bio-proteomics-peptide-identification

Database Search with pyOpenMS

Goal: Identify peptide sequences from tandem mass spectra by matching against a protein database.

Approach: Load a FASTA database, perform in-silico tryptic digestion to generate theoretical peptides, then match experimental spectra against theoretical fragment ion patterns to identify peptide-spectrum matches (PSMs).

from pyopenms import MSExperiment, MzMLFile, FASTAFile, ProteaseDigestion
from pyopenms import ModificationsDB, AASequence

## In-silico digestion

digestion = ProteaseDigestion()
digestion.setEnzyme('Trypsin')
digestion.setMissedCleavages(2)

peptides = []
for entry in fasta_entries:
    seq = AASequence.fromString(entry.sequence)
    result = []
    digestion.digest(seq, result)
    peptides.extend([(entry.identifier, str(p)) for p in result])

Read mzIdentML results

psms <- readMzIdData('results.mzid')