Proteomics

Proteomics refers to tools that investigate and analyze the whole of proteins occuring on differing scales (cell, tissue or organism).

This page will provide information about the tools used in proteomics. Feel free to add more tools, websites and tips if your are an expert on this topic!

Mass Spec

Mass spectrometry can be used to determine peptide sequences and as such to determine the protein composition of a mixture.

Tools

• http://www.expasy.ch/tools/#proteome: mass-spec data identification tools at expasy.

Protein databases

• UniProt database - the best annotated protein database in the world. The mission of UniProt is to provide the scientific community with a comprehensive, high-quality and freely accessible resource of protein sequence and functional information. A merge between trEMBL, PIR and SwissProt.
• Protein Research Foundation Sequence Database (PRF/SEQDB) - Database of protein sequences included and not-included in EMBL, GenBank and SwissProt since it is constructed from sequences reported in literature. 1/ Allows retrieving all articles in which your protein of interest appears. 2/ Very quick retrieval of exact motifs in protein sequences.
• DAD datebase - CDS from DDBJ, maintained at NIG/CIB (Mishima, Japan)

Protein structure visualisation tools

See Protein structure

Protein network

Databases of protein interaction

See Interaction databases

Protein meta-data

• Human Protein Atlas - Localize (tissue level) the expression of your gene based on antibody proteomics