A lot of these tools have been out for a while (programs out in advance of this great recent paper)....
...but this is a great compendium of the tools that are available and the super simple command that you can use through the REST interface (what's a REST? here ya go) to pull up proteomics data from anywhere and basically anything!
Proteomic informatics is getting better every day, and we might be leading the way for -omics when it comes to data sharing and transparency (having significantly smaller files might be helpful in this regard, but still)!
There is so much power here that you're basically only limited by your own imagination. Need a good example?
What if you were really interested in 2 proteins and wanted good experimental spectra from situations where you'd find them?
You could make a line like this.
www.omicsdi.org/ws/dataset/search?query=UNIPROT:P08648%20AND%20UNIPROT:Q99714%20AND%20omics_type:Proteomics.
...after the "UNIPROT:" put in any protein identifiers that you want (in this case I put in Integrin Alpha 5 for humans in place of the example the authors used, the second one appears to be a mitochondrial thing of some sort) and hit enter!
WHOOOOOA! Overwhelmed with data? Yes you are!
Note at the end of the line where it says "type:Proteomics."?? You know what that means? You don't need to restrict yourself to proteomics. Obviously, I would start with the best -omics, but if you wanted data from the inferior ones, they're available as well!
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