It's that time of year again for are Annual proteomics chart course! Going on almost 20 years! Honestly it's a good class for those wanting to add proteomics to your research. And Proteomics really is the best Omics if I don't say so myself #proteomics #massspec #proteome #massspectrometry

🚨AI trigger warning🚨 So I’m realizing that since the winter we moved from “cute little scripting” to legit big time fun with LLMs, I’m going to try and document my journey better. This “build” captures a lot of my general approach and experience. neely.github.io/tiltMaze/

No credit for these popping up on my radar (my weekly gems found it), but I have them on my "to read" list now: Evaluation of deep and dynamic proteomic screening strategies at sub-50Hz scan rate and without automation www.biorxiv.org/content/10.6... Radiant DIA www.biorxiv.org/content/10.6...

This week on #THEProteomicsShow, Ben @proteomicsnews.bsky.social and I finally get to sit down with @jochwenk.bsky.social and talk blood (this has been on my wish list for a while, and didn't disappoint). Find it wherever you find fine podcasts or here: anchor.fm/theproteomic...

We have chamber of commerce weather today with brisk temps, lowish humidity, and not a cloud in the sky. I have already encouraged 2 people to take leave and bug out, and might even do so myself.

Well, its out. Honored to play a small part in this huge project using multi-omics to profile human biology and variations at unprecedented scale. www.sciencedirect.com/science/arti... Thanks to a great team of co-authors and collaborators! @fbmh-uom.bsky.social @uom-dcs.bsky.social

Behind the scenes with #THEProteomicsShow: we are mostly done recording the first 12 episodes of All the Parts, and today I was labeled an agent of chaos by Ben @proteomicsnews.bsky.social. "Are we talking to a chef or the most famous rehab scientist on the planet?" No way to know till we hit go!

Not science: there’s some songs you hear everywhere but, for me at least, can’t seem to remember the source. Like pieces from Kashmere Stage Band. Well, this jam from The Meters lives rent free in my mind. youtu.be/Nd3yDoOyvbY?...

Our latest review on Single Cell Proteomics is out. Honored that it is a Feature Review in the @cp-trendsbiochem.bsky.social special series: TIBS at 50 - Foundations and Frontiers. #Proteomics www.sciencedirect.com/science/arti...

Did you always want to know more about snot and all the things it can tell you? Well do I have a show for you! This week's #THEProteomicShow me and Ben @proteomicsnews.bsky.social sit down with Jennifer Mulligan to talk snot. Find it wherever you find fine podcasts or anchor.fm/theproteomic...

I am editing a recently recorded episode of the pod, topic is blow, and I must have had some allergies, but all the sniffling plus the title makes me think it is some hilarious meta joke. I am removing them though.

Since it might not have been apparent unless you were following the drama, @arstechnica.com @andrewwrites.bsky.social wrote about this. tl;dr it was a vibe coded unofficial port without endorsement or permission to use name and logo. 😿 arstechnica.com/gadgets/2026...

I love that because of Claude Code there’s all these words I feel more comfortable using. Ex. I just used smoosh in a professional email. That said, every time I see “flibbertigibbit” I think of Joe v the Volcano (fav movie btw), and one of the 3 Meg Ryan characters. youtu.be/IBIQU6_VCzU?...

Not science, gross local trend: people looking for Bapple (Busch Lite Apple). Busch Lite may be the grossest beer ever. But here we are. Reminiscent of the previous ~’19 crazy for Natty Lite Pink Lemonade “Naturdays”. Ugh. That said, our local baseball park had some good natty lite “milk shakes”.

So I guess I haven't submitted a paper in a while, but the new JPR (or I guess ACS at large) submission process is super smooth and quick now.

After using a Norman Rockwell calendar (the free one state farm sends me) for years, I am convinced he was a time traveler using gen AI. Okay, I kid, but how the heck did he paint so much?!

Using project and handoff docs, even with chat LLMs, along with new context for most tasks, is so much better than how I was working. I didn’t appreciate a good plan (use the smart model here) then sub tasks (to “dumb” model) works really well. Of course this gets infinitely better in agentic land.

All the Parts continues on #THEProteomicsShow, this week with Charlie Schurman talking to me and Ben @proteomicsnews.bsky.social about bones (not Star Trek). No joke, learned way more than I expected. Find it wherever you find fine podcasts or here anchor.fm/theproteomic...

Not science: when I first set up my “nameplate” url, way back when, it was a custom domain pointing at a GitHub repo, but before GitHub pages. DNS IP addresses and used a CNAME file. Just migrated to using cloudflare for DNS management and it’s about 1M x easier. 🤦‍♂️

So today is the first legit rain we’ve gotten in maybe 2 months, and so we have running jokes about how we’ve all forgot what to call this moisture falling from the clouds. My vote is sky water. It might even continue sky watering for a couple days! 🤯

Now here’s some news: notepad++ coming to Mac!!! www.macrumors.com/2026/04/29/n...

A Selective History of Protein Sequencing and the Impact of Donald F. Hunt on Protein Sequencing by Tandem Mass Spectrometry pubs.acs.org/doi/10.... --- #proteomics #prot-paper

So I think it was over the winter break there was a drop in proteomics skywalker traffic, or appearance of it in my custom algo, and I thought it would bounce back but I haven’t seen it. Is it just my vibe on it or legit? We going back pre 2017 twitter where it’s ~30 (of the coolest!) chatting?

Whelp, Ben @proteomicsnews.bsky.social, I am realizing we are missing a Blood, Sweat, and Tears opportunity, but I sweat was not on my 'All the Parts' bingo card. (tears and blood are locked down)

I think it was over on the Twitters, but I ran into issues analyzing stuff grown in FBS and @ronbeavis.bsky.social pointed me at his FBS fasta, which I’m not sure I still have the url for (have the fasta). But yeah, Ben @proteomicsnews.bsky.social it’s got lotsa annoying stuff, including glycos.

Almost forgot, you can find the latest episode of #THEProteomicsShow out today as we continue our biological voyage. This week me and Ben @proteomicsnews.bsky.social talked to Lekha Sleno about tears. No crying it was awesome. Find it wherever you find fine podcast or here anchor.fm/theproteomic...

I’ve talked extensively about how as commercial AIs hoover up web traffic and at the safe time enormously lower the cost to generating low quality content, high-quality content will disappear from the web, and AI slop will predominate. It’s just a matter of time until this is a top search result.

Is there a way to help non-coder proteomics pros, AI-pros who don't know proteomics, or total novices vibe code proteomics software with confidence? Maybe. We are proposing a epistemic grounding context file, but there is still a ton left to do: arxiv.org/abs/2604.21744 @magnuspalmblad.bsky.social

Choice B is pretty hilarious too.

Each passage into the nucleus is guarded by a jumble of proteins. These bouncers work together to determine which VIPs (very important proteins) are allowed in and out of the most exclusive part of the cell. Tune in to The Quanta Podcast:

Was looking for some old info today and I am so glad late 90s sites are archived so you too can experience the geocities-esque nature of the internet. I mean, check out that sweet NOAA animated gif. web.archive.org/web/19980218...

Back from 🌄Spring Break🏖️, a new episode of #THEProteomicsShow is out. Ben @proteomicsnews.bsky.social and I sat down with Drs. Sasha Singh @toleafgirl.bsky.social and Sarah Parker to chat all things blood vessels. Find it wherever you find fine podcasts, or here anchor.fm/theproteomic....

Science adjacent: I am not sure sending Endurance to Shackleton Crater is the right naming convention based on history, but maybe? BUT, I do recommend anyone to read Lansing's book Endurance, watch Disney's 2024 Endurance doc (cool gen-AI voice work, really), or build the Lego Icons Endurance set.

Did I just ask an actual tear proteomics expert about this... yes. And again, it was you eagle eye @cashwood.proteaglyco.com, but Ben @proteomicsnews.bsky.social again thinks I am insane. For the pod of course.

Robot vacuuming and the pattern it took to "clean" seems completely inefficient and wrong. Watching reasoning of agents makes me think of this. On one hand, I can hand it off to them, on the other, I can definitely see how just a little mental effort by me would be 1000x better. Planning is smart.

A [not actually in a] movie couple that would definitely have a podcast. #THEProteomicsShow

Excellent work. In some ways we (👀 @colincarlson.bsky.social) were proposing/hoping to do something like this across species, but turns out it’s legit hard as I’m sure these authors know.

There are tons of ELI5 explanations for LLMs, but this one from @quantamagazine.bsky.social seemed especially apt. "Chatbots are “yes, and” improv machines designed to spit out strings of words that sound plausible because they’re statistically likely." The parallels with this movie are spot on.

Kinda science: on vacation at Airbnb in Valle Crucis, owned by Parley Rasmussen [a biochemist in the Standards Division, Department of Agriculture (from obit)], who gifted 500 acres to state for park. When sold house in ‘22 they left some of his old stuff. But haven’t found his publications yet. 🤷‍♂️

Not sure why @jradoff.bsky.social hasn’t posted here yet, but they did over on reddit. Pretty awesome use case, imagine resurrecting and maintaining defunct proteomics tools @magnuspalmblad.bsky.social. Spoiler, you can play it now here lofp.metavert.io meditations.metavert.io/p/resurrecti...

Building small apps to fulfill your own needs feels super empowering and fun, we're truly in a new age of software hannahilea.com/blog/housepl...

I can’t tell if this amalgamation is the best thing ever and pure brilliance, or just super weird. But if you’re ever in the south side of Soda City, this exit has it all.

MS proteomics skywalkers... can I again iterate that we might have a problem. This 👇 is "proteomics space".

A consistent message in both Dario’s and now Sam’s, aside from doomsday, is they realize if we don’t get a little socialism/UBI, that it will break the system. I can’t tell if it’s cause the “break” is revolution or just they need people to have money to buy things. openai.com/index/indust...

It really is silly all the little static html “webapps” you can make. This one is for my son since he never writes things down but he’s trying to keep track in his brain. The import/export is a little json file since I’m using persistent memory which can get wiped. apps.benneely.com/media-tracker

I’ll save people a click, FTL is not Faster Than Light protein but is ferritin light chain. Whomp whomp. Also transcriptomics not proteomics. Rats aren’t giant mice and humans aren’t giant rats, but still fun I’m sure for aging research colleagues. www.nature.com/articles/s43...

Not science: soft shell crab season (it’s like a week tbh) is about to be over and it’s magical. Strong local feels about where to eat or not eat it. James island has the winners btw. B-) www.instagram.com/reel/DWtbn2l...

1) Proteomics has a severe problem. We keep pretending database search is “good enough”, while systematically missing everything that isn’t already known. No genome/proteome → no ID Variant peptide → invisible Novel biology → filtered out

Not science: hearing Calexico in episode 6 of Ponies was a surprise. Not the music you’d expect in a show set in 1970s Moscow, but I do love Calexico.