ProtSeq -- The most complicated way to analyze a proteome yet?

 

I'd been meaning to get to this one since the holidays, in particular because some of the leaders of our field seemed to be such fans of it. 

ProtSeq is more evidence that biology and medicine is really really interested in proteomics right this second and they will go to any lengths to avoid mass spectrometrists. As one EXTREMELY prominent medical researcher said on a webinar I recently sat in on mass spec based proteomics was described in flattering terms which included "toxic" and "short-sighted." We were largely detailed as a group that doesn't care about medicine, only about one-upping each other with incremental improvements and it was implied that our field leaders were essentially just extensions of the marketing departments of instrument vendors. Which...well....honestly might not have been directed at me, but I sure spend a lot of my time promoting new toys from vendors and now I feel like kind of a like a gross old puppet. Oh, my notes say the speaker also said "miss the forest, for the trees". I'll see if it is up where I can share it. I bet I can find a bunch.

I won't even go into how ProtSeq works here. Not just because I don't understand it, but because I'm really really sleepy from moving instruments for expensive incremental hardware improvements. I need to join in on the cycle here that goes like:

1) Prominent mass spec researcher publishes data on unreleased prototype instrument. This should be 2-4 months before ASMS. 

2) We see 4 million posters at ASMS. Noisy sleep deprived blogger amplifies all of these

3) Early adopters get the instrument (a lot of the functions don't work and it's highly unstable, bug fixes will roll out every month for the first year or so and taper off to every 2 or 3 months 

4) Our "big" journals will publish literally anything from the instrument during the unstable period Yeast? Sure! HeLa? Of course! This is partially to marvel at how anyone somehow got the thing to do absolutely anything. But we only get a couple freebees. One yeast paper is okay and 2 HeLa papers. Bonus points if half the authors on the paper are vendor R&D team who were largely necessary to keep the instrument from burning down the hospital where it was housed. 

5) 24 months later -- a bunch of papers from the early adopters are finally published. More conservative facilities, or ones where funding needs to be requested 1-2 years in advance finally get their purchases through and the stable instrument starts showing up in tons of labs. 

6) 6-9 months later, prominent mass spec reseracher publishes data on new unreleased prototype instrument for the next ASMS and the cycle begins again. 

I'm a hardware instrument nerd. I'm super impressed with the physics and math that goes into making these things work and a lot of our field is. We're a minority. I'm increasingly seeing young people who want to do proteomics but do not care in the slightest how the thing works that gets them there. But maybe that was everyone all along? 

ProtSeq and O-Glink and SOMAProteinGuesser and a bunch of other things rolling out are pretty clear that no one wants to play these games with us. To be honest, after writing out how it works, I can see the point. It sounds like it's great for the shareholders of instrument vendors and not for science.