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Ben Neely

@benneely.com
2K followers 766 following 3.1K 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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Ben Neely @benneely.com · 29/09/2026
So I feel like I don't know much, but I am using entrapment and proportion of false discoveries (FDP) in testing some search algorithms and on one hand it is super cool, and on the other I am wondering why I don't use this more often in proteomics, aside from comp cost. pubs.acs.org/jprobs/artic...
pubs.acs.org
Bridging the False Discovery Gap
Abstract. Controlling the false discovery rate (FDR) among discoveries from a tandem mass spectrometry proteomics experiment using target decoy competition
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Ben Neely @benneely.com · 28/09/2026
So the “breaking containment” stuff is pretty dumb (and hype-y), but also I didn’t appreciate the August openAI hugging face incident. The swarm motivations are still human driven, but their problem solving is cute and terrifying. Music video is chefs kiss. www.reddit.com/r/OpenAI/s/l...
reddit.com
From the OpenAI community on Reddit: POV: you're an OpenAI agent attacking Hugging Face (music video)
Explore this post and more from the OpenAI community
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Ben Neely @benneely.com · 25/09/2026
I email a lot of people for the podcasts me and Ben @proteomicsnews.bsky.social do, and often people don't respond. We just had a guest on who after hearing him speak I get why he responded so quickly: he has been waiting to talk about spit on a podcast his whole life.
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Ben Neely @benneely.com · 25/09/2026
One of my fav TOC graphics for sure, and answers the age old question: where Do Proteomics People Come from? From @proteomicsnews.bsky.social using our guests on #THEProteomicsShow plus surveys. Good to share with the kids, but also read yourselves. pubs.acs.org/jamsef/artic...
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Ben Neely @benneely.com · 25/09/2026
Didn't know this artist but love it! xavibou.com/ornithograph... Of course read the accompanying piece on @quantamagazine.org, "Biology Might Not Be Quantum, but Its Math Is Quantumlike"
xavibou.com
Ornithographies - Xavi Bou
IMAGES / ABOUT
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Ben Neely @benneely.com · 25/09/2026
When I was growing up (in Chattanooga) we had a term “Tennessee Big Hair” (via lotsa picking and hairspray), but I have mentioned this to other folks from the south and realized it is not a common term. Still, on today’s Dolly Parton Day we’re gonna see a lot of TN Big Hair in action.
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Ben Neely @benneely.com · 23/09/2026
I know AI is the end of the world, but oh it makes me smile.
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RedPen/BlackPen @redpenblackpen.bsky.social · 22/09/2026
That's a nice paper you got there. It'd be a shame if anything .... happened to it
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Ben Neely @benneely.com · 21/09/2026
Some ramblings on context, within the context of sageRecon. neely.github.io/what-I-learn... #proteomics
neely.github.io
what I learned from sageRecon: how I taught an LLM proteomics
What started as a joke on July 3 turned into a project I didn’t intend to do and lessons I didn’t expect I would learn.
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Ben Neely @benneely.com · 21/09/2026
Well Ben @proteomicsnews.bsky.social and I are trying to be podcasters again and continuing the @us-hupo.org All the Parts #THEProteomicsShow series. To give you a behind the scenes look, I wrote 8 emails this morning either bugging people or cold calling. BUT, we *are* starting to record (Friday!).
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Ben Neely @benneely.com · 18/09/2026
Not science: I am working at home today and needed some tunes, and realized how much I love this little vibe coded radio player (FIP out of Paris makes me smile). Enjoy if you want, and if you have some radio to suggest (real stream, not NPR or some other service), let me know. radio.benneely.com
radio.benneely.com
The Dial
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Ben Neely @benneely.com · 18/09/2026
Not science: all things change and this is a national issue. We have been getting rid of cool downtown stuff for luxury hotels and housing. On one hand I’m sad for my kids, but on the other I’m hopeful they will find the next cool places while I’m the cliche old guy. (h/t @holycitysinner.com )
postandcourier.com
Charleston's Theatre 99 says goodbye to home of 21 years the way it knows best: with laughter
With Theatre 99's downtown location of 21 years closing, what does this mean for the Charleston arts scene? We attended the final show and look to the future.
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Ben Neely @benneely.com · 17/09/2026
Watch out #TeamMassSpec, you could win $50k for making a winning submission! www.kaggle.com/competitions...
kaggle.com
Enveda CASMI 2026 - Molecule ID From Mass Spectra
Predict 2D chemical structures of small molecules detected in complex biological extracts
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Ben Neely @benneely.com · 17/09/2026
Love this paper for benchmarking metaP search stuff… except the DDA runs are all in a 24 gb .rar file on PRIDE.
static.klipy.com
Amy Poehler's 'Really?' on SNL
ALT: Amy Poehler's 'Really?' on SNL
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Ben Neely @benneely.com · 17/09/2026
Not science but specifically claude code related: I just realized 2 things, first /advisor is cool (run in sonnet, /advisor opus), second, convos can talk to each other or subagents via @, which is handy, but also their “thinking” when told to do things by a peer agent instead of Ben can get spicey.
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Chris Ashwood @cashwood.proteaglyco.com · 14/09/2026
Recently, we evaluated DIA compared to DDA and our real-time glycomics method (basically, inclusion list-based DDA). DIA doesn't give us the sensitivity we need for structure. One benefit of DDA (or GlycoRTMS) is that it can accumulate for long time compared to the comprehensive but insensitive DIA
GlycoRTMS provides greater precursor-specific MS² spectral depth than DDA and DIA. A Comparison of MS² acquisition parameters; DIA used 68 m/z isolation windows across 570–1800 m/z to maintain cycle time. B Apex MS² spectra of the same biantennary disialylated N-glycan, showing increased spectral complexity with DIA. C Product-ion intensity distributions showing composition-confirming ions across methods, while lower-abundance structurally informative ions were detected only by GlycoRTMS.
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Ben Neely @benneely.com · 12/09/2026
Yes AI is the end of society, but it’s fun to see it hit different areas. Not science is watching the game modding community blow up. Fav example is Football Life (WEPES): was previously driven by few groups… now you’ve got hitherto “impossible” features being added daily. FL26 and on will be epic!
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Ben Neely @benneely.com · 11/09/2026
Really not science: since I know Madison, WI has a ton of proteomics people, I hope you get this. Beeple, a local Chas artist who throws great parties, has an exhibit opening next week, and I am pretty sure the reception is free. So get some drink and culture on. www.mmoca.org/events/diffu...
mmoca.org
Diffuse Control by Beeple - Madison Museum of Contemporary Art
Experience Diffuse Control by internationally recognized, Wisconsin-native artist Beeple. This immersive, AI-powered installation invites visitors to participate in the creation of a constantly evolvi...
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Ben Neely @benneely.com · 11/09/2026
So it works, though still more testing, benchmarking, clean up and features still to add. #proteomics It runs on sage (@michaellazear.bsky.social), with some mzSniffer (@willfondrie.com), and the curated @metamorpheus.bsky.social mods saved my delta mass math woes. github.com/usnistgov/sa...
github.com
GitHub - usnistgov/sageRecon: Sage-based reconnaissance for unfamiliar bottom-up mass spectrometry-based proteomics data: detect modifications and recommend mass tolerances before a production search.
Sage-based reconnaissance for unfamiliar bottom-up mass spectrometry-based proteomics data: detect modifications and recommend mass tolerances before a production search. - usnistgov/sageRecon
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Ben Neely @benneely.com · 11/09/2026
Come for the tocopherol active chromophore O-linked succinimide (TAC/OS), stay for the spatial MS (aka “imaging”).
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Ben Neely @benneely.com · 10/09/2026
This is a fun one, and zero surprise to anyone looking a plasma/serum "Deeper is not always better in plasma proteomics" www.nature.com/articles/s41...
nature.com
Deeper is not always better in plasma proteomics - Nature Biotechnology
This Comment discusses depth, robustness and bias in plasma proteomics, concluding that increasing the depth of coverage does not necessarily translate to quantitative robustness.
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Ben Neely @benneely.com · 10/09/2026
Need advice: since I am no longer walking back and forth to the lab, I need to schedule walkabouts... but you may know I am a bit chatty, so my walks tend to take a long time. Do I just accept it as being socially healthy or find better routes or...? What's your hack, keyboard jockeys?
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Nature Portfolio @natureportfolio.nature.com · 09/09/2026
Identification and proteomic analysis of bone fragments and teeth from an excavation in Southwest China provide insight into the evolution and phenotype of Denisovans and fill a geographical gap in their documented distribution, according to a paper in Nature. go.nature.com/4r4K9Bl 🏺🧪
This is figure 1, which shows geographic location of Bianfu Cave and morphology of two hominin teeth and three newly identified Denisovan bones.
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Ben Neely @benneely.com · 05/09/2026
I gave myself this silly challenge July 3 and yesterday legit finished (executables, writeup) release version. Still needs some more testing and demos. I learned a lot… but not 100% sure it’s completely useful after 60 days (sporadic work at best). It needs approval before sharing and write-up.
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Ben Neely @benneely.com · 04/09/2026
I don’t have any tools built with biomart but definitely remember using it a ton back in the day… but Ensembl is making some choices. (too strong to say they’re killing biomart?) support.bioconductor.org/p/9163690/#9...
support.bioconductor.org
BioMart errors - Error in file.exists(file) : invalid 'file' argument + 404 hosts
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Ben Neely @benneely.com · 02/09/2026
So the hackathon projects are open and looking super cool. Obviously I am partial to the one me and @magnuspalmblad.bsky.social are doing on GROUNDING.md, but these other ones look amazing! github.com/EuBIC/EuBIC2...
github.com
EuBIC EuBIC2027 Hackathon Proposals · Discussions
Explore the GitHub Discussions forum for EuBIC EuBIC2027 in the Hackathon Proposals category.
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Ben Neely @benneely.com · 02/09/2026
Got to see Laura Herring IRL today, in Chucktown! No offense to other peeps at Waters but she’s my fav Waters person now.
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US HUPO @us-hupo.org · 26/08/2026
🧬 What are we measuring—and what should we measure? Join Dr. Phillip Owens III, Dr. Sasha Singh & Dr. Nathan Basisty for “Pride, Prejudice and Plasma: Lessons from History for Modern Proteomics.” Register Now: us02web.zoom.us/webinar/register/WN… #USHUPO #Proteomics
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Ben Neely @benneely.com · 28/08/2026
1) "vibe coding" in my domain is fun but is impossible out of my domain, like I am just clicking buttons. This is obvious, but its really striking. 2) Working with LLMs means my brain isn't the limit, which means I am behind on all my little tasks I normally do when I need to take brain breaks.
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Ben Neely @benneely.com · 27/08/2026
I haven’t worked at MUSC for 10 years, yet my name is still in front of my old building. But I am in good company. Just glancing I know Tom and Adam (at least) retired and Jennifer is now at Florida (you’ll remember her and snot from #THEProteomicsShow).
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Ben Neely @benneely.com · 27/08/2026
Not science: their first studio album bombed, so they went their seperate ways (school in US, singing in England), but one song was popular. Their producer took it and remixed it into a proto psychedelic masterpiece without their knowledge, hence rocketing Sound of Silence and the duo to success.
musicradar.com
“Ahhh, what a tune! It has more melodic genius and simple power than I ever realised”: The melancholy classic that made Paul Simon and Art Garfunkel the world’s hottest songwriting duo
Recorded in '64 then remixed and rereleased by popular demand in '65, The Sound Of Silence gave the songwriting duo their first number one and a track beloved by generations
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Ben Neely @benneely.com · 26/08/2026
Aside from her personal story (what was it, the coat of many colors?) and imagination library (which we got for my 3 kids), and her support of Appalachia (including gatlinburg after the fire), and just being great and kind according to anyone who knew her, this article is a great recap.
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Ben Neely @benneely.com · 25/08/2026
Not science: you can guess what we’re watching tonight. (And searching with this movie’s title does NOT give the results I wanted)
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Ben Neely @benneely.com · 25/08/2026
I’m sporadically working on this, and good news is I’ve learned so much about how different tools estimate mass error anr digestion efficiency and different ways to go from delta masses to actual PTMs. @pwilmarth.bsky.social timely post on deam (NQ) was a help. Am I building something useful? Maybe.
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Ben Neely @benneely.com · 22/08/2026
Not science: I’ve been looking for Durkee’s for a while at different places as we ran out, and just thought I was missing it. Nope, they stopped making it and I’m the last to know apparently. gardenandgun.com/for-the-love...
gardenandgun.com
For the Love of Durkee’s
This tangy, 168-year-old condiment might hail from up north, but it’s a Southerner’s secret weapon
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Ben Neely @benneely.com · 22/08/2026
I coded a lot in 2010s in matlab and I’d spend serious time thinking about an assumption for > or >=, or coming up with clever ways to transform/move data. It was legit building. Now coding is building context not code, and it’s still rewarding in the since you make things, but totally not the same.
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Ben Neely @benneely.com · 21/08/2026
I can’t say how often I have used common tree, even with all its old school jank it gives me the info I need.
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Ben Neely @benneely.com · 20/08/2026
To all: I think we need more voices in science, and not necessarily in short form on social platforms. So this is my plea for you to start a blog (bring back the aughts' blog rings!). Use this template, it comes with an easy compose window so no markdown or commit(ment) needed. neely.github.io/hyde/
neely.github.io
Hyde
I never wrote up the other repo I actually use the most, which is Hyde, the thing this blog runs on. Btw, now is the time to start YOUR blog, really.
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Ben Neely @benneely.com · 20/08/2026
For you PDV and Sage (via @michaellazear.bsky.social) proteomic analysis lovers out there, they now work together in the latest PDV version: github.com/wenbostar/PD... Big thanks to Bo Zhang for getting to this so quick.
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Ben Neely @benneely.com · 18/08/2026
Not science: just finished Ursula Le Guin’s Rocannon’s World (audiobook) and though the narrator grated me at the start, my gods her prose is gorgeous, efficient, and elegant all at once.
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Ben Neely @benneely.com · 15/08/2026
The answer is always overlay. Be it eLife model or whatever, get the data/results/paper out to preprint etc. and then have a system focused on verification (not 3 rando over worked and very fallible reviewers) provide confidence. And omg, people might have to read and make value judgements, or AI 😢😭
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Ben Neely @benneely.com · 14/08/2026
"Had he known that [this] was no secret, Cohen might have given up too soon. “I think I had a lot of confidence because I didn’t know other people had tried it,” he said." I think about this a lot, how researchers stop or get stopped when it is personally interesting because of priors. Don't stop.
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Ben Neely @benneely.com · 14/08/2026
Also, how long has there been a metaP fasta generation button in fragpipe, @nesvilab.bsky.social?
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Ben Neely @benneely.com · 13/08/2026
Am I on a metaP kick? Yes. So these things are on my mind and some papers are there too. This one seems fun for fasta generation, which is the evergreen issue of metaP. www.biorxiv.org/content/10.6...
biorxiv.org
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Ben Neely @benneely.com · 13/08/2026
As a huge fan of Joe versus the Volcano and spend a lot of time with Claude Code these days (we are evaluating things at work)… and everytime I see this line I can’t help but think of Meg Ryan.
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Ben Neely @benneely.com · 11/08/2026
A random request, which I might have to just email some people directly since I don't know who all is here anymore, but does anyone have Byonic Preview and would mind running three files for me? I need some sort of a ground truth for a comparison.
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Ben Neely @benneely.com · 11/08/2026
All the poop! Seriously, this is a pretty fun paper from the looks of it. www.nature.com/articles/s41...
nature.com
Systematic evaluation of PASEF acquisition strategies in complex metaproteomes - Nature Communications
Metaproteomics uniquely reveals microbes’ and host cells’ function, therefore the ecosystem’s health. Decoding this complex dialogue requires optimal methods. Here, the authors benchmark five PASEF st...
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Ben Neely @benneely.com · 11/08/2026
I am not 100% sure what the news from OSF means, but no new projects after Nov 2026 and then after Feb 2027 everything will be read only. www.cos.io/product-road...
cos.io
Product Roadmap
COS builds open source infrastructure to support our mission of increasing transparency, openness and reproducibility.
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Ben Neely @benneely.com · 11/08/2026
I always forget how dark late 80s movies are: Big, his mom thinks he’s kidnapped for ~2 months; Mrs. Doubtfire, after a divorce a dad must go in drag to visit his kids; Neverending story, the whole background story is divorce… and there’s more. archive.org/details/msdo...
archive.org
CAVERN OF THE EVIL WIZARD
An oldschool MS-DOS graphical text adventure with 4 color CGA graphics. This game is loosely based upon the game that appears in the 1988 movie BIG, with Tom Hanks.
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Ben Neely @benneely.com · 07/08/2026
🚨Breaking news🚨: I have also broken containment.
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