Wednesday, September 5, 2018

Deep diving in spinal fluid proteomics!

Human body fluids have unbelievable dynamic ranges in terms of protein abundance. Spinal fluid is no different. Which is surprising, honestly, if you look at it, because it just looks like water.

(Not my freakishly large hands).

Just like the blood/serum/plasma proteome, we don't know with 100% certainty what proteins are present in the fluid under normal conditions, but this brand new JPR study does the best job yet of thorough characterization.

Cool stuff from this study -- there are just companies where you can buy commercial human body fluids from! They just bought a bunch of CSF!

They digest the CSF, TMT6-plex and then they break out the OFF-GEL and use the high resolution fractionator (24 isoelectric peptide fractions).

It looks like they take the peptides directly from the OFF-GEL and desalt online (! awesome if true !) and run a complex 171.354 minute gradient (my math) on a 50cm column into an Orbitrap Fusion Lumos running in OT-OT mode (120k MS1 15k MS/MS).

That's 68 hours of Lumos time and the highest number of peptides and proteins from CSF to-date, by a large margin!   Now that there is an improved baseline for "normal" is it time to re-evaluate some of these historic datasets from studies on different pathologies?  I'd think so!

All RAW files from this great new reference dataset are available at PRIDE/ProteomeXchange here.

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