Proteomics Python Packages

pyopenms

The codebase of the OpenMS project

gget

🧬 gget enables efficient querying of genomic reference databases

alphabase

Infrastructure of AlphaX ecosystem

ms2pip

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

nmdc-schema

National Microbiome Data Collaborative (NMDC) unified data model

rustyms

A library to handle proteomic mass spectrometry data and match peptides to spectra.

depthcharge-ms

A deep learning toolkit for mass spectrometry

pypdb

A Python API for the RCSB Protein Data Bank (PDB)

deeplc

DeepLC: Retention time prediction for (modified) peptides using Deep Learning.

lobster-ai

The self-evolving agentic framework for bioinformatics

lobster-ai-tui

The self-evolving agentic framework for bioinformatics

psm-utils

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

mopepgen

Multi-Omics Peptide Generator

sdrf-pipelines

SDRF official validator and converts SDRF to pipeline configuration files

alphastats

An open-source Python package for automated and scalable statistical analysis of mass spectrometry-based proteomics

directlfq

Fast and accurate label-free quantification for small and very large numbers of proteomes

peptdeep

Deep learning framework for proteomics

pridepy

Python Client library for PRIDE Rest API

mokapot

Fast and flexible semi-supervised learning for peptide detection in Python

alphadia

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

pyxlms

A python package to process protein cross-linking data.

im2deep

Collisional cross-section prediction for modified and multiconformational peptides

ms2rescore

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

spectrum-fundamentals

Fundamental functions, annotation pipeline and constants for oktoberfest