There are many free web resources available to analyze proteomic data.
Here are a few:
http://www.uniprot.org/
- Accession names of proteins identified in proteomic data (gene names are not usually used)
- Proteomes available for searching
- GO annotation of each protein
- PTM/processing
- Expression, inteaction, structure
https://david.ncifcrf.gov/
- Identify enriched biological themes, particularly GO terms
- Identify pathways linked to your protein list (KEGG and Biocarta)
- Multiple species, not just eukaryotes
- More...
fmol of proteins identified in the endocytic pathway from 200ng HeLa cell lysate mapped unto KEGG pathway
http://www.phosphosite.org/homeAction.action
- Resource for the study of post-translational modifications
- Phosphorylation, ubiquitination, acetylation and methylation
- Links to cell signaling antibodies available for specific PTM studied
- Gives overview of the protein (MW, function, gene name, associated disease...)
- Gives crystal structure if available
http://string-db.org/
- Protein-Protein interactions network
- Multiple species, not just eukaryotes
- GO analysis of proteins in network
String analysis of all 1833 proteins identified in a 200ng HeLa lysate. High Stringency
http://www.reactome.org/
- Reactome is a curated database of pathways and reactions (pathway steps) in human biology
- Extensively cross-referenced to other resources e.g. NCBI, Ensembl, UniProt, UCSC Genome Browser, HapMap, KEGG (Gene and Compound), ChEBI, PubMed and GO
- Inferred orthologous reactions are available for over 20 non-human species including mouse, rat, chicken, puffer fish, worm, fly, yeast, rice, Arabidopsis and E.coli
Reactome analysis of all 1833 proteins identified in a 200ng HeLa lysate. Overrepresentation of pathways is shown in yellow