ProteomicsSURF is a site dedicated to disease proteomics which aims to identify proteins involved in human disease and to understand how their expression, structure and function cause illness.

Multi-Q provides an automated data analysis tool for multiplexed protein quantitation based on iTRAQ labeling.

The Global Proteome Machine (GPM) project facilitates the analysis of proteomes for researchers using tandem mass spectrometry. The aims of the project include providing a common validation and testing platform for results, making the results more portable, and improving the quality of the analysis. The GPM uses the X! TANDEM Spectrum Modeler to match peptide sequences to tandem mass spectra. Both the GPM interface and X! TANDEM are open-source.

sgTarget is a structural genomics resource that helps to select and prioritize good targets for structure determination from a list of sequences. Target selection is based on multiple factors including homology searches and a range of physiochemical properties.

Software tools and integrated databases to facilitate analyzing the output from protein mass spectrometry experiments.

Proteome Analyst is a high-throughput tool for predicting properties for each protein in a proteome. The user provides a proteome in fasta format, and the system employs Psi-blast, Psipred and Modeller to predict protein function and subcellular localization. Proteome Analyst uses machine-learned classifiers to predict things such as GO molecular function. User-supplied training data can also be used to create custom classifiers.

The Proteome Analysis Database at EBI provides statistical and comparative analyses of the predicted proteomes of organisms for which there are fully-sequenced genomes.

Proteios is an initiative to create an open-source storage, analysis and organization system for proteomics experiments.

Various tools used for sequence database mining in connection with mass spectrometry experiments.

PeptIdent is a tool that allows the identification of proteins using pI, Mw and peptide mass fingerprinting data.