⚖️ Best AI tools for Proteomics & metabolomics (2026)
Mass-spec proteomics and metabolomics: DIA search, spectrum and retention-time prediction, de novo peptide sequencing and metabolite annotation.
12 tools · 10 open source · each entry links to its website, code and paper.
Self-supervised transformer foundation model for tandem mass spectra of small molecules.
Transformer and diffusion models for de novo peptide sequencing from tandem mass spectra.
Feature-free DIA proteomics search engine with transfer learning from AlphaPeptDeep.
Transformer for de novo peptide sequencing directly from MS/MS spectra.
Deep learning framework predicting peptide MS2 spectra, retention time and CCS for proteomics.
Siamese neural network predicting structural similarity between MS/MS spectra for metabolomics.
Python library for importing, cleaning and comparing mass spectra for metabolomics.
Deep learning retention-time predictor that generalizes to unseen peptide modifications.
Metabolomics software for molecular formula and structure annotation from MS/MS with CSI:FingerID and CANOPUS.
Predicts peptide fragmentation spectra (and with DeepLC/IM2Deep) for spectral libraries and rescoring.
Neural-network-powered data-independent acquisition (DIA) proteomics processing software.
Open-source platform for LC-MS and imaging-MS data processing in metabolomics.