msms

PDV: an integrative proteomics data viewer

metaX: a flexible and comprehensive software for processing omics data.

Convert mass spectrometry imaging data (Bruker, Waters, PHI, imzML), with ion mobility and MS/MS, into the open SpatialData/Zarr format

A Deep Learning Framework to Interpret Raw Mass Spectrometry (m/z) Data

DeepRescore: rescore PSMs leveraging deep learning-derived peptide features

Local-first MS/MS annotation against local spectral libraries: target-decoy FDR, provenance with every result. Python, CLI-first.

proteoQC: an R package for proteomics data quality assessment.

pClean: a tool for MS/MS spectrum preprocessing

Mobitel Sri Lanka's SMS Library for Laravel. PHP / JS / TS

A package for MSMS spectral library prediction models from the field of (phospho-)proteomics, intended to facilitate the testing and comparison of different neural network architectures and existing models.

An MCP server exposing mass spectrometry tools to AI clients. Spectra stay out of the context window via server-side references with provenance.

Calibrated trust and abstention for MS/MS molecular annotations

MSM tutorials modeled on the useful PyEmma tutorials but using the more up-to-date deeptime package

A tool to identify intra-protein crosslinks using non-canonical amino acids and mass spectroscopy

Request management system for analytical labs