Ummm....wow....
In big data studies you can generally go one of two ways, right? Loads of samples at lower coverage or fewer samples with extensive coverage. This huge and ambitious study did the former.
1) I massively respect the amount of work that went into this. This is almost 1,000 different cancer cell lines metabolically profiled for around 225 total metabolites. The controls and different chromatography methods used are so impressive that it doesn't matter that it's QTrap data. I'd normally --
-- if asked to validate an MS1 identified lipid that was qualified by a 0.3Da window -- but -- the power here is in the great n -- 1,000 cell lines??! I don't think Jeff Bezos could afford to send that many samples to the great big company that does all the awesome metabolomics, so this group did it in house with their 2 QTraps.
MASSIVE BONUS for any of y'all thinking about doing metabolomics. The supplemental material has all the settings and transitions for the 150 or so polar metabolites (these are surprisingly hard to find out there in the world) only the lipids were knocked out by what appears to be MS1.
MORE MASSIVER SUPER BONUS -- All this data on these 1,000 cell lines is available online at the Broad (which -- I'll remind you -- is pronounced like "TOAD") -- you'll need to register and make some promises about how you'll use the data and that you'll report the errors back to them -- but WHAT A RESOURCE!! The metabolomics is just the top of the iceberg. There is genetics stuff galore!
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