Mass Spec insights in PTMs introduced during EV sample processing...

Google: please read our updated Terms of Servitude...

At tonight's Ultimate Fascist Club bash at the Spite House, enjoy 80-year old men in pissing contests, see nerdy tech bros try to hurt each other with mean words, and, in the main event, watch Stephen Miller and the ICE dancers brutally separate babies and toddlers from their asylum-seeking parents!

Another heavy lift from the titins of proteomics podcasting!

Ha-ha. Watching the Apple WWD keynote and they are talking about parental controls and how parents are in control. That is as delusional as saying that I am in control of my cats.

Out now, a lovely tour de force led by Brooke Genovese @brookegenovese.bsky.social. The comp and statistical tools Brooke developed for non-model proteomics work are legit and worth a look. (her periodic calls to discuss methods were a bright spot on my cal) www.nature.com/articles/s41...

So, @edzitron.com ate his Wheatties this morning

Time to call it like it is and refer to Google as Gobble and its search engine as Gobbledygook...

Preemptive joke apology. If you use nanopore sequencing to study urine proteins, would that be piss poor proteomics? #proteomics

Protein corona proteomics is today's version of SELDI (or maybe the next big thing like aptamers). Snake oil proteomics is still going strong. Now with AI!

"Based on the dataset you shared, US and UK responses differ mainly in tone, intensity, and wording style, even though they express similar emotional states" New post on what happened when I got Copilot to do some data analysis: kucharski.substack.com/p/real-signa...

#Proteomics desperately needs a meeting without any vendor presence. No product seminars, no new instruments, no new methods. No fucking AI. No new tech shit at all. Call it "Back to Biology" and try to remember how to do science. Get off of the hamster wheel, for God's sake.

If you have missing values in DIA, something is below the quant level. End of story. If your answer to shit is to add more shit, you have a real shit problem. Can we get back to doing #proteomics and learning how to do actual analytical work? It is about physical concepts not computational magic.

Every friggin' day in America is a new low with no end in sight.

I don't understand why "A" and "I" are being used as an abbreviation for "bullshit" and/or "piece of shit" when BS and POS were so well established. I guess that is the disruptive part of this new frat-boy-mansplaining investor-defrauding rent-seeking surveillance scam tech.

Does it work properly? No. Are the people making it acting in good faith? No. Have they ensured it can't be used maliciously? No. Does it make people's lives better? No. Will it make people's lives better? No. Is it profitable? No. Is it popular? No. Is it harmless? No. The argument for AI.

Unlocking the silent proteome?? Are silent proteins the products of silenced genes? Maybe they are just real quiet and you can't hear them over the rough pump noise? Are they withdrawn because of early translation trauma? Are they non-interacting? Who locked them up? So many questions for AI...

If you find the news headlines don't make any sense, add the two words "for Billionaires" to the end of any headline. Even if you still can't figure it out, at least it will be true.

'OpenAI, the company behind ChatGPT, is on track to lose $14bn this year. Its market share is collapsing, and its own CEO, Sam Altman, has admitted it “screwed up” an element of the product. All it takes to accelerate that decline is 10 seconds of your time.' www.theguardian.com/commentisfre...

In the 35 years since Python was first released, lots has changed. One constant has been that "Learning Python" by MarK Lutz is the best book out there. There's a 6th edition (learning-python.com/about-lp6e.h...). If your code is shit, you'll end up with 10 lb. of shit in a 5 lb. Docker container.

We have a PhD studentship available!

Great. Thermo is going to transition to Windows 11 instead of Linux. I can have CoPilot hallucinate some instrument parameters, acquire scans to OneDrive where every 4th scan is an ad, and search my data with Bing. That is, if any runs finish without a security update reboot in the middle...

Now that table of contents figures are all AI-generated crap can we just get rid of them? Please. I want to scroll through the TOC to see the article titles and authors, not the shit pictures.

Can we figure out how to combine spacial proteomics with laser tattoo removal to provide population-level health care screening for millions of people? I know, the Mann Lab probably had a preprint but it might be fading over time...

Giuseppe really likes to nap in the hammock in the cat tower we have in the basement. He also enjoys catnip (maybe too much). Have you ever really looked at your foot? I mean REALLY looked at your foot, man???

It's time for cat stories. Giuseppe (a 12-yr old orange tabby that lives 4 house up the street from us) likes spending time with our youngest cat Chip (3-yr old). They hang out, in the better weather, on the front porch chairs. This winter Giuseppe spends his days (everyday!) at our house.

If you’re going to #ASMS2026 and are a student, it’s a great idea to apply for these. When I did my assistant work, I was lucky enough to assist with the polymer session, which meant I was paid to learn about Kendrick mass defects!

I have a 3-year postdoc position available at University of Manchester for a mass spec expert in proteomics. The person will be involved in exciting projects in single cell proteomics, drug discovery and innate immunity - on timsTOF Ultra AIP & HF & Astral Zoom. www.jobs.ac.uk/job/DQJ093/r...

If your opinion of AI for use in science/academia is neutral (going along to get along), somewhat positive (it can be amazing) or you feel forced into it (can' keep up w/o it), this blog is a good read to get some perspective. www.garfieldtech.com/blog/selfish...

Getting an email to keep my computer protected with Microsoft Defender is like getting an email from Hannibal Lecter to eat more liver...

If you are interested in how modern proteomics can shed light on rare childhood diseases, check out this new paper: www.frontiersin.org/journals/mol... TMTpro quantitation works really well. Heads up: it is not a short story. There are decades of knowledge behind the interpretation of the results.

It's what all of the super users will be doing!

I have improved my mental health with one little hack. Whenever I see the term "AI" in posts, news articles, emails, paper titles, etc., I mentally substitute "nazis". It really helps me tune out anything AI-related. This current incarnation of coal-powered auto completion is f-ing embarrassing.

Congratulations orange buffoon on your receipt of the Ebay Prize!!! It is a regifted, second-hand medal, trophy, or prize awarded sporadically to the most needy white male on the planet. Shipping and handling are not included...

One less thing to learn. No AI for me. Not today, not ever. I can figure things out all by myself. I don't need mental training wheels. "It is better to keep your mouth shut and appear stupid than to use AI and remove all doubt..."

Happy Holidays to all with the energy left to celebrate! I will be glued to the TV watching the cyclocross Kerstperiode racing. Total respect for the top riders and I hope everyone survives. It has been a great season so far and now it "goes to eleven" for the rest of the year.

Let's take an instrument that is even more expensive than Tribrids, use a TMT mode (MS2 reporter ions) that does not work well *at all*, and do DDA masquerading as DIA to do exactly what? Generate an even bigger pile of crap data? Where the F is proteomics headed and how did we get here?

FDR estimation in DIA data is simple. The DDA FDR est. is like this: Johnny has 5 apples and gives 2 apples to Jane. How many apples does Johnny have left? The DIA est. is: Johnny has an unknown number of apples. He gives an unknown number of apples to Jane. How many apples does Johnny have left?

AI lets you fuck up everything everywhere all at once. Welcome to the multicurse.

I don't need any AI tooling to summarize my daily news feeds (newspaper, apple news+, etc.). Every single article/story can now be summarized as "you are fucked".

@asms.org has sent out ballots for the BOD election. There is a strong slate of candidates this year. I know from other organizations only 20-25% of the membership vote in society elections so make your voice heard & vote. It took me 15 seconds to vote. I’m asking for your vote as VP for Programs.

Chip and I want to remind everyone to put your feet up, recharge the batteries, and sleep through black Friday.

I see modified peptides. All of the time. They are everywhere. proteomicsnews.blogspot.com/2025/11/pros...

I am looking for a PostDoc to join my group at Genentech to drive the development of proteomics technologies to fuel target and therapeutic discovery and development. Check out the link below! careers.gene.com/us/en/job/20...

Are you curious about what steps you need to do to analyze very large multi-plex TMT datasets? This is a reanalysis of some Gygi Lab mouse liver data from 2015 and 2021 with 14.5 million MS2/MS3 scans in total. The big data needed a big discussion (kind of a long read). github.com/pwilmart/mou...

We’ve been considering creating an announcement mailing list for #PRIDE @pride-ebi.bsky.social; to share new features, releases, datasets, known issues, and more. If you think this would be useful, please Like and RT!

Lucinda Brand just made 50 elite women's cyclocross podiums (placing 1, 2, or 3) in a row. That is like submitting your last 50 manuscripts to Nature, Science, or Cell and all getting accepted with no or minor revisions. It is an epic accomplishment by one of the true legends of the sport. Chapeau!

I grew up during the cold war where we had fascist "tools" using science and scientists to make weapons. Now we have scientists using fascist tools and weapons (ML and AI) in some failing effort to do good. If AI worked, it could do its own white washing. This is some real next generation absurdity.

In the early days, artificial limbs were made out of wood. Since it is still the early days of artificial intelligence, I am going to substitute "wooden head" for "AI" every time I see it in scientific paper titles, in conference talks, and social media posts. It puts the work in a proper context...