glutenTAG - Spatial proteomics of 100 targets with IHC and MALDI-MS!

 

For an entry into best new method name of 2025 - look no further than glutenTAG! 

This preprint is simply stunning and overlays high-plex IHC with MALDI mass spectrometry. 

Biggest ASMS for hardware launches in a long time? Ever? Maybe!

If you're registered for ASMS you can now dig through the hardware posts.

Chris just posted what he's already got through digging through the ASMS app

I know of at least 2 things that didn't make his initial list. Probably he knows about them but ran out of characters to post them. 

I think there is some chance that 2025 is the year that we started thinking about 100 Hz high resolution scans as kinda fast and there is a decent chance we stop thinking of PCR as the most sensitive technique. Disclaimer - I haven't done PCR personally in a really long time. 

And as funny as it is to think that Agilent's launch is a single quad - I'd actually really like to have a simple inexpensive and not crippled single quad around. 

Attention freeloaders! Skyline needs your support! It takes 60s to sign this thing!

 

I even signed it and 99% of my interaction with Skyline is complaining about how I'm not smart enough to ever make it do what I want.

Please drop in here and sign the stuff! 

Sad reddit thread - scientists concerned to travel to the US for ASMS....

 

....yeah....

I'll just leave this here. 

An update on the proteomics of extracellular vesicles!

 

Are you also confused by what an extracellular vesicle is? And or why people want you to do proteomics on them? Did you get two collaboration requests this week to work on them while also remembering that you already ran 400 for someone and you aren't entirely sure where you put the .d files that you are supposed to be using to write a grant. 

This isn't me I'm talking about. There is no way a single lab move would make me so disorganized to have 20 cases of p20 tips and no way to pipette a larger volume without adding to a large list on my tablet that says "I owe Matt MacDonald lab..." And I absolutely have every file and every file backed up. It just might be in the hard drives with the p200 tips that I absolutely have on a shelf...somewhere.... 

To whoever you are you hypothetical person who needs to know about EVs I present this really nice and succint and new review - 

OH! And this is important! I just found this out and you guys should know this. 

There is a Qiagen kit out there for EV enrichment. The buffer that they use in the final step to lyse the EVs contains Triton X-100. I got suspicious when I checked the MSDS and it was essentially a blank document. Of course, a vendor won't tell you what is in their secret buffer, so I put in a help ticket and I asked - does this contain X-100, Tween-20 or any other scary detergents I should know about. And - yes - it contains a low amount of X-100. 

Deep spatial proteomics of ovarian cancer precursors!

 

Wow - this is just another stunning example of spatial proteomics and what it can do! 

Highlights? 

The cuts are made with a little Leica LMD7 system which can drop cuts directly into 96 or (as used here) 384 well plates. These smaller systems appear a bit more approachable, but might not have the resolution to do some of the really precise cuts (?) I'm not sure.

Here the regions that were excised were in the 50-100 cell range and guided by histological stains (I think? not my field and I can't spend all morning on it).

Cells were digested in plate - ACN first to lyse - that's dried off then LysC then trypsin. 

The cleanup was done on EvoTips and analysis was on a TIMSTOF Ultra(? I forget, but pretty sure) using the EvoSep 30SPD method.

Analysis with DIA-NN allowed them to quantify 10,000 protein groups?? From 50-100 cell cuts! Just stunning work I can't wait to circulate to my colleagues this morning! 

AI IN PROTEOMICS! An ABRF / US HUPO Crossover event is go!

 

Yeah! It's happening!

My favorite session from ABRF 2025 is now open to all you bums who weren't heavily exposed to second hand smoke for 4 days in Las Vegas so you could see it when I did.

You can register for it here - and, like all US HUPO webinars, it'll be recorded if you've already got plans or are in a suboptimal time zone.

Pirates of the proteome!

Too funny and well done to not share! I'm going back home to Baltimore, Hon!  

True story, I'm somehow presenting exclusively in the mornings so I don't even think I can stay at my house because I-83 in the morning isn't the most fun you can have. 

Multiplexed method allows hydroxyproline enrichment and quantification!

 

This is a really interesting approach - and application! Ever thought much about hydroxyproline? It looks like it might play a role in the progression of prostate cancer! Bonus - 12 plex DiLeu labeling makes an appearance! 

A tissue proteome specificity map that is actually good!

 

I am so excited by this great new resource!  

And not just because the most recent big paper purporting to do such a thing (this one - still out there and still misdirecting people!) was such a pile of garbage! 

In this new cell paper, this group did the work to FIND PROTEINS that legitimately appear to be organ specific! 

Don't want to read and just want a list of proteins that are -by protein - and by RNA - basically almost entirely produced by specific organs? Check out their nifty little portal! 

 Their RAW data is publicly available? What?!? What an amazing concept! They actually compare data from protein level and RNA measurements before claiming a protein in plasma originated in said organ? Amazing. For proteomic nerds - the organ data was acquired by DDA on a QE Plus running nanospray on 2 hour gradients. The plasma proteomics was done by DIA proteomics on a QE HF-X. High accuracy high precision measurements. I'll dig into it more soon, for sure, but it's absolutley worth checking out now.