This new study might be a textbook example of how to study limited samples and work your way to a biological conclusion.
How sample limited were they? They got little left over little pieces of eyeball material from patient volunteers following cataract surgery. They didn't get all of that for proteomics, they had to share some of it for microscopy work as shown in the really nice picture above (check out the paper, I just snipped it so the resolution dropped).
Samples were S-Trapped, TMTPro labeled, and analyzed by 2D LCMS on an Orbitrap Fusion (2? I forget now, I think it was a 2) using SPS MS3. Interestingly Comet was used for the data analysis using a "1.25 Da monoisotopic peptide mass tolerance, and a 1.0005 Da monoisotopic fragment ion tolerance." I suspect this is to allow for incorrect monoisotopic assignments made by the instrument on the fly.
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