Proteomics Python Packages

pyopenms

The codebase of the OpenMS project

gget

🧬 gget enables efficient querying of genomic reference databases

ms2pip

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

rustyms

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

nmdc-schema

National Microbiome Data Collaborative (NMDC) unified data model

alphabase

Infrastructure of AlphaX ecosystem

deeplc

DeepLC: Retention time prediction for peptides carrying any modification.

psm-utils

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

lobster-ai

The self-evolving agentic framework for bioinformatics

pypdb

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

sdrf-pipelines

SDRF official validator and converts SDRF to pipeline configuration files

lobster-ai-tui

The self-evolving agentic framework for bioinformatics

depthcharge-ms

A deep learning toolkit for mass spectrometry

im2deep

Collisional cross-section prediction for modified and multiconformational peptides

pmultiqc

A library for QC report based on MultiQC framework

directlfq

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

peptdeep

Deep learning framework for proteomics

mopepgen

Multi-Omics Peptide Generator

alphadia

modular & open DIA search

ms2rescore

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

alphastats

Python Package for the downstream analysis of mass-spectrometry-based proteomics data

quantms-utils

A python library with scripts and helpers classes for quantms workflow

alphapept

A modular, python-based framework for mass spectrometry. Powered by nbdev.

pridepy

Python client for PRIDE Archive Rest API.