Mass Spectrometry Python Packages

pyopenms

The codebase of the OpenMS project

pymzml

pymzML - an interface between Python and mzML Mass spectrometry Files

matchms

Python library for processing (tandem) mass spectrometry data and for computing spectral similarities.

molmass

Molecular mass calculations.

openwraw

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

alphabase

Infrastructure of AlphaX ecosystem

brain-isotopic-distribution

A Python implementation of Baffling Recursive Algorithm for Isotopic distributioN calculations

psm-utils

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

pyms-nist-search

PyMassSpec extension for searching mass spectra using NIST's Mass Spectrum Search Engine.

spectrum-utils

Python package for efficient mass spectrometry data processing and visualization

alphatims

An open-source Python package for efficient accession and visualization of Bruker TimsTOF raw data from the Mann Labs at the Max Planck Institute of Biochemistry.

ms2pip

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

alpharaw

An open-source Python package to unify raw MS data accession and storage.

ms-deisotope

A library for deisotoping and charge state deconvolution of complex mass spectra

sdrf-pipelines

SDRF official validator and converts SDRF to pipeline configuration files

glypy

Glycan Analysis and Glycoinformatics Library for Python

depthcharge-ms

A deep learning toolkit for mass spectrometry

thyra

A modern Python library for converting Mass Spectrometry Imaging (MSI) data into standardized SpatialData/Zarr format, enabling seamless integration with spatial omics analysis workflows.

pyxlms

A python package to process protein cross-linking data.

riassigner

RIAssigner is a python tool for retention index (RI) computation for GC-MS data.

pymassspec

Python Toolkit for Mass Spectrometry

spec2vec

Word2Vec based similarity measure of mass spectrometry data.

maldiamrkit

Comprehensive toolkit for MALDI-TOF mass spectrometry data preprocessing for antimicrobial resistance (AMR) prediction purposes

opentfraw

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