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mass-spectrometry

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OpenMS /OpenMS

The codebase of the OpenMS project

windows macos linux c-plus-plus algorithms proteomics metabolomics mass-spectrometry openms ms-data analyses hacktoberfest 3-clause-bsd

UpdatedMar 21, 2025
C++

sage

lazear /sage

Proteomics search & quantification so fast that it feels like magic

bioinformatics proteomics mass-spectrometry

UpdatedFeb 13, 2025
Rust

Nesvilab /FragPipe

A cross-platform proteomics data analysis suite

gui proteomics mass-spectrometry label-free-quantification command-line-interface isobaric-quantification data-independent-acquisition data-dependent-acquisition

UpdatedMar 21, 2025
Java

matchms /matchms

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

analysis fuzzy-search fuzzy-matching python3 similarity-measures metabolomics mass-spectrometry

UpdatedMar 20, 2025
Python

sneumann /xcms

This is the git repository matching the Bioconductor package xcms: LC/MS and GC/MS Data Analysis

r feature-detection bioconductor metabolomics mass-spectrometry peak-detection

UpdatedMar 14, 2025
R

MannLabs /alphapept

A modular, python-based framework for mass spectrometry. Powered by nbdev.

bioinformatics proteomics mass-spectrometry alphapept-ecosystem

UpdatedApr 19, 2024
HTML

pymzml /pymzML

pymzML - an interface between Python and mzML Mass spectrometry Files

bioinformatics mass-spectrometry mzml-files mzml-interface

UpdatedMar 18, 2025
Python

bittremieux-lab /spectrum_utils

Python package for efficient mass spectrometry data processing and visualization

mass-spectrometry

UpdatedMar 21, 2025
Python

lgatto /MSnbase

Base Classes and Functions for Mass Spectrometry and Proteomics

bioinformatics r visualisation bioconductor proteomics mass-spectrometry proteomics-data

UpdatedMar 17, 2025
R

philosopher

Nesvilab /philosopher

PeptideProphet, PTMProphet, ProteinProphet, iProphet, Abacus, and FDR filtering

go bioinformatics data-analysis proteomics mass-spectrometry ms-data

UpdatedMar 19, 2025
Go

Nesvilab /MSFragger

Ultrafast, comprehensive peptide identification for mass spectrometry–based proteomics

bioinformatics proteomics mass-spectrometry database-search

UpdatedJun 20, 2024
HTML

sirius-ms /sirius

SIRIUS is a software for discovering a landscape of de-novo identification of metabolites using tandem mass spectrometry. This repository contains the code of the SIRIUS Software (GUI and CLI)

java science bioinformatics cheminformatics molecular-structures sirius metabolomics mass-spectrometry ms-data denovo molecular-formulas ms-spectra structure-elucidation fragmentation-trees csi-fingerid fingerid isotope-pattern mass-spectra

UpdatedJan 22, 2025
Java

nh2tran /DeepNovo

Protein Identification with Deep Learning

machine-learning deep-learning tensorflow sequencing mass-spectrometry dynamic-programming peptide-identification

UpdatedNov 27, 2020
Python

lgatto /RforProteomics

Using R and Bioconductor packages for the analysis and comprehension of proteomics data.

tutorial r bioconductor proteomics mass-spectrometry bioconductor-packages proteomics-data

UpdatedMay 12, 2023
TeX

OpenChrom /openchrom

Visualization and Analysis of mass spectrometric and chromatographic data.

open-source nmr mass-spectrometry chromatography nmr-spectroscopy

UpdatedMar 21, 2025
Java

ElucidataInc /ElMaven

LC-MS data processing tool for large-scale metabolomics experiments.

c-plus-plus qt metabolomics mass-spectrometry lc-ms lc-msms

UpdatedJul 11, 2022
C++

MassBank /MassBank-data

Official repository of open data MassBank records

library repository mass-spectrometry massbank

UpdatedMar 3, 2025
Shell

MannLabs /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.

python cli gui dia dda mass-spectrometry ms ion-mobility tof max-planck-institute tims lc-tims-msms pasef

UpdatedMar 13, 2025
Python

MannLabs /alphamap

An open-source Python package for the visual annotation of proteomics data with sequence specific knowledge.

visualization python gui proteomics mass-spectrometry peptide-level

UpdatedMar 19, 2025
Jupyter Notebook

depthcharge

wfondrie /depthcharge

A deep learning toolkit for mass spectrometry

framework deep-learning pytorch proteomics metabolomics mass-spectrometry

UpdatedJul 24, 2024
Python

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