Ummm…..whoa….I'm just going to leave this here. This is far too large of a resource for me to tackle on a Sunday morning.
Here is an overview and a lot of links to/around/about the study — including an query-able — SQL database in case you're not sure where to put 4,000 Fusion RAW files….
And here is a short paper about it….
Okay....are you guys ready for this one? I wish I could say I was, but it's too important for us as a field to not think about.... Matrix matching? "Analytical figures of merit"?? Hey! This is the proteomics party, don't you come in here with all your boring analytical chemistry validation stuff....oh.....ugh...okay.... (Yes. I had to make that. You're welcome.) Why is this (study) important? In part because it addresses 2 separate concepts that need to be separated -- and they're right in the abstract: "....Our results demonstrate that increasing the number of detected peptides in a proteomics experiment does not necessarily result in increased numbers of peptides that can be measured quantitatively....." What? First of all, this study is like 4 pages or something and it represents an absurd amount of work. SRMs and DIA experiments (QE HF, I think) and a bunch of different HPLCs and the matrices are all sorts of fun -- CSF and FFPE and yeast digest and maybe I mi..