Search Packages

pyopenms

The codebase of the OpenMS project

matchms

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

molmass

Molecular mass calculations.

pyms-nist-search

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

ms2pip

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

rustyms

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

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.

ms-deisotope

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

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

sdrf-pipelines

SDRF official validator and converts SDRF to pipeline configuration files

pymassspec

Python Toolkit for Mass Spectrometry

glypy

Glycan Analysis and Glycoinformatics Library for Python

maldiamrkit

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

depthcharge-ms

A deep learning toolkit for mass spectrometry

im2deep

Collisional cross-section prediction for modified and multiconformational peptides

pmultiqc

A library for QC report based on MultiQC framework

pyopenms-viz

Streamlining Mass Spectrometry Data Visualization with Pandas

alpharaw

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

alphadia

modular & open DIA search

alphastats

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

pridepy

Python client for PRIDE Archive Rest API.