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.

opentfraw

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

alphabase

Infrastructure of AlphaX ecosystem

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

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.

glypy

Glycan Analysis and Glycoinformatics Library for Python

brain-isotopic-distribution

A Python implementation of Baffling Recursive Algorithm for Isotopic distributioN calculations

candycrunch

Predicting glycan structure from LC-MS/MS data

alpharaw

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

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)

ms2pip

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

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.

psm-utils

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

msbuddy

a python package for molecular formula analysis in MS-based small molecule studies

ms-deisotope

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

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