Sunday, November 2, 2014
The NCI-60 proteomics project has awesome online tools!
I've mentioned the NCI-60 proteomics project a couple of times over the last year or so since the publication came out in Cell. If you aren't familiar, the NCI-60 is probably the most well-characterized set of cancer cell lines in the world. The National Cancer Institute picked these lines years and years ago and hundreds, if not thousands, of papers have been written comparing and contrasting them. One of the most common uses is for drug sensitivity comparisons. You invent a new chemotherapy agent and someone at the NCI is going to dose all of these cells with tons of different doses of your drug under different, clinically relevant, circumstances.
Despite talking about it a few times, I've never actually got onto the tools TUM has provided for analyzing this amazing resource. I've had some time this weekend and they are really really good. You can use the online web tools to look at comparisons of virtually any proteins against these lines. You can break them down by chromosome or by function. The tools are fast, simple, and intuitive.
Best of all, the file downloader is simple and fast. I'm benchmarking some functions in Proteome Discoverer 2.0 and I wanted a big dataset. So I downloaded one of the cell lines that they studied "in depth". Minor minor criticism -- it would be nice if it was easier to separate the files that belong to each cell line. If you want every MCF-7 fraction, for example, you need to scroll down and pick each on individually. Told you it was minor!!!
And while I'm talking about the RAW data. Whoever set up the Orbi Elite that acquired this data knew what they were doing! Part of my day job is to look at other people's methods and see where a tweak here or there might improve their data. I'm pretty good at that part. I wouldn't change a thing in the files I downloaded from this resource. That method is perfect for the chromatography conditions they used.
Anyway, if you haven't checked out this resource, I strongly recommend that you do. You can link to it directly here!