HUGE ramifications for our understanding of host-pathogen response reutilizing those systems for good. Crazy paper, I pulled off the road while driving to post this. Looks like better grammar than usual!
They do test this versus earlier versions of Prosit and with what appears to be HLA class 1 and it is much better and it has functions that you can only access on PrositDB while waiting your turn. All good stuff!
Details here! Also -- new lightning talks for the discussion group start in October (great idea!)
I knew this was happening, for real. I just didn't know that today's date was also in September of 2023 until just about now.If you are unfortunate enough to be doing proteomics or mass spectrometry in the midAtlantic where you still have to tell people mRNA abundance doesn't correlate with protein abundance every day (maybe that is everywhere) - we can commiserate at this thing Monday night. Either I got very lucky with the final verb in that 40 word sentence, or the spell check is off again on this wacky blog thing.
This preprint was just posted and I'm largely leaving it here to remind me to run it on some things later!
What is important to note here is that an awful lot of our contaminant testing things require that we fragment the grossness that is in our runs. HowDirty does MS1 based feature extraction (through Skyline, which is the gold standard for MS1 extraction analysis). HowDirty is going to let you see a lot of things that the workflows I use will simply miss.
https://www.sciencedirect.com/science/article/pii/S2666166723005038
All the DIA tools seem able to predict your peptide ion mobility values now, but what if you want to use something else?
And for a change of topic, sorta --
....so...hmmm....6,000 proteins in plasma is generally something reserved for fiction or especially scammy proteomics startup companies, or those next gen things that we still don't have evidence work at all with any quantitative accuracy.
What might be most impressive is how much of this is actually the Seer nanoparticle technology vs. how much is the OrbiToF. The figures are broken up for publication, but I'd recommend checking out Figure 3B which is the Seer technology things vs a neat plasma digest on the Exploris 480 - BIG NUMBERS out of a 4 year old instrument! Now....the abstract says 6k proteins for the Asstral, but I'm having trouble figuring out the numbers from the body of the text support this statement in the abstract. Either way - big numbers. And some of the highest I've ever seen for plasma (from reputable sources).
Like the prominent proteomic scientist Bini Ramachandran stated earlier this morning on social media, I'm also struggling some with the quantitative comparisons. What I think they are doing is using a spike in of known ratios to estimate their true ratio compression. That way when they look at a protein that appears to be a certain ratio (observed) they can decompress it to true. However, this is my second paper this morning and I really have to go figure out what is up with a QQQ an hour drive from where I'm sitting, so I can't put more time into it.
Today you can buy "mass spectrometry grade" trypsins from a bunch of vendors. Are they all the same? How do they perform on easy stuff (HeLa cell line digest) or super hard stuff (single cells and plasma)?
On the list of - thank you for doing this because it sounds like zero fun whatsoever - check this out.
I won't ruin it for you, it is a fun read, but on the easy stuff, maybe it isn't a problem. On the hard stuff, there do appear to be some differences - and there is some evidence that you should really keep it consistent (don't swap trypsins in experiments). The thing I found the most alarming was the decrease in trypsin performance at recommended storage conditions. While the authors indicate that this decrease is within their error bar, it is still a drop. We'd do this thing in the government of buying lots of trypsin right at the end of our fiscal year -- and sometimes it was a LOT. Like -- years worth. If you don't spend that money it goes back! With detection of a decrease in performance over a period of months it may make you very concerned when you are keeping some surplus trypsin over a course of years.
Solid, well executed work that answers questions I think just about everyone has wondered about and I sure wasn't going to ever do it!
