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