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.

opentfraw

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

alphabase

Infrastructure of AlphaX ecosystem

nmdc-schema

National Microbiome Data Collaborative (NMDC) unified data model

sdrf-pipelines

SDRF official validator and converts SDRF to pipeline configuration files

peptacular

Parse ProForma 2.1 peptide sequences and calculate masses, fragments, and isotopic distributions in Python.

tacular

Python lookups for amino acids, elements, and proteomics PTM ontologies (UNIMOD, PSI-MOD, RESID, XLMOD, GNOme)

protspace

Explore protein language model embeddings in your browser — surface relationships sequence similarity misses, overlay annotations, and transfer labels (EAT). Nothing uploaded.

ms2pip

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

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

protlabel

Explore protein language model embeddings in your browser — surface relationships sequence similarity misses, overlay annotations, and transfer labels (EAT). Nothing uploaded.

tdfpy

Python reader for Bruker timsTOF (.d) data: DDA/DIA/PRM, fast centroiding and noise filtering

mzmlpy

Fast, lazy mzML reader for Python: typed models, gzip random access, validation, Numpress/zstd decoding

depthcharge-ms

A deep learning toolkit for mass spectrometry

directlfq

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

paftacular

Parse and serialize HUPO-PSI mzPAF fragment-ion annotations for mass-spectrometry proteomics in Python.

psimodpy

Python library, API, and MCP server for the PSI-MOD protein modification ontology

unimodpy

Python library, API, and MCP server for the UNIMOD mass spectrometry modifications database

mzlib

mzLib for Python - mass spectrometry and proteomics from the mzLib C# library, with no .NET to install

pefftacular

Python library for reading and writing PEFF (PSI Extended FASTA Format) files. PEFF is a superset of FASTA used in proteomics that carries rich per-entry annotations.

fastatacular

Pure-Python library for reading and writing FASTA sequence files with UniProt-style header parsing.