Peptide Identification Python Packages

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

alphadia

A novel proteomics search engine for DIA data based on end-to-end transfer learning.

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

Pepid: a Highly Modifiable, Bioinformatics-Oriented Peptide Search Engine