Mass Spectrometry Python Packages

pyopenms

The codebase of the OpenMS project

96K 589 427

matchms

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

48K 256 78

molmass

Molecular mass calculations.

21K 66 13

pyms-nist-search

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

19K 22 6

ms2pip

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

10K 49 19

rustyms

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

9K 46 10

spectrum-utils

Python package for efficient mass spectrometry data processing and visualization

9K 168 33

alphabase

Infrastructure of AlphaX ecosystem

7K 55 13

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

ms-deisotope

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

7K 41 17

brain-isotopic-distribution

A Python implementation of Baffling Recursive Algorithm for Isotopic distributioN calculations

6K 23 12

psm-utils

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

6K 31 10

sdrf-pipelines

SDRF official validator and converts SDRF to pipeline configuration files

5K 32 29

pymassspec

Python Toolkit for Mass Spectrometry

4K 43 12

depthcharge-ms

A deep learning toolkit for mass spectrometry

4K 89 26

glypy

Glycan Analysis and Glycoinformatics Library for Python

4K 37 14

im2deep

Collisional cross-section prediction for modified and multiconformational peptides

3K 13 2

pmultiqc

A library for QC report based on MultiQC framework

3K 30 24

maldiamrkit

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

3K 3 1

pyopenms-viz

Streamlining Mass Spectrometry Data Visualization with Pandas

3K 23 20

alpharaw

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

3K 32 14

alphadia

modular & open DIA search

2K 108 11

alphastats

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

2K 87 17

quantms-utils

A python library with scripts and helpers classes for quantms workflow

2K 6 5