Peptide Identification Python Packages

psm-utils

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

ms2pip

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

alphadia

modular & open DIA search

ms2rescore

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

peptacular

A Python package for peptide sequence analysis built around ProForma 2.1 notation. Calculate masses, generate fragments, predict isotopic patterns, and more.

pepid

Highly customizable research-oriented peptide search engine