Proteomics Mass Spectrometry Datasets for Machine Learning
PSI-MOD ontology for modified and unmodified amino acid residues
An ensemble-based approach for prediction of protein S-nitrosylation sites integrating supervised word embedding and embedding from protein language model
Code to generate the PTMTorrent dataset
Pipeline for analysing and visualising CyTOF datasets, with a focus on PTM signalling networks.
PTM-X: a prediction tool for Post-Translational Modification cross-talk
Lightweight polynomial texture map viewer based on PySide2 and OpenGL
Summarize post-translationally modified amino acid sites, peptides and proteins for Proteome Discoverer output
Python library, API, and MCP server for the UNIMOD mass spectrometry modifications database
Python lookups for amino acids, elements, and proteomics PTM ontologies (UNIMOD, PSI-MOD, RESID, XLMOD, GNOme)
Python library for reading and writing PEFF (PSI Extended FASTA Format) files. PEFF is a superset of FASTA used in proteomics that carries rich per-entry annotations.
Python library, API, and MCP server for the PSI-MOD protein modification ontology
Python library, API, and MCP server for the UniProt PTM controlled vocabulary
Reproducible PTM 45 nm HP/LP NMOS analysis using ngspice and Python
Proteoform- and PTM-level reanalysis of public aging proteomics data: PRIDE discovery, download, spectra QC, MetaMorpheus search + FlashLFQ, with a provenance record on every output.
Generate annotated PEFF files from UniProt accessions, taxonomy IDs, or search queries, using pefftacular.
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