Question: Can I Search Pride On Drugs?
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gravatar for Egon Willighagen
7.4 years ago by
Maastricht
Egon Willighagen5.2k wrote:

I tried searching paracetamol in PRIDE, to see the differential effect on the proteome when a cell or organism is dosed with a drug, but could not find anything. Browsing PRIDE shows that it has room for species, tissue, cell type, GO term, and disease, but not a word about small molecules, like drugs, hormones, or other chemical entities of biological interest...

Does PRIDE contain proteomics for drug/metabolite perturbation studies? And if so, how can I search based on a drug/metabolite name?

Update: OK, I am educated by @prideebi and @ChrisEvelo now: PRIDE is a protein/proteome database, more than a proteomics database... like the HMDB is a metabolome rather than a metabolomics database.

Update2: @pride_ebi further details that 'separation' dimensions and intensities are present, and suggest searching via PubMed abstracts for useful differential protein abundances, and use the PubMed ID to search PRIDE.

proteomics drug • 1.7k views
ADD COMMENTlink modified 3.6 years ago by Biostar ♦♦ 20 • written 7.4 years ago by Egon Willighagen5.2k
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Best Phrased Question of the Day

ADD REPLYlink written 7.4 years ago by Jeremy Leipzig18k
1

I believe Crick may have experimented with LSD to help come up with the structure of DNA, so maybe it will help you search PRIDE too.

ADD REPLYlink written 7.4 years ago by Torst900
3
gravatar for Chris Evelo
7.4 years ago by
Chris Evelo10.0k
Maastricht, The Netherlands
Chris Evelo10.0k wrote:

You might first want to check the answer to this question: http://biostar.stackexchange.com/questions/13048/what-are-the-proteomics-data-repositories

It indicates that pride is really just about protein identification. The terms you mention that are searchable in Pride are also useful for proteins themselves.

Now I am not sure what kind of perturbation you are looking for. If the protein itself changes, for instance by drug protein adduct formation you would in fact see that from the spectrum and the change might be relevant for the spectra stored in Pride. But... Most often the change will affect protein levels and as mentioned in that other question these are not stored in Pride.

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)

ADD COMMENTlink modified 7.4 years ago • written 7.4 years ago by Chris Evelo10.0k

Ah, OK. I had indeed not realize that PRIDE content was decoupled from whole-sample analysis... proteomics database vs protein database... thanx for the clarification!

ADD REPLYlink written 7.4 years ago by Egon Willighagen5.2k
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