Boringest study of 2025 so far! 9,000 harmonized QC samples ran by a bunch of labs over 4 years!

 

In case you're new here or my sarcasm doesn't translate well - this study is amazingly fantastic and probably very very very very boring.

Quick summary? These nerds did the stuff that everyone hates to do and they came up with a QC standard that they could run at every site. FOR YEARS. Actually FOR FOUR (4, vier, quattro, cuatro, fier, quatro [cause they like t's less in Portugal than in Italy]) YEARS! 

Why is this super fantastic? I mean, besides the 9,000+ QC files? 

1) The mass spec instrument methods are completely harmonized (settings are the same for each piece of hardware regardless of which lab it is in). 

As an aside - if you've got an Orbitrap instrument and you're writing your method section and you are wondering what parameters to include in that section - DO IT THIS WAY. PLEASE. Everything that is actually important for me to go to an Exploris 480 and replicate your experiment is right there. 

2) They didn't standardize the HPLCs or settings! Look, I ain't going to use a Waters HPLC unless you give me one for free. I have close friends who are otherwise very informed and rational who will always use those HPLCs. (They do seem very nice except for that whole "they will never ever pick up all the sample in that well no matter what, and they seemingly last forever in the hands of people who know them. I just don't know them and I have my favorites already). This is real world stuff. 

3) They don't hide the results or the variation! No joke, between two core facilities using the same mass spec one lab gets almost 2x the peptides as another lab. It's totally worth looking at why this is the case. And don't get me wrong, it isn't because one lab is better than the other or one go a bum instrument, they're doing it different and delivering a different end product. Super interesting (yes, and very very boring). 

Ben Neely and I did a podcast (actually, out today? maybe) where we walked through our favorite papers of 2024 and he pointed out that 2024 was a huge year for good valuable QC/QA proteomics stuff. 2025 ain't off to a bad start either!