As a field, we have a tendency to ignore what is going on in other fields. I understand, for real! This field is awesome. New technology, new software, new techniques. Its almost impossible to keep up with what is even happening in your favorite subsection of proteomics on your favorite PTM. However, there are times when we should probably lift our heads up and look around. Maybe that time is when people keep getting sued for studying and releasing data on a particular cell line.
So... its with a little hesitation that I write about this awesome compilation of data. The work is top notch. I wish it was on K562 or MCF-7 or one of the other amazing and well characterized cell lines out there. But it isn't. Its on HeLa, and despite my reservations, Confetti is a great contribution to our field and deserves to be acknowledged as such.
Off the soap box! This paper is currently open access at MCP, but won't be for long. So grab it here!
What they did: They extracted protein and digested it (with FASP! )in different combinations of 7 different enzymes. They used a variety of run techniques, including unfractionated and SAX fractionation to get a huge coverage. How huge?
8539 proteins.
44.7% coverage over the sequences of these 8539 proteins! Seriously. QExactive power!
Big deal? People have gotten numbers like this before. With UniprotHuman as the only database? Very very few people have ever obtained coverage this deep vs a manually annotated genome. Very few. Still not impressed?
Well, what if this group made a simple web application so that you could directly build and test SRMs off of this data set? Guess what. They did.
I'd put up a screenshot, but it is currently down. The paper hasn't officially been released yet, so the application may be going through some growing pains still. But the figures in the paper make it seem easy to use and powerful. Hopefully it will be up soon. Regardless, check out this paper. This is an idea of what we can get with proteomics when we really need to go deep and get awesome coverage.
When the application is back up, you can check it out here!
Update 4/15/14: The Confetti application had a minor web address issue, now resolved (see comments below). The resource is up and looks great!
0 comments:
Post a Comment