Monday, January 6, 2014

Data access in proteomics

I need access to RAW data.  Lots of it.  There are so many cool papers out there right now with new studies and new techniques, some of which are so fantastic that they defy my beliefs in the current capabilities of instruments and methods.  Unfortunately, I (and if I believe what I've been told out there, you as well!) have a lot of trouble getting ahold of these results.

It's weird.  It used to be easy.  You'd pull up a paper, you'd go to the last page to figure out whether they put it on Tranche or ProteomeCommons or whatever and you'd download that data.  Super easy.  Check the RAW results, get the method they used for every file and you could replicate the study lickity-split.

Then things changed.  The data files got too big.  The databases could no longer hold all the data that we generated.  The turning point?  February 22, 2011.  This was the day that  MCP no longer required the uploading of data before considering an article for publication.

While this simplified the publication process for the authors, it sure made reproducing the studies out there a whole lot harder for everyone else.  Ultimately, this is slowing down the progress in the field.

Solution?  We need to require the public repository of proteomics data.  And I think we have the tools now.  The solution I propose?

I wrote about the Chorus project last summer as my favorite thing to come out of ASMS.  And this was exactly what I was thinking we need it for.  A cloud based (HUGE storage) site for uploading data.  And you don't have to download the data once its there, you can search it and view it and interrogate it all on the cloud.  So when the next amazing paper pops up demonstrating 2,800 proteins quantified in 10 minutes on an old triplequad we can find out that we really are looking at the next revolution in proteomics (or the other thing...) by seeing the data with our own eyes.

Currently the Chorus website states that the site is still in beta mode. However, I talked to Nate Yates and Mike MacCoss and that beta level should be off soon.  Lets all get behind Chorus and start moving forward!

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