Centroided LC-MS datasets
in mzML (MetaProSIP is mainly tested on data generated by orbitrap instruments)Fasta Database
in Fasta (aminoacid sequences)
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)
- MSGFPlusAdapter parameter
- Fixed modifications
- Variable modifications
- Labeled element
- 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