People outside our field have a tendency to give proteomics a harder time than they do genomics technologies. I think it comes down to a couple of reasons:
1) Genomics is older stuff. Everybody's had classes on PCR
2) We come off as jerks a lot of the time. All our acronyms and all our complaining about "all you gave me...again...was your keratin...can I please process your sample myself?" Or "umm...if you were interested in <insert PTM here> could you have told me about this before you occupied an instrument for a month?" The genomics cores never give you crap like that cause they 1) can (generally) amplify the crud out of the tube and 2) they haven't heard of PTMs yet. 💃💃💃💃 (Dancy man, emoji!)
You know where we win -- HANDS DOWN? -- TRANSPARENCY! Between ProteomeXchange, MASSIVE, PRIDE, the CPTAC portal and other sites anybody can access anyone's proteomics data and nerds like me do it all the time. Some of us even gave up video games because it's more fun to snoop through your mass spec data. I was about to give someone a call because I couldn't replicate their PTM, then I realized I didn't learn math too good in WV and everything was fine. Maybe they should pay their teachers more...
Don't believe me (about the transparency)? Try getting the transcriptomics data from that newest Nature paper. (Or metabolomics study....but I think they're trying!). WAY easier to check your nemesis's proteomics data while you prepare that scathing rebuttal.
And now -- targeted mass spec gets the transparency treatment with Panorama Public, which you can read about In Press at MCP here!
If you're already using Skyline and Panorama this gives you a super easy way to port your data for reviewers and for the community at large. If you aren't using these (and you're allowed to use open software), you probably should be!
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