I just sat through a great talk by Oliver Kohlbacher detailing the power of OpenMS for label free quantification. The great algorithms he detailed are old news, apparently, as I was able to find a paper his group published last year where they do a thorough review of label free quantification algorithms. You can find this paper (open source) here.
What isn't old news, is the work that Oliver's lab has been doing preparing to bring OpenMS functionality to Proteome Discoverer 2.0. It sounds like they are well developed and I even saw screenshots showing the nodes in Compound Discoverer. PD nodes may only be a few months away!!
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