The Global Proteome Machine Organization was set up so that scientists involved in proteomics using tandem mass spectrometry could use that data to analyze proteomes. The projects supported by the GPMO have been selected to improve the quality of analysis, make the results portable and to provide a common platform for testing and validating proteomics results.

Additions to GPMDB interface (2008/05/09)

Several new ways of accessing information in the GPMDB have been added.

Normal Clinical Tissue Alliance site opens (2008/03/24)

The Normal Clinical Tissue Alliance was formed to provide information about the proteins that can be observed in clinically derived tissues. Lists of proteins for each of the tissue types can be obtained and manipulated. The tissues are "normal" (non-diseased) and the lists represent composites of proteins obtained from multiple studies. The protein lists are dependent on the availability of proteomics data: the lists are compiled directly from MS/MS identification data, which is also made available through the site.

Change to protein coverage display (2008/03/23)

The protein sequence coverage displays have conventionally showed the regions of a protein that have been observed in red. The displays have been updated to show the regions of a protein that are predicted to be difficult to observe (using MS/MS-based proteomics) in green.

Species added to GPM servers (2008/03/12)

Twenty-two new eukaryote species have been added to the GPM Tornado cloud server system. These species include 14 new fungi, 2 insects and 6 protists. A list of these new species is as follows:

1. Aspergillus nidulans FGSC A4
2. Candida albicans
3. Candida glabrata CBS138
4. Cryptococcus neoformans var JEC21
5. Debaryomyces hansenii CBS767
6. Encephalitozoon cuniculi
7. Eremothecium gossypii
8. Gibberella zeae
9. Kluyveromyces lactis NRRL Y-1140
10. Magnaporthe grisea 70-15
11. Pichia stipitis
12. Ustilago maydis
13. Yarrowia lipolytica
14. Yarrowia lipolytica CLIB122
15. Nasonia vitripennis
16. Tribolium castaneum
17. Cryptosporidium parvum
18. Dictyostelium discoideum
19. Leishmania infantum
20. Plasmodium falciparum
21. Theileria parva
22. Trypanosoma brucei

These new proteomes were all obtained from NCBI.

GPM changes to a peer-to-peer grid computing system (2008/02/25)

Starting on Feb. 23, 2008, a peer-to-peer grid computing system (called Tornado) is being rolled out for the GPM search servers. When a search is submitted to any of the genome, human, mouse or rat search pages, the system will determine which server on the grid is the fastest and least busy and send your search to that computer. This system has the effect of increasing the effective capacity of the existing system by approximately 10-fold.

Note: In order to use this system, the search form must say "GPM Tornado" at the top of the page. If it does not say Tornado, please press the reload button on your browser to get the most recent version of the search form.

KEGG pathways analysis added (2008/01/24)

A new display using the Kyoto Encyclopedia of Genes and Genomes (KEGG) metabolic pathways database is now available for all data sets that have used the ENSEMBL proteomes for human, mouse, rat or yeast. The new display categorizes the identified proteins by metabolic pathway, with about 190 pathways available for human proteins. The pathways are linked through to their KEGG cartoon representations.

Annotated modifications added (2008/01/20)

Starting with the 2008.02.01 release of X! Tandem, the search engine will now have the capacity to set the potential modifications being tested on a protein by protein basis. This new feature can be activated in either the first round of searching or the subsequence refinement rounds by setting the "Use sequence annotations" control to be "yes".

The way that this new feature works is quite simple. A file is constructed that contains a list of sequence accession numbers and potential sequence modification specifications, e.g. several lines from the human modification file look like the following:

<protein label="ENSP00000166244" pmods="79.966331@Y" />
<protein label="ENSP00000350614" pmods="79.966331@S" />
<protein label="ENSP00000372956" pmods="79.966331@S,79.966331@T" />
<protein label="ENSP00000372947" pmods="79.966331@S,79.966331@T" />
<protein label="ENSP00000363773" pmods="15.994915@P" />

The first line indicates that the protein sequence ENSP00000166244 is known to be tyrosine phosphorylated. If the "Use sequence annotations" feature is turned on, then that sequence will be tested for tyrosine phosphorylation, in addition to the other potential modifications you have specified for your search to be applied to all protein sequences. Similarly ENSP00000350614 will be checked for serine phosphorylation, ENSP00000372956 and ENSP00000372956 will be checked for phosphorylation at serine and threonine residues, while ENSP00000363773 will be tested for the possible presence of hydroxyproline residues.

Files of this type have been constructed for human, mouse, rat, chicken and brewer's yeast proteomes, using publically available annotation sources such as Uniprot and GPMDB. This capability is now available on all of the public GPM search servers. The annotation files are available here.

GPM system updates (2008/01/06)

Over the Holidays, several system changes have been made to the GPM system and interface pages. While most of these changes are minor, they do change some default behaviors.

1. The "peptide clustering" control on the protein page has been changed to be consistent with the similar control on the "peptide" page. For both pages, the default setting is now "all", meaning that all identified spectra will be represented on the page. This change was made at the suggestion of a number of users, because of some confusion caused by having only the "best" identification for each peptide sequence shown as the default.
2. More information about the distribution of proteins amongst Gene Ontology categories has been added to the "GO" display, including p-values for enrichment or depletion each category.
3. Shading and other small formatting and navigations changes have been made to make the interface as consistent as possible.