We know with 100% certainty that some peptides "fly" better than others. We exploit this fact when we're picking the best peptide targets for our best possible targeted assays.
Does this impart some sort of a systematic bias? Sure it does! But what are you going to do about it?
These people are really good at math and write about half the paper in Greek with funny variations in the font sizes used (example):
...which makes the study seem a little on the daunting side, however, there is a Github up here and my role here might be to be enthusiastic about what a great idea this is so that someone integrates it into tools that I use!
They run through a ton of previously published work and apply Prepper and results that didn't make quite as much sense, now make more sense than they did.
We all bash the transcript abundance to protein abundance correlation stuff, but -- ultimately there are classes of proteins that are going to be regulated primarily by transcription/translation. You'd think more would match up than they do. Some of this might very well be us! (Of course, many proteins are regulated by degradation, in which case transcription levels are largely meaningless in terms of protein abundance.)
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