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...

Joe is a great scientist and a wonderful collaborator. If you want to know more about platelets, this would be a good starting point.

To be honest, when I see conferences announced that have a majority of male invited speakers, I think the organisers are not trying hard enough. We have so many excellent #FemalesinMS and resources available there is really no excuse for it anymore #massspec #teammassspec #lipidomics #metabolomics

Some new content at GitHub: github.com/pwilmart/pow... We have been measuring proteomes for a long time but almost never think about our data and results at the whole proteome level. We lose a lot of information when we think one protein at a time. We need to multiplex our thinking.

Thermo announces partnership with big coal to develop new line of coal-powered liquid chromatography and Mass spectrometry solutions (pollutions?). It's even easier for senior PIs to "get their hands dirty" in the lab. Pull down Hibachi facilitates spur-of-the-moment lab BBQs and team building...

This week's top headline from the Department of Redundancy Department: MTG says that there are a lot of weak Republican men...

They may be a few anti-Pho folks here in Portland but they would be hard to find on a cool rainy day. As some French lady said many, many years ago, "let them eat soup!"

US HUPO short course topic suggestions: You are doing it wrong because no one knows how to do it correctly. Techniques that actually work (*extremely* short course). AI is to science like creationism is to evolution. Experimental designs that tell you something: finding needles in haystacks.

ChatStat or StatChat??? I bet this protein is always differentially something or another: www.uniprot.org/uniprotkb/Q5...

I gave a quick listen to Taylor Swift's new album. My first thought was that I hope they are not making a video for Wood...

Maybe the Government shutdown means the Federal Government won't be able to terrorize "we the people" of the US as much, or are those the "essential functions" now?

Boy, I'm sure glad federal troops are coming to get crime under control here in Portland. On my walk today, I saw some cars not come to complete stops at stop signs. There were a few cars exceeding the speed limit. There were some pedestrians that jay walked. I saw some litter. It is out of control!

and btw, here is a much better write-up by @pwilmarth.bsky.social from 2021. pwilmart.github.io/blog/2021/04... I just did my own internal write-up and leaned on this completely.

I'm amazed at academics using AI. You are whitewashing the AI field for tech bros and they have rewarded your efforts with funding cuts, job losses, and incredible stress. But go ahead and keep writing those AI papers and having AI conferences. Maybe you'll raise your h-index before you're erased.

Size matters. How big is your embedding? Maybe we should call AI what it really is: Alpha-male Insecurity. If your research work involves AI, just stop. It is like saying you found a couple of non-mass-murder uses for assault rifles, so you recommend all researchers start using them.

ECD is back! That took about 20 years. Proteomics must be slowing down. The length for proteomic idea recycling is more like 10 years. Maybe ECD results in longer time distributions? Since it is shooting electrons at big things, I hope it uses a manual joystick. Turn MS into a mass player e-game!

I can confidently predict that "inflammation" and "immune response" will be associated with many diseases...

When you are mostly concerned about the size of your study, can we all agree to call that a search for bromarkers?

Windows (10 or 11) is total shit thanks to AI and MS being the World's worst company. Win10 virtual machine makes my iMac fans run all the time. Pausing Win10 stops the energy wasting. Resuming Win10 results in *several* unusable minutes of 100% CPU use as Win10 tries to catch up on spying. FU MS.

Ha-ha. Proteomics methods from 15 years ago are not ready for prime-time. How many wrongs (bad sample prep, bad enrichment, bad LC, bad MS, bad data acquisition, bad data analysis, bad experimental design, bad QC) does it take to make a right? We need more AI! AI beads, AI LC, AI MS, AI marketing...

If your issue with Cracker Barrel is the logo, then you must have your own portable defibrillator...

We are lucky that proteins are robust molecules. No spontaneous peptide bond breaking, no artifactual modifications from oxygen or buffers, and they never stick to any surfaces! Why were we ever so stupid to digest with trypsin and try (with limited success) to use mass specs to sequence peptides?

I'm co-author on a paper that was submitted to MCP. It was rejected because it was not *novel* enough. It used thoroughly tested quantitative proteomic techniques and had reliable, believable results. I think that makes the paper *extremely* novel for MCP (or any other proteomics journal).

I wanted to get a couple more years of work in before retiring. Was that too much to ask? Now, there's funding uncertainty, and GitHub is being forced to all AI crap by Microsoft. Is there nothing that MS can't turn to shit? I will be looking for a GitHub alternative and wasting time migrating...

Do you need an AI's help to write a blank review???

If this was for microscope data, they could have called it CryptoEM...

It is the 100th anniversary of the Pig -n-Ford races this year: www.tillamookheadlightherald.com/news/pig-n-f... The racing starts today and the World Champion will be crowned on Saturday! My money is on Wout van Aert...

A really dumb question that just won't die is: "when are they going to make the women's Tour de France more like the men's race?" The question should be when are they going to make the men's race more like the women's race. This year's women's tour is absolutely amazingly great. OMG!!!

The $10 proteome is interesting. Assuming 100 nanograms of digest per sample to get a really shitty result, that is $100 million per gram. There are 453 grams per pound, so that is 45.3 billion dollars a pound for manure. I should have stayed on the dairy farm. Talk about cash cows!

It looks like Sydney Sweeney's "great jeans" ads might be a big bust...

I fixed the title: "Non-random extracted ion chromatogram peak areas as a novel complex, computationally-heavy data imputation method for non-quantifiable proteins in quantitative proteomics: imaginary data solves the complex number proteomic crisis in experiments with negative replicate numbers."

Finally, the real Tour de France starts today. This 3-week Tadej de France snooze fest is so over. If they had a mercy rule in grand tours, it would have ended two seeks ago. Now it is time for some real bike racing.

The NIH NCI announces that cancer research funding is in near total remission...

Didn't get enough #TeamMassSpec at the Cascadia Proteomics conference last week? Did our @talusbio.bsky.social presentations pique your curiosity? Say no more because Bruker has you covered. I'm speaking at the "Bringing ASMS 2025 to Seattle" event TODAY! Registration still open! lnkd.in/gTs62ePq

I can't believe how many attractive young women with cute user names are really into proteomics! You know it is a healthy social media platform when you have such a diversity of followers!. Do the women scientists get a lot of proteomics-loving hunky young men with rugged user names as followers?

I wonder how UAE and Tadej will attack his rivals on the rest day. Can he win the rest day? How much time can he put into his rivals? Did the team recon the rest day? What is the best rest day bike setup? What time bonuses and points are on offer for the rest day?