Proteogenomics is some great stuff. But it isn't easy stuff yet. You might notice from recent blog posts that its starting to become a bit of an obsession of mine... The promise is there. The data is there, but integrating RNA-Seq data with Proteomics is still no easy task.
For an overview of where we are (as of 2014) you should check out this great review in Nature Methods from Alexey Nesvizhskii. It is open access, remarkably clear, and very thorough.
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