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...

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...