Mass Spectrometry Python Packages

pyopenms

The codebase of the OpenMS project

181K 593 429

matchms

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

54K 256 79

molmass

Molecular mass calculations.

22K 67 13

pyms-nist-search

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

10K 22 6

alphabase

Infrastructure of AlphaX ecosystem

9K 54 13

spectrum-utils

Python package for efficient mass spectrometry data processing and visualization

8K 169 33

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.

7K 95 29

brain-isotopic-distribution

A Python implementation of Baffling Recursive Algorithm for Isotopic distributioN calculations

6K 23 12

ms2pip

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

6K 49 19

rustyms

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

5K 47 10

depthcharge-ms

A deep learning toolkit for mass spectrometry

5K 90 26

pymassspec

Python Toolkit for Mass Spectrometry

5K 43 12

ms-deisotope

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

5K 41 17

psm-utils

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

4K 31 10

maldiamrkit

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

3K 3 1

sdrf-pipelines

SDRF official validator and converts SDRF to pipeline configuration files

3K 32 29

alpharaw

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

2K 32 14

alphastats

An open-source Python package for automated and scalable statistical analysis of mass spectrometry-based proteomics

2K 87 17

glypy

Glycan Analysis and Glycoinformatics Library for Python

2K 37 14

pyopenms-viz

Streamlining Mass Spectrometry Data Visualization with Pandas

2K 23 20

spec2vec

Word2Vec based similarity measure of mass spectrometry data.

2K 84 20

massivechem

MASSIVEChem is a pip-installable package centred around mass spectrometry

2K 15 1

alphadia

A novel proteomics search engine for DIA data based on end-to-end transfer learning.

2K 108 11

thyra

A modern Python library for converting Mass Spectrometry Imaging (MSI) data into SpatialData/Zarr format - your portal to spatial omics

2K 20 1