Cognitive impairment at high altitude? Proteomics (and metabolomics) to the rescue!

 

I don't know about you, but I'm waaaaaay dumber than usual when I'm at really high elevations. Not only dumb, but also lazy and tired and 2 glasses of wine and I might just fall right off of a ski lift. 

I went to a wine convention thing in Colorado at a Ski resort years ago and found out all of these things. 

This study tried to get to the bottom of this by collecting proteomic and metabolomic samples from people who went to work in high elevations for 6 months. Holy crap. Some of this work was at 4,800 meters in elevation. There isn't anything in Colorado that tall. The highest lift I fell off of wasn't even 4,000 meters. I'd be useless up there. 

These authors compared serum proteomics (TIMSTOF Pro with....ummm....I'm not sure I understand what else. SDS-PAGE fractionation? Online? At high pH? And an Ultimate 3000 was used on the TIMSTOF but no details seem to be here for the column, flow rate, gradient length) and the data was processed by ....umm....magic....? No software was mentioned that made the PSM/Peptide or Protein Assignments.  I suspect the person doing the actual proteomics was not consulted by the authors on that section. Or they're author 7 and they're like "f' you guys, figure it out yourself" which I've heard sometimes happens. 

The metabolomics was done on a Q Exactive and there are details. Waters BEH 2.1mm x 10 cm column at 350uL/min for a completely secret gradient length. It literally says "over time" and if you want to know about how they ran the Q Exactive - you did not come to the right authors. No joke, check this out. 

We optimized it for best performance and we will never ever tell you what that was and it's weird you'd want to know. The reviewers were not on top of their game for this one. Weird to see something like this in JPR. Nature something or other? Sure. Not JPR or MCP. Meh. 

The data does appear to be publicly available if you're all nosy and want to know or...you know...if you thought this was cool and you wanted to reproduce this work.

The plots are really nice, though. MSStats was used for the super secret proteomics data and an R wizard was onboard who tells you what packages he/she/they used. Hmm...no version info - but AHA there is a github and it is populated. The biology looks cool and I really dig some of the graphs, so Imma post it. The authors could put the complete mass spec methods in the Github later since it doesn't appear to be published to Zenodo or something that will lock it from alterations.