Ben Neely
@benneely.com
1.9K followers 700 following 2.2K posts
Analytical biochemist attempting molecular cartography across the tree of life, powered by MS-based proteomics. Opinions expressed are solely my own. he/him benjaminneely.com Charleston, SC, USA
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benneely.com
As of right now, it is not an exaggeration that I am getting many fold better science/proteomics content and interactions here, as well as some of my pop culture (eventually sports) and local info! A good time to get mine folks that *you* make the algorithm.

bsky.social/about/blog/7...
Algorithmic Choice with Custom Feeds - Bluesky
Our implementation of algorithmic choice lets users customize one of the most important parts of their social media experience: their feed.
bsky.social
Reposted by Ben Neely
willfondrie.com
I'm a huge fan of this proposal!

If we can get vendor buy-in to an open, common format, it could bring more computational folks into the field. How can these folks be excited about #proteomics when its hard to even read the already complicated data?

pubs.acs.org/doi/10.1021/...
mzPeak: Designing a Scalable, Interoperable, and Future-Ready Mass Spectrometry Data Format
Advances in mass spectrometry (MS) instrumentation, including higher resolution, faster scan speeds, and improved sensitivity, have dramatically increased the data volume and complexity. The adoption of imaging and ion mobility further amplifies these challenges in proteomics, metabolomics, and lipidomics. Current open formats such as mzML and imzML struggle to keep pace due to large file sizes, slow data access, and limited metadata support. Vendor-specific formats offer faster access but lack interoperability and long-term archival guarantees. We here lay the groundwork for mzPeak, a next-generation community data format designed to address these challenges and support high-throughput, multidimensional MS workflows. By adopting a hybrid model that combines efficient binary storage for numerical data and both human- and machine-readable metadata storage, mzPeak will reduce file sizes, accelerate data access, and offer a scalable, adaptable solution for evolving MS technologies. For researchers, mzPeak will support complex workflows and regulatory compliance through faster access, improved metadata, and interoperability. For vendors, it offers a streamlined, open alternative to proprietary formats. mzPeak aims to become a cornerstone of MS data management, enabling sustainable, high-performance solutions for future data types and fostering collaboration across the mass spectrometry community.
pubs.acs.org
benneely.com
Ha, I definitely helped with that!
benneely.com
I mean, there was that paper (paleoproteomics?) where they had the dog naw on bones in the lab.

So it’s not something you’ve concern for or seen evidence of? I figured asking you was the quickest way to an answer. Thanks.
benneely.com
Hey @ronbeavis.bsky.social, me and @proteomicsnews.bsky.social were chatting about your cRAP and I recall you saying you could identify certain European labs by their wool sweaters. Did you ever see if you could identify labs that had cats or dogs as pets, and include those keratins in cRAP? Thanks!
benneely.com
Yeah, absolutely imo. Primm- just comes across as pretentious or awkward to me.
benneely.com
But what about the movie or the nucleotide sequence? Come on dictionary people, give me real info!
benneely.com
I also liked it when it came out! though it was incredibly unpopular at the time.
benneely.com
Live footage of me taking kids to school next couple days.

Charleston is a glimpse into the future. King Tide means flood, and a little rain or onshore wind makes it real big. But tides go up and down quick. Still, planning trips to avoid high tide downtown. @chswx.com

water.noaa.gov/gauges/chts1
two people are standing on a boat in the ocean .
ALT: two people are standing on a boat in the ocean .
media.tenor.com
benneely.com
Ha, I guess for all my genomics skywalkers. Hopefully it’s better than Peptide: a protein building game (which I do own).
tabletopgamedeals.bsky.social
While not as big a deal as the other two our favourite Genius Games Game Genotype is also on sale.

It's 19% off, a Prime Big Deal

#ad amzn.to/4h0Ktw1

This is a great dice drafting worker placement game about Mendelian genetics and growing pea plants.
benneely.com
I definitely got a couple games not on my list because of you. Big thanks.
benneely.com
I was playing a pre-determined part, which was for the guests.
benneely.com
Since I’ve started this thread: “feedback” was 3 people legit tried to fight us, and one guy was coming to work the event (gigpro) but quit to protest with us. He got super pissed when he found out we were fake, like security had to escort him away and report him.

Point: AI emotions run hot.
benneely.com
Nearly every patron both nights was taping us out of safety, annoyance or laughter. This is from night one with matching shirts. Second night we looked more legit in normal clothes and had more “feedback” from guests. And all those uber drivers were freaked out!

www.instagram.com/reel/DPZFTUa...
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Welcome back to Instagram. Sign in to check out what your friends, family & interests have been capturing & sharing around the world.
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benneely.com
… which I guess is the point of performance art and this event specifically. AI is great, but even satirically it does have a dark underside to the promised future.
benneely.com
So… for two nights I was a paid extra, first protesting outside the event, then a patron yelling at hecklers inside, and got to see the show 3 times. Seeing people’s reaction for and against, I can 100% see real (large and violent too) protest being a thing in the near future.

synthetic-theatre.ai
This is not part of the show but is a recent thread on bluesky that feels pretty close to a sentiment I see. Only one half of our protest, which was like 50 people with signs and bullhorns making our voices known. Lots of stories here. The ad for the gig. I was brought in late after they realized they wanted more people inside. This was posted Tuesday night when I realized I wasn’t gonna be working Wednesday.
Reposted by Ben Neely
rhuttenhain.bsky.social
My lab @stanfordmedicine.bsky.social is recruiting! We are looking for a postdoc at the interface of quantitative proteomics and G protein-coupled receptor (GPCR) biology:
postdocs.stanford.edu/prospective/...
#TeamMassSpec #Proteomics #GPCR #Postdoc
Open Postdoctoral position, faculty mentor Ruth Huttenhain | Office of Postdoctoral Affairs
postdocs.stanford.edu
benneely.com
It felt pretty on brand for the meeting, especially with their announcement from Germany involving hockey uniforms. When in Rome!

But you know, the show is a bit all over, so no promises what you’ll find.
a man in a suit sits on a park bench with two older people
ALT: a man in a suit sits on a park bench with two older people
media.tenor.com
benneely.com
I think just moving to “proteomes”, as in a complete annotated proteome, is paramount. The whole tr v sp thing needs to be gone, especially for human searches, but also for any other species. BUT, you can still gain or lose genes between assemblies and annotations, which is a bit of a can of worms.
benneely.com
I’m late to this news, but Melvyn Bragg is stepping down as host of In Our Time. I can’t emphasize enough how much this show has meant to me, and Melvyn’s style is what makes it awesome. Definitely hit the back catalog, or one of my fav recent ones is this one on lungs… there’s so much more to it.
BBC Radio 4 - In Our Time, The Evolution of Lungs
From the mechanics of the first breaths on Earth to the reason we hiccup.
www.bbc.co.uk
benneely.com
This morning instead of proteomic-ing, I went to a rehearsal for what I guess will be performance art. I have a very small role but it’s gonna be a blast to do this for real Friday and Saturday night… and get paid to do it! The show itself is great btw.
benneely.com
First step for shutdown Ben was to apply to some local calls for extras in a live show this week. I would recommend reading the article as it describes the upcoming experiment of creativity with AI, which is front and center in our science world.

charlestoncitypaper.com/2025/08/01/s...
'Synthetic Theatre' will be colorful mix of McBride, Beeple - Charleston City Paper
Imagine, if you will, an unassuming warehouse in a no-frills industrial strip on the outskirts of a South Carolina town.
charlestoncitypaper.com
benneely.com
It’s definitely an interesting question to ask someone, but not cheating.
benneely.com
I think all the calls for the season finale of Outer Banks are over, but that would be cool too.
benneely.com
Of course, just like how washing your car insures it rains, if I get a callback that means the shutdown ends early. 🤷‍♂️
benneely.com
First step for shutdown Ben was to apply to some local calls for extras in a live show this week. I would recommend reading the article as it describes the upcoming experiment of creativity with AI, which is front and center in our science world.

charlestoncitypaper.com/2025/08/01/s...
'Synthetic Theatre' will be colorful mix of McBride, Beeple - Charleston City Paper
Imagine, if you will, an unassuming warehouse in a no-frills industrial strip on the outskirts of a South Carolina town.
charlestoncitypaper.com