Global Proteome Machine Database - constructed to utilize the information obtained by GPM servers to aid in the difficult process of validating peptide MS/MS spectra as well as protein coverage patterns
HIPD - Human Protein Interaction Database
HUPO - Human Proteome Organization
Human Interactome Map - a dynamic browser for the human protein-protein interaction map. HiMAP allows users to begin with a single protein or a set of proteins and explore both known and predicted protein-protein interactions.
Human Plasma Proteome - a comprehensive resource for all human plasma proteins along with their isoforms. The database includes information pertaining to isoform specific expression, disease, localization, post translational modification and single nucleotide polymorphism
Human Protein Reference Database - a centralized platform to visually depict and integrate information pertaining to domain architecture, post-translational modifications, interaction networks and disease association for each protein in the human proteome
INTEGRATOR - a collection of interactive, graphical search tools for exploring protein-protein interaction networks
IntNetDB - An integrated protein-protein interaction network database generated by a probabilistic model
Mouse Proteomics Database - combine subcellular fractionation with exhaustive tandem mass spectrometry-based shotgun sequencing to examine the protein content of four major organellar compartments (cytosol, membranes [microsomes], mitochondria and nuclei) in six organs (brain, heart, kidney, liver, lung and placenta) of the laboratory mouse, Mus musculus
Open Proteomics Database - a public database for storing and disseminating mass spectrometry based proteomics data. The database currently contains roughly 3,000,000 spectra representing experiments from 5 different organisms
OPHID - Online Predicted Human Interaction Database
Peptide Atlas - a multi-organism, publicly accessible compendium of peptides identified in a large set of tandem mass spectrometry proteomics experiments
PIANA - (Protein Interactions And Network Analysis) is a software framework that facilitates the work with protein interaction networks by 1) integrating data from multiple sources in a centralized database, 2) providing a library that handles all operations related with the network and 3) automating the analysis of protein-protein interactions networks
Point2006 - protein-protein interaction database system. You can input the NCBI gene name or gene id to query the interaction results of gene products.
PrenBase - a database of large-scale predictions of protein prenylation substrates ranked by evolutionary conservation of the motif
PRIDE - PRoteomics IDEntifications database is a centralized, standards compliant, public data repository for proteomics data
ProFunc - to help identify the likely biochemical function of a protein from its three-dimensional structure
Protein Atlas - isplays expression and localization of proteins in a large variety of normal human tissues and cancer cells
PROTEIOS - a comprehensive database server to manage the massive amounts of data generated by proteomics experiment and analysis
Proteome (Biobase) - compendium of proteome database
ProteomeCommons.org - An open-source framework for referencing common mass spectrometry data such as atoms and residues. This framework provides a programmer with an easy to use library for writing programs that rely on common mass spectrometry data
Proteomics.org - For resources and information on Proteomics and Mass spectrometry
Proteomics Database Portal - a centralized, web-based resource for tracking and managing the data generated by proteomics research projects
Proteomics Tutorials - Tutorials on Proteomics For Scientists
SHARP(2) - predicts the location of protein interaction sites on the surface of the 3D structure of a protein
UniHI (Unified Human Interactome) - a database that includes more than 150 000 distinct interactions between more than 17 000 unique human proteins
Unipep - a project to provide access to proteomics data from the Serum Biomarker group at the Institute for Systems Biology
UbiProt - a public resource offering comprehensive information on ubiquitylated proteins