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MetaProSIP OpenMS 2.8

Automated inference of stable isotope incorporation rates in proteins for functional metaproteomics

  • Author(s):
  • Matthias Bernt
  • Release: 0.2
  • License: MIT
  • UniqueID: b03da1a7-fc6f-419f-aa2c-431a670f9a96

MetaProSIP: automated inference of elemental fluxes in microbial communities

Inputs dataset

  • Centroided LC-MS datasets in mzML (MetaProSIP is mainly tested on data generated by orbitrap instruments)
  • Fasta Database in Fasta (aminoacid sequences)

Inputs values

  • Precursor monoisotopic mass tolerance (ppm): This value is passed to
    • MSGFPlusAdapter parameter Precursor monoisotopic mass tolerance (-precursor_mass_tolerance)
    • MetaProSIP parameter Tolerance in ppm (-mz_tolerance_ppm)
  • Fixed modifications
  • Variable modifications
  • Labeled element

Processing

  • DecoyDatabase: Add decoy sequences to the Fasta database (for FDR calculation)
  • FeatureFinderCentroided: identify eluting peptides that correspond to isotopologues with natural isotopic distributions
  • MSGFPlusAdapter: identify peptides through peptide fragment fingerprinting (database search)
  • FeatureFinderMultiplex: detect elution profiles of unlabeled peptides
  • PeptideIndexer: annotate protein association to identified peptides
  • FalseDiscoveryRate: Calculate FDR
  • IDMapper: map identified spectra to elution profiles
  • MetaProSIP: calculate the protein-SIP features, to perform functional grouping, and for protein inference