Peptide Identification Python Packages

peptacular

Parse ProForma 2.1 peptide sequences and calculate masses, fragments, and isotopic distributions in Python.

ms2pip

MS²PIP: Fast and accurate peptide spectrum prediction for multiple fragmentation methods, instruments, and labeling techniques.

psm-utils

Common utilities for parsing and handling peptide-spectrum matches and search engine results in Python

ms2rescore

Modular and user-friendly platform for AI-assisted rescoring of peptide identifications

alphadia

modular & open DIA search

pepid

Highly customizable research-oriented peptide search engine