Proteomics Python Packages

pyopenms

The codebase of the OpenMS project

gget

🧬 gget enables efficient querying of genomic reference databases

openwraw

Pure-Rust reader for Waters MassLynx .raw mass-spectrometry directories, with Python bindings.

alphabase

Infrastructure of AlphaX ecosystem

nmdc-schema

National Microbiome Data Collaborative (NMDC) unified data model

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.

pypdb

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

sdrf-pipelines

SDRF official validator and converts SDRF to pipeline configuration files

deeplc

DeepLC: Retention time prediction for peptides carrying any modification.

directlfq

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

depthcharge-ms

A deep learning toolkit for mass spectrometry

lobster-ai

The self-evolving agentic framework for bioinformatics

pyxlms

A python package to process protein cross-linking data.

opentfraw

Pure-Rust reader for Thermo Fisher .raw mass-spectrometry files, with Python bindings.

pmultiqc

Python package for quality control of proteomics datasets, based on multiqc package

rustyms

A Rust library for peptide centric mass spec calculations centered around PSI standards and handling complex cases robustly

peptdeep

Deep learning framework for proteomics

mokapot

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

lobster-ai-tui

The self-evolving agentic framework for bioinformatics

opentimstdf

Pure-Rust reader for Bruker timsTOF .tdf / .tdf_bin files, with Python bindings.

pixelgen-pixelator

A command-line tool and library to process and analyze sequencing data from Molecular Pixelation (MPX) and Proximity Network (PNA) assays.

alphastats

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

alphadia

modular & open DIA search