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I put together a guide a few years ago about what to do after you have proteomics data. I'm glad to hear some people have found it useful, but I know it isn't very good. Truth is...I don't really know what you do next to work out a mechanism if GiaPronto or Ingenuity doesn't say "It's this one!!"
This amazing paper in a journal I've never heard of brings new set of tools on stage and goes through them in painstaking detail.
I strongly recommend reading it in the HTML format over the PDF because having the references side-by-side makes it much easier to pop a tab open and figure out what they're doing (in case it's a word of stack of letters in a row you've never heard of).
...which...makes me wonder why everything isn't formatted this way!!
Don't get me wrong, the proteomics here is stellar. (They run a Fusion in HighSpeed mode using 50cm columns and 150min gradients and combine this with data from another cohort that used a QE Plus). Most of the methods and basic data analysis are based directly on the spatially resolved mouse brain study Max Planck did a few years ago, but its the amazing level of detail in both the experimental design and downstream analysis that makes this something I'm very glad I read this weekend!
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