Okay — so, despite all appearances, methionine oxidation (Met-Ox)is actually a really important thing. Before I get distracted, you should check out this really smart way of studying whether it is a biological Met-Ox or a sample prep Met-Ox artifact here.
This is an aside, but — holy cow — the first 11 papers I tried to find to prove this from home were all locked behind paywalls. I had to go back to this 1997 PNAS paper for something that was open access.
Are you a US citizen and do you think that if your tax dollars funded some research then those results should have to be openly accessible to you? If so, check out this thing some guy set up….
Here is a direct access link to this petition.
With that out of the way — back to Met-Ox. For real — this is important. It can be used as a metric for ROS scavenging and for a long time has been thought to be impaired in a lot of diseases and may even be a generic metric of aging. It just turns out that we don't have a great way of determining what is real Met-Ox and what is an artifact of the myriad ways our field extracts and digests proteins. And now we do! If it looks like Met-Ox might be playing a key role in your biology you can get some heavy labeled hydrogen peroxide and — ouch — it is surprisingly expensive, at least at the first suggestion Google had for purchasing it and find out for sure!
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..