What Are The Proteomics Data Repositories?

Question

[Larry_Parnell]

I'm updating 2-year old slides for a course that will introduce genomics and computational analysis to graduate students in nutrition. I have a segment on proteomics that begins with data repositories and that, at the moment, is limited to PRIDE at the EBI.

How useful is PRIDE? What other proteomics data sites should I include?

Thanks for your help!

Answer 1

[Julian]

Another one to consider is GPMDB. Data is submitted by running a public X!Tandem against the GPM database and selecting to add the data to the GPM. The GPM is split into species based sections (e.g., searching Human: http://human.thegpm.org/tandem/thegpm_tandem.html).

The Peptide Atlas repository exits. It has several spin-offs including information relating specifically to phospho-peptides, SRM's, etc. You can browse through the repository at http://www.peptideatlas.org/repository/.

However, I still use PRIDE, and encourage the students and people I work with to use it. It encourages a high degree of annotation or metadata to the mass spectrometry data. The team involved in maintaining PRIDE are also actively involved in the various proteomics standards efforts (PSI-MS), and these standards are being adopted in PRIDE. It does a number of other things such as trying to reconcile protein annotation from different databases (PICR). It also provides tools to easily assemble a new entry (PRIDE Converter) from raw spectra and identifications, and there is great support to placing data into the repository.

You might also find this review article by Conrad Bessant's group useful (although it was written a couple of years ago): **Recent developments in public proteomic MS repositories and pipelines**, J. Mead, L. Bianco, C. Bessant, Proteomics, 2009, 9 (4), 861-881.

[Laurent]

You beat me by a couple of second! Great answer, by the way.

Answer 2

[Laurent]

PRIDE (PRoteomics IDEntifications database), as it's name suggests, is currently focused on identification data. It's main advantage are structured data and meta data, powerful query capabilities and, recently, nice visualisation functionality through PRIDE Inspector. It is also worth noting that they also allow private submissions that are accessible to reviewers and authors only prior to paper/data publication. Since NCBI's Peptidome has been discontinued, PRIDE is, AKAIK, the main generalist structured data repository.

Tranche is very different. It's main goal is the unstructured cloud storage or raw/binary data.

Another big player is PeptideAtlas, from ISB's Proteome Center. They reprocess data sets with their pipeline and then make this processed data available to the community.

Another significant player is the GPMDB. There are many other specialised data bases out. This review from 2009 by Mead, Bianco and Bessant might be a good read.

Finally, these data bases do not work in glorious isolation. They do interact quite a lot, as illustrated by the ProteomExchange consortium, that will provide a single point of submission to proteomics repositories.

Update: you did not specify whether you were interested in MS repositories only. Protein Atlas, for instance, provides protein expression profiles based on immunohistochemistry and sub-cellular localisation data.

[Larry_Parnell]

Also some very useful info. Thank you, Laurent.

Answer 3

[Chris Evelo]

We recently had a look at PRIDE and found that it is more about identification of mass patterns than about final protein content results. In our experience it was thus not very useful as a real proteomics repository, although probably very useful for analysts thrying to make sense of MS spectra.

Edit

There were a number of updates from people on Twitter that knew about the most recent developments at Pride. It turns out that Pride now actually does store protein concentration information, at least for a number of studies.

PRIDE is also storing protein expression information now. http://www.ebi.ac.uk/pride/q.do?accession=16649 (use PRIDE Inspector). You can also check out 16649 - 16656. (@pride_ebi and @juan_vizcaino)

[Attila Csordas]

could you provide an (MS-based) example for "final protein content results"?

[Chris Evelo]

The edit should help and we published an example here: J Renes, J van Tilburg, R van Haaften, F Bouwman, A Kodde, C Evelo, J P Noben, J Robben, E Mariman (2006) Thiazolidinediones regulate expression of proteins involved in triglyceride storage and fatty acid oxidation in 3T3-L1 pre-adiopocytes. Adipocytes 2: 75-92. Available from here: http://bit.ly/t2LWpm

Answer 4

[Mary]

You might be interested on an ENCODE track in the UCSC Genome Browser that is proteogenomics:

http://genome.ucsc.edu/cgi-bin/hgTrackUi?hgsid=217204403&c=chr21&g=wgEncodeProtGenoSuper

and read this too:

http://genome.ucsc.edu/cgi-bin/hgTrackUi?hgsid=217204403&c=chr21&g=wgEncodeUncBsuProt

[Larry_Parnell]

Thanks, Mary. The tracks in UCSC are indeed useful.

Answer 5

[Simon Cockell]

You should also consider Tranche from Proteome Commons. It is a distributed file store, designed as a repository for large amounts of proteomics data. It is less structured than PRIDE, but I believe much easier for data deposition.

Answer 6

[Jax Adams]

You can also consider proteomicist.org.

[Larry_Parnell]

Thank you. Loading 60+ recent PubMed entries (abstracts) on the homepage, though, was not so neat. Nonetheless, I will give this a try later.

Answer 7

[enunvillafer]

Hi, I recommend PeptideAtlas database as well. You can also keep the track of the C-HPP (chromosome-centric human proteome project) at http://www.c-hpp.org/, http://www.peptideatlas.org/hupo/c-hpp/.

Cheers!