeted Metabolomics Columns

For targeted metabolomics, the following fields are also supported:

  • CompoundName ** (synonyms: CompoundId)
  • SMILES
  • SumFormula

Grouping Columns

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:

  • TransitionGroupId (free text, designates the transition group [e.g. peptide] to which this transition belongs; synomys: TransitionGroupName, transition_group_id)
  • TransitionId (free text, needs to be unique for each transition [in this file]; synonyms: TransitionName, transition_name)
  • Decoy (1: decoy, 0: target, i.e. no decoy; determines whether the transition is a decoy transition or not, synomys: decoy, isDecoy)
  • PeptideGroupLabel (free text, designates to which peptide label group (as defined in MS:1000893) the peptide belongs to<sup>2</sup>)
  • DetectingTransition (1: use transition to detect peak group, 0: don’t use transition for detection; synonyms: detecting_transition)
  • IdentifyingTransition (1: use transition for peptidoform inference using IPF, 0: don’t use transition for identification; synonyms: identifying_transition)
  • QuantifyingTransition (1: use transition to quantify peak group, 0: don’t use transition for quantification; synonyms: quantifying_transition)

Warning

If you are unsure about these columns, TargetedFileConverter and the downstream tools OpenSwathAssayGenerator and OpenSwathDecoyGenerator will generate them automatically for you.

Optional Columns

Optionally, the following columns can be specified but they are not actively used by OpenSWATH:

  • CollisionEnergy (float; synonyms: CE)
  • Annotation (free text, e.g. y7)
  • UniprotId (free text; synonyms: UniprotID)
  • LabelType (free text, optional description of which label was used, e.g. heavy or light)

Fields indicated with * are strictly required while fields indicated with ** are only required in the specific context (proteomics or metabolomics).

Conversion

Once the generic transition list is generated by the user (or TPP or Skyline), peptide query parameters can be derived by the OpenSWATH tools part of OpenMS. Please follow the instructions on how to install OpenSWATH prior to the next steps.

# Import from SpectraST MRM
TargetedFileConverter -in transitionlist.mrm -out transitionlist.TraML

# Import from Skyline or generic transition list format (TSV)
TargetedFileConverter -in transitionlist.tsv -out transitionlist.TraML

# Import from Skyline or generic transition list format (CSV)
TargetedFileConverter -in transitionlist.csv -out transitionlist.TraML

References

[1]Röst HL, Rosenberger G, Navarro P, Gillet L, Miladinović SM, Schubert OT, Wolski W, Collins BC, Malmström J, Malmström L, Aebersold R. OpenSWATH enables automated, targeted analysis of data-independent acquisition MS data. Nat Biotechnol. 2014 Mar 10;32(3):219-23. doi: 10.1038/nbt.2841. PMID: 24727770
[2]Röst HL, Sachsenberg T, Aiche S, Bielow C, Weisser H, Aicheler F, Andreotti S, Ehrlich HC, Gutenbrunner P, Kenar E, Liang X, Nahnsen S, Nilse L, Pfeuffer J, Rosenberger G, Rurik M, Schmitt U, Veit J, Walzer M, Wojnar D, Wolski WE, Schilling O, Choudhary JS, Malmström L, Aebersold R, Reinert K, Kohlbacher O. OpenMS: a flexible open-source software platform for mass spectrometry data analysis. Nat Methods. 2016 Aug 30;13(9):741-8. doi: 10.1038/nmeth.3959. PMID: 27575624