JPOST (Japan Proteome Standard Repository Database)
jPOSTrepo (Japan ProteOme STandard Repository) is a new data repository of sharing MS raw/processed data.
Proteopedia helps to bridge the gap between 3D structure & function of biomacromolecules.
RCSB Protein Data Bank (PDB). See also the RCSB PDB-101 training materials.
STRING provides Protein-Protein Interaction Networks Functional Enrichment Analysis
UCSD: Center for Computational Mass Spectrometry: Proteomics: MassIVE (Mass Spectrometry Interactive Virtual Environment)
UCSD: Center for Computational Mass Spectrometry: Proteomics: ProteoSAFe
UCSD: Center for Computational Mass Spectrometry: Proteomics: Submitted MassIVE Datasets
UM: HPSF (Human Proteome Structure and Function) database
Uniprot: Proteomes and Reference Proteomes
CHO Proteome Database hosts proteomic data generated from CHO cell lines.
Human Liver Proteome Database (HLPD)
Human Plasma Proteome Project (HPPP)
Human Protein Atlas, The open access resource for human proteins
Human Salivary Proteome Wiki is a collaborative, community-based portal to more than 1,000 unique human saliva proteins identified by high-throughput proteomic technologies.
Human Skin Atlas is a research initiative aiming to advance translational skin research by providing a resource with mass spectrometry-based proteome data from healthy and diseased skin.
LIPID MAPS® Proteome Database (LMPD) of lipid-related genes and proteins contains data for over 8,500 genes and over 12,500 proteins from Homo sapiens, Mus musculus, Rattus norvegicus, Saccharomyces cerevisiae, Caenorhabditis elegans, Escherichia coli, Macaca mulata, Drosophila melanogaster, Arabidopsis thaliana and Danio rerio.
MitoProteome Human Mitochondrial Protein Database is an object-relational mitochondrial gene/protein sequence database and annotation system.
Office of Cancer Clinical Proteomics Research (OCCPR) Data Portal includes Proteomic Data Commons (PDC) represents the NCI's largest public repository of proteogenomic comprehensive tumor datasets, essentially a Proteogenomic Cancer Atlas.
Plant Proteome Database for Arabidopsis thaliana and maize (Zea mays). See also The Arabidopsis Information Resource (TAIR) data repositories and protein location databases lists.
PlantPReS Database for plant proteome response to stress
Plasma Proteome Database (PPD) is one of the largest resources on proteins reported in plasma and serum.
Saliva Proteome Database is a public data portal for searching and retrieving custom-curated information about the proteome of human saliva.
PASSEL (PeptideAtlas SRM Experiment Library)
Pep2Pro (complete peptide dictionary)
PRIDE PRoteomics IDEntifications (PRIDE)
TopFIND, The public knowledgebase for protein termini and protease processing
EXAMPLES
CRAPome (UofM)
DIA-Umpire (UofM)
MAP-DIA (UofM)
MSFragger (UofM)
REPRINT (Resource for Evaluation of Protein Interaction Networks)
SuperPose was a protein superposition server. Superpose calculates protein superpositions using a modified quaternion approach.
Trans-Proteomic Pipeline (TPP)
COLLECTIONS
Alexey Nesvizhskii Lab: Software (UofM)
Bioinformatics tools for proteomics
Minnesota Supercomputing Institute: Proteomics software available in the public domain
Wikipedia: List of mass-spectrometry software: Proteomics software
ABOUT
Välikangas T, Suomi T, Elo LL. A comprehensive evaluation of popular proteomics software workflows for label-free proteome quantification and imputation. Briefings in Bioinformatics, bbx054, https://doi.org/10.1093/bib/bbx054