Sunday, December 11, 2011

Something Bioworks does better than Proteome Discoverer

Proteome Discoverer 1.2 is a great piece of software.  Now that I've got the module thing down, I don't know how I got anything done with Bioworks.  We did, of course, process hundreds of GB of data with Bioworks, but it is so much faster and easier now with Discoverer.
There is, however, one thing that Bioworks does better, much better, than Discoverer.
If you are trying to put together a presentation to show off your SILAC quantification data, would you rather show this:


The top is the graphical output for a protein that is ~10 fold down-regulated in the heavy labeled cell line that you would get with Bioworks.
The bottom is an example of the output you get with Discoverer.  Not nearly as pretty, or as sciencey!

Summary:  Bioworks still has value.  Keep an old Windows XP computer around so that you can still run it if you need to!

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