HAHAHAHAHHAHAHA!
We didn't have the time to do an unveiling of the winners of this year's US HUPO video competition.
But now they're live!
and Omics Family Therapy from UC Davis!
Monday, March 3, 2025
Spend 3 days doing a pulldown and analyze it in 7 minutes of LCMS time!
I do have to wonder if that is the most effective use of resources. And - yes - I'd have the same question if this was a TIMSTOF Ultra or other super high end instruments, but only because the pull-downs I've seen seem to take students 2 days to do a pair.
Presumably...you know....the instrument isn't just sitting there after it does it's 14 minutes of work....
It is super cool that the bottlenecks would fall back on sample prep and maybe through robotics and stuff you could find antibodies to do pull-downs on all the things.
But you do have to wonder if maybe it is a tiny bit of overkill? Like...could you do this on an Exploris 240 for 1/4 the price and just run a 30 minute gradient instead of a 7min? It's tough to imagine a scenario where this is a superb use of resources.
However - if you're in a busy core facility and you've got 40 people who do IPs and you the 3rd Thursday of every month is IP day (yay!) knocking out 40 pairs of IPs in triplicate in
40 x 2 x 3 x 7 / 60 in 28 hours would be pretty great, particularly if you're paid by sample injection for 240 in about a day's time.
The Harvard thing where they've done just an absurd number of pull-downs is one of my favorite resources ever (and completely under-utilized by the scientific community) - PlexBio or something? And the thought that you could do that label free between now and ABRF (if you had the samples) is super compelling.
Sunday, March 2, 2025
The Proteomics Show is officially top 3 proteomics podcasts on a service that lists...one!
This guy wrote me this morning from something I'd never heard of to tell me the good news! Out of a field of 1 proteomics podcasts - THE Proteomics Show had made THE TOP 3!
On further investigation, the show is actually ranked #1 out of all 1 proteomics podcasts!
Huge thank you to whatever this thing is called and whoever votes and for not picking up the much more professional proteomics podcasts by Nautilus and O-Link.
In the latter case, we were just on that show!
As always, thank you US HUPO for paying our editing fees and annual software subscription and for our new microphones. Well....I got an open box/refurbished microphone and saved US HUPO $15 and that is starting to seem like a mistake, as you might catch from the show from time to time. I'll be super bummed if I have to buy a new one for $90 later and use this glitchy one for parts.
Most of all, thank you to everyone who replies to emails when we invite you on the show! Without 60 amazing and often famous guests over the last few years, it would just be Ben and I rambling at each other and we can't really get away with that more than once each season. The magic of the show is that we have smart guests saying smart things and then Ben and I dilute it down with our mouths and brains.
Fingers crossed we just proposed something completely different for a Season 7!
Also for not podcast people - your phone probably has a podcast app and you can just open it and type "proteomics" and ...that's probably us.... or Amazon music or Spotify or other things.
Saturday, March 1, 2025
Phosphoproteomic analysis of different CHO - Antibody producing cell lines!
I don't manufacture antibodies, and I honestly only have a loose understanding of the process. If I really like you, or your project I've got a 7 minute gradient, really expensive Thermo column and even more expensive high temperature heater necessary to make the column work properly to knock out standards that look like this
...and data from your mAB that look more like this ...
Which is clearly your protein, cause my standard looks a great. It isn't that it was selected from a broad range of possible proteins to find the one that was absolutely the most amenable to mass spectrometry, or at a level of clean that is completely impossible in a production environment.
I know that CHO cells (Canadian Hippo Organoid - name suggested by a 4 year old, it actually might be something that sounds far more disturbing) cells are often used for production.
Want to know more about the process? Check out this new paper!
It turns out that there are multiple lines of CHO cells and some are good at making some antibodies and not others. This group investigated some cell lines that were good and less good at making particular proteins to see what the difference is. I'm not entirely clear on why they went straight to phosphoproteomics, but US HUPO 2025 was amazing but my work backlog wasn't and my brain is still toasty from digging myself out.
Turns out, though, that they are really excited by the patterns of phosphoproteomic alterations. From a production standpoint I'm not sure if the idea is that they could leverage some cell types and selected conditions to force advantageous production conditions - or if the idea is better applied to selecting the right cell lines for product production based on these information. Either way - antibody based drugs aren't going anywhere and it's cool to see proteomics addressing riddles beyond host cell contamination!
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