Ben Neely
@benneely.com
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
benjaminneely.com
Charleston, SC, USA
Pinned
Ben Neely
@benneely.com
· 9d
Me and Ben @proteomicsnews.bsky.social are bringing you some holiday science cheer with this week’s #THEProteomicsShow with @lingjun2025.bsky.social. We expect that soon everyone will want to do research they can eat, we do! Find it wherever you find fine podcasts or here anchor.fm/theproteomic...
December 31, 2025 at 6:15 PM
Did you wake up wondering how you could make tonight more nerdy, and maybe you hate things dropping* as the clock hits zero? Well this video is for you!
youtu.be/kS43BrnzetQ?...
* things dropping that I know of: balls, pickles, and flip flops (thats folly beach btw). I bet there’s more.
youtu.be/kS43BrnzetQ?...
* things dropping that I know of: balls, pickles, and flip flops (thats folly beach btw). I bet there’s more.
2026 New Year Countdown Timer with Professor Second
YouTube video by National Institute of Standards and Technology
youtu.be
December 31, 2025 at 1:01 PM
Did you wake up wondering how you could make tonight more nerdy, and maybe you hate things dropping* as the clock hits zero? Well this video is for you!
youtu.be/kS43BrnzetQ?...
* things dropping that I know of: balls, pickles, and flip flops (thats folly beach btw). I bet there’s more.
youtu.be/kS43BrnzetQ?...
* things dropping that I know of: balls, pickles, and flip flops (thats folly beach btw). I bet there’s more.
What were you fluent in when AI hit is key. Those who know things won’t lose that, and not to sound like a Luddite, the future generations seem in trouble if used too much as a crutch. There’s also the current business practice of removing entry jobs to make 5 years profit for collapse in 10 years.
Not really, no? What we label "AI" came into being long after I reached competence and fluency in my writing. Professionally it's not useful to me, other than to occasionally poke at it to understand its current state. Also there are less environmentally destructive ways to spur ideas/structure.
Have you ever been tempted, to have AI write something, then basically challenge yourself to do something better. Not just changing every word, but going in different directions & basically using it as a roadmap of what not to do?
December 31, 2025 at 12:53 PM
What were you fluent in when AI hit is key. Those who know things won’t lose that, and not to sound like a Luddite, the future generations seem in trouble if used too much as a crutch. There’s also the current business practice of removing entry jobs to make 5 years profit for collapse in 10 years.
Only 10 years later and my name is still up in the lobby. Considering how many new fancy mass specs they have now at the MUSC Proteomics Center, I wonder if i could just move back in and no one would notice?
December 29, 2025 at 2:37 PM
Only 10 years later and my name is still up in the lobby. Considering how many new fancy mass specs they have now at the MUSC Proteomics Center, I wonder if i could just move back in and no one would notice?
Make a bond movie academic
North by Northwest: finding out society journals were always better to begin with
(Backstory, this is arguably a top 5 bond film by Hitchcock released before Dr. No, the first Bond film.)
North by Northwest: finding out society journals were always better to begin with
(Backstory, this is arguably a top 5 bond film by Hitchcock released before Dr. No, the first Bond film.)
Make a Bond movie academic
Diamonds Are Forever: challenges in long-term sustainability for aspirational open access financial models
Diamonds Are Forever: challenges in long-term sustainability for aspirational open access financial models
Make a Bond movie academic
Goldfinger: Bitcoin & the Semiotics of Digital Goldbugs
Goldfinger: Bitcoin & the Semiotics of Digital Goldbugs
December 27, 2025 at 2:07 PM
Make a bond movie academic
North by Northwest: finding out society journals were always better to begin with
(Backstory, this is arguably a top 5 bond film by Hitchcock released before Dr. No, the first Bond film.)
North by Northwest: finding out society journals were always better to begin with
(Backstory, this is arguably a top 5 bond film by Hitchcock released before Dr. No, the first Bond film.)
PSA for parents (or old “kids”) giving/getting Legos: I didn’t know this till very recently, but if you open a Lego box on one side (I don’t use the finger tabs), the box becomes a self-contained Lego holder/tray. Maybe everyone but me already knew.
December 26, 2025 at 9:06 PM
PSA for parents (or old “kids”) giving/getting Legos: I didn’t know this till very recently, but if you open a Lego box on one side (I don’t use the finger tabs), the box becomes a self-contained Lego holder/tray. Maybe everyone but me already knew.
#AminoAcidAdvent Day 21: Tyrosine (Tyr; Y)
This is the end my friend, tomorrow is the big day. Gird your loins and have lots of merry on hand! tYrosine is the last of the three phosphomusketeers, a fun F derivative. Why 21? Well, U know Y.
Source for Dayhoff: biology.arizona.edu/biochemistry...
This is the end my friend, tomorrow is the big day. Gird your loins and have lots of merry on hand! tYrosine is the last of the three phosphomusketeers, a fun F derivative. Why 21? Well, U know Y.
Source for Dayhoff: biology.arizona.edu/biochemistry...
December 24, 2025 at 1:32 PM
#AminoAcidAdvent Day 21: Tyrosine (Tyr; Y)
This is the end my friend, tomorrow is the big day. Gird your loins and have lots of merry on hand! tYrosine is the last of the three phosphomusketeers, a fun F derivative. Why 21? Well, U know Y.
Source for Dayhoff: biology.arizona.edu/biochemistry...
This is the end my friend, tomorrow is the big day. Gird your loins and have lots of merry on hand! tYrosine is the last of the three phosphomusketeers, a fun F derivative. Why 21? Well, U know Y.
Source for Dayhoff: biology.arizona.edu/biochemistry...
#AminoAcidAdvent Day 20: Asparagine (Asn; N)
You know how sometimes you over do it when nogging your eggnog and you wake up feeling like ass(n), well, that’s the penultimate day of this. It’s like mini glutamine, but also maybe hydrolizes to Asp in aging 🤷♂️. FYI was asparagiN according to Dayhoff.
You know how sometimes you over do it when nogging your eggnog and you wake up feeling like ass(n), well, that’s the penultimate day of this. It’s like mini glutamine, but also maybe hydrolizes to Asp in aging 🤷♂️. FYI was asparagiN according to Dayhoff.
December 23, 2025 at 1:53 PM
#AminoAcidAdvent Day 20: Asparagine (Asn; N)
You know how sometimes you over do it when nogging your eggnog and you wake up feeling like ass(n), well, that’s the penultimate day of this. It’s like mini glutamine, but also maybe hydrolizes to Asp in aging 🤷♂️. FYI was asparagiN according to Dayhoff.
You know how sometimes you over do it when nogging your eggnog and you wake up feeling like ass(n), well, that’s the penultimate day of this. It’s like mini glutamine, but also maybe hydrolizes to Asp in aging 🤷♂️. FYI was asparagiN according to Dayhoff.
Me and Ben @proteomicsnews.bsky.social are bringing you some holiday science cheer with this week’s #THEProteomicsShow with @lingjun2025.bsky.social. We expect that soon everyone will want to do research they can eat, we do! Find it wherever you find fine podcasts or here anchor.fm/theproteomic...
December 22, 2025 at 5:12 PM
Me and Ben @proteomicsnews.bsky.social are bringing you some holiday science cheer with this week’s #THEProteomicsShow with @lingjun2025.bsky.social. We expect that soon everyone will want to do research they can eat, we do! Find it wherever you find fine podcasts or here anchor.fm/theproteomic...
Doping testing will be for non-human hemoglobin (proteomics hint hint). Funny article btw with "Lance" mice getting M101 injections, an extracellular hemoglobin from the blow lugworm with ridiculous O2 binding capacity.
(here is a 2020 paper on the molecule btw: pubmed.ncbi.nlm.nih.gov/35536914/ )
(here is a 2020 paper on the molecule btw: pubmed.ncbi.nlm.nih.gov/35536914/ )
Remember the marine worm with blood that inspired research and a medical start-up to make blood substitutes? On a sports radar for doping possibilities. Corriere reports labs are now making the molecule for doping. Can be tested for, but has short half-life www.corriere.it/sport/25_dic... (🇮🇹)
December 22, 2025 at 3:23 PM
Doping testing will be for non-human hemoglobin (proteomics hint hint). Funny article btw with "Lance" mice getting M101 injections, an extracellular hemoglobin from the blow lugworm with ridiculous O2 binding capacity.
(here is a 2020 paper on the molecule btw: pubmed.ncbi.nlm.nih.gov/35536914/ )
(here is a 2020 paper on the molecule btw: pubmed.ncbi.nlm.nih.gov/35536914/ )
#AminoAcidAdvent Day 19: Valine (Val; V)
No, this GoT reference will *not* happen. (val's name comes from similarity to an acid from a certain plant, not a rare alloy)
We will never forgive you D&D for Seasons 7 and 8!!!
In general I find it hard to get excited about branched-chain amino acids.
No, this GoT reference will *not* happen. (val's name comes from similarity to an acid from a certain plant, not a rare alloy)
We will never forgive you D&D for Seasons 7 and 8!!!
In general I find it hard to get excited about branched-chain amino acids.
December 22, 2025 at 2:16 PM
#AminoAcidAdvent Day 19: Valine (Val; V)
No, this GoT reference will *not* happen. (val's name comes from similarity to an acid from a certain plant, not a rare alloy)
We will never forgive you D&D for Seasons 7 and 8!!!
In general I find it hard to get excited about branched-chain amino acids.
No, this GoT reference will *not* happen. (val's name comes from similarity to an acid from a certain plant, not a rare alloy)
We will never forgive you D&D for Seasons 7 and 8!!!
In general I find it hard to get excited about branched-chain amino acids.
#HUPO2025 really should’ve had this kid getting by people stoked to visit. youtube.com/shorts/DZnak...
Poutine - Cooking with Carter
YouTube video by Cooking with Carter
youtube.com
December 21, 2025 at 9:33 PM
#HUPO2025 really should’ve had this kid getting by people stoked to visit. youtube.com/shorts/DZnak...
#AminoAcidAdvent Day 18: Aspartic Acid (Asp; D)
Apologies to all you Hofmann fans, there’s no fear and loathing in peptides going on here, though Dayhoff’s “asparDic” seems a bit sus. Shorter than its acid brethren, it can still cyclize, which seems biologically important. Google it, I’m on break.
Apologies to all you Hofmann fans, there’s no fear and loathing in peptides going on here, though Dayhoff’s “asparDic” seems a bit sus. Shorter than its acid brethren, it can still cyclize, which seems biologically important. Google it, I’m on break.
December 21, 2025 at 3:47 PM
#AminoAcidAdvent Day 18: Aspartic Acid (Asp; D)
Apologies to all you Hofmann fans, there’s no fear and loathing in peptides going on here, though Dayhoff’s “asparDic” seems a bit sus. Shorter than its acid brethren, it can still cyclize, which seems biologically important. Google it, I’m on break.
Apologies to all you Hofmann fans, there’s no fear and loathing in peptides going on here, though Dayhoff’s “asparDic” seems a bit sus. Shorter than its acid brethren, it can still cyclize, which seems biologically important. Google it, I’m on break.
#AminoAcidAdvent Day 17: Alanine (Ala; A)
I heard Paul Simon wanted to use Ala instead of Al, but no one got the reference. This tiny aliphatic residue is the Switzerland of amino acids (aka non-reactive), but does have some roles in structure and signaling motifs. 🤷♂️
I heard Paul Simon wanted to use Ala instead of Al, but no one got the reference. This tiny aliphatic residue is the Switzerland of amino acids (aka non-reactive), but does have some roles in structure and signaling motifs. 🤷♂️
December 20, 2025 at 2:46 PM
#AminoAcidAdvent Day 17: Alanine (Ala; A)
I heard Paul Simon wanted to use Ala instead of Al, but no one got the reference. This tiny aliphatic residue is the Switzerland of amino acids (aka non-reactive), but does have some roles in structure and signaling motifs. 🤷♂️
I heard Paul Simon wanted to use Ala instead of Al, but no one got the reference. This tiny aliphatic residue is the Switzerland of amino acids (aka non-reactive), but does have some roles in structure and signaling motifs. 🤷♂️
2 days in a row my 10 year old has written really good short stories. Pre 2022 we would instantly be amazed. But in the current world we immediately think she used some LLM. She didn’t btw.
But this has also been happening in science for a while and it stinks. The juice is not worth the squeeze.
But this has also been happening in science for a while and it stinks. The juice is not worth the squeeze.
December 19, 2025 at 10:48 PM
2 days in a row my 10 year old has written really good short stories. Pre 2022 we would instantly be amazed. But in the current world we immediately think she used some LLM. She didn’t btw.
But this has also been happening in science for a while and it stinks. The juice is not worth the squeeze.
But this has also been happening in science for a while and it stinks. The juice is not worth the squeeze.
"We're likely to see sunshine with highs in the lower 70s on Christmas Eve and Day... should be in the top ten warmest (out of over 100 Christmases as far as the 1880s)."
@ronbeavis.bsky.social it can be cold or warm... this year we are going legit warm.
@ronbeavis.bsky.social it can be cold or warm... this year we are going legit warm.
December 19, 2025 at 5:05 PM
"We're likely to see sunshine with highs in the lower 70s on Christmas Eve and Day... should be in the top ten warmest (out of over 100 Christmases as far as the 1880s)."
@ronbeavis.bsky.social it can be cold or warm... this year we are going legit warm.
@ronbeavis.bsky.social it can be cold or warm... this year we are going legit warm.
#AminoAcidAdvent Day 16: Phenylalanine (Phe; F)
If you like it then you should've put a ring on it (i.e., alanine). This essential hydrophobic amino acid is often buried inside protein structures, and is useful to make tyrosine.
Dayhoff named F cause P was taken and the obvious phonetics.
If you like it then you should've put a ring on it (i.e., alanine). This essential hydrophobic amino acid is often buried inside protein structures, and is useful to make tyrosine.
Dayhoff named F cause P was taken and the obvious phonetics.
December 19, 2025 at 1:49 PM
#AminoAcidAdvent Day 16: Phenylalanine (Phe; F)
If you like it then you should've put a ring on it (i.e., alanine). This essential hydrophobic amino acid is often buried inside protein structures, and is useful to make tyrosine.
Dayhoff named F cause P was taken and the obvious phonetics.
If you like it then you should've put a ring on it (i.e., alanine). This essential hydrophobic amino acid is often buried inside protein structures, and is useful to make tyrosine.
Dayhoff named F cause P was taken and the obvious phonetics.
Not science: the late great Sharon Jones has the best holiday album ever and I strongly encourage listening.
youtu.be/iRENaUQc5No?...
youtu.be/iRENaUQc5No?...
Sharon Jones & The Dap-Kings: Tiny Desk Concert
YouTube video by NPR Music
youtu.be
December 18, 2025 at 11:03 PM
Not science: the late great Sharon Jones has the best holiday album ever and I strongly encourage listening.
youtu.be/iRENaUQc5No?...
youtu.be/iRENaUQc5No?...
#AminoAcidAdvent Day 15: Glutamic Acid (Glu; E)
Don't get too excited about this tasty amino acid! Dayhoff wasn't thinking just about about gluE but also "glutamEke" when naming it. And yes, this terminal residue will cyclize to pyro-Glu with loss of water (like Q), so be warned search algorithms.
Don't get too excited about this tasty amino acid! Dayhoff wasn't thinking just about about gluE but also "glutamEke" when naming it. And yes, this terminal residue will cyclize to pyro-Glu with loss of water (like Q), so be warned search algorithms.
December 18, 2025 at 2:22 PM
#AminoAcidAdvent Day 15: Glutamic Acid (Glu; E)
Don't get too excited about this tasty amino acid! Dayhoff wasn't thinking just about about gluE but also "glutamEke" when naming it. And yes, this terminal residue will cyclize to pyro-Glu with loss of water (like Q), so be warned search algorithms.
Don't get too excited about this tasty amino acid! Dayhoff wasn't thinking just about about gluE but also "glutamEke" when naming it. And yes, this terminal residue will cyclize to pyro-Glu with loss of water (like Q), so be warned search algorithms.
#AminoAcidAdvent Day 14: Glutamine (Gln; Q)
Maybe one of the funnier Dayhoff naming moments ("Q-tamine"), this amide of glutamic acid will spontaneously cyclize and deamidate when on the N-terminus (not a rare event! Ig beware)... making this new post-doc convinced his SIS peptide was contaminated.
Maybe one of the funnier Dayhoff naming moments ("Q-tamine"), this amide of glutamic acid will spontaneously cyclize and deamidate when on the N-terminus (not a rare event! Ig beware)... making this new post-doc convinced his SIS peptide was contaminated.
December 17, 2025 at 1:19 PM
#AminoAcidAdvent Day 14: Glutamine (Gln; Q)
Maybe one of the funnier Dayhoff naming moments ("Q-tamine"), this amide of glutamic acid will spontaneously cyclize and deamidate when on the N-terminus (not a rare event! Ig beware)... making this new post-doc convinced his SIS peptide was contaminated.
Maybe one of the funnier Dayhoff naming moments ("Q-tamine"), this amide of glutamic acid will spontaneously cyclize and deamidate when on the N-terminus (not a rare event! Ig beware)... making this new post-doc convinced his SIS peptide was contaminated.
Reposted by Ben Neely
Experience in #archaeological #proteomics?
Interested in #Roman economy / organic artefacts?
Background in data analysis for #ZooMS?
Then apply for a 3-year RA post working to join PELLIS project with the wonderful @gtaylortu.bsky.social to investigate Roman leather economy
Apply by 12/01/2026
Interested in #Roman economy / organic artefacts?
Background in data analysis for #ZooMS?
Then apply for a 3-year RA post working to join PELLIS project with the wonderful @gtaylortu.bsky.social to investigate Roman leather economy
Apply by 12/01/2026
T: 01642 342201
E: HRrecruitment@tees.ac.uk
tuwpapps.tees.ac.uk
December 16, 2025 at 2:39 PM
Experience in #archaeological #proteomics?
Interested in #Roman economy / organic artefacts?
Background in data analysis for #ZooMS?
Then apply for a 3-year RA post working to join PELLIS project with the wonderful @gtaylortu.bsky.social to investigate Roman leather economy
Apply by 12/01/2026
Interested in #Roman economy / organic artefacts?
Background in data analysis for #ZooMS?
Then apply for a 3-year RA post working to join PELLIS project with the wonderful @gtaylortu.bsky.social to investigate Roman leather economy
Apply by 12/01/2026
My fav memory in grad school was coming in early before anyone was in the lab, sitting at my bench planning experiments or making media, with my back to the window as the sun came up over the marsh. Weirdly I work in this building now, though they’ve blocked my old window (and that PI is long gone).
December 17, 2025 at 12:39 PM
My fav memory in grad school was coming in early before anyone was in the lab, sitting at my bench planning experiments or making media, with my back to the window as the sun came up over the marsh. Weirdly I work in this building now, though they’ve blocked my old window (and that PI is long gone).
Whoa, I didn’t know DIA was for more than proteomics now. It’s also one of those new agentic AI web browser things no one wants. Wohoo.
www.diabrowser.com
www.diabrowser.com
Dia Browser | AI Chat With Your Tabs
Dia is the AI browser from The Browser Company. Chat with your tabs, write in your own voice, learn and plan faster, shop, and more — all with privacy that you control.
www.diabrowser.com
December 17, 2025 at 2:00 AM
Whoa, I didn’t know DIA was for more than proteomics now. It’s also one of those new agentic AI web browser things no one wants. Wohoo.
www.diabrowser.com
www.diabrowser.com
I’m friends with one of the guys mentioned (James), but it really is a wild thing that there’s a whole passionate community spending decades trying to find these treasures, and all the hoops they must jump through to even test their ideas. No banging through stone floors as a librarian stamps books.
A hidden treasure was buried in Charleston decades ago. A Summerville man thinks he's found it. www.postandcourier.com/charleston_s...
A hidden treasure was buried in Charleston decades ago. A Summerville man thinks he's found it.
Summerville resident Chris Enfinger believes treasure referenced in Byron Preiss’s “The Secret” is buried somewhere at Patriots Point in Mount Pleasant.
www.postandcourier.com
December 16, 2025 at 5:16 PM
I’m friends with one of the guys mentioned (James), but it really is a wild thing that there’s a whole passionate community spending decades trying to find these treasures, and all the hoops they must jump through to even test their ideas. No banging through stone floors as a librarian stamps books.
#AminoAcidAdvent Day 13: Selonocystein (Sec; U)
Not one of the classic 20 but U love it! Fenyo and @ronbeavis.bsky.social showed you need to think about its alkylation (Unimod #1008). Pro tip 2: check that the MS1 agrees with Se-78 and Se-80 abundance (it might not).
pubs.acs.org/doi/10.1021/...
Not one of the classic 20 but U love it! Fenyo and @ronbeavis.bsky.social showed you need to think about its alkylation (Unimod #1008). Pro tip 2: check that the MS1 agrees with Se-78 and Se-80 abundance (it might not).
pubs.acs.org/doi/10.1021/...
December 16, 2025 at 1:01 PM
#AminoAcidAdvent Day 13: Selonocystein (Sec; U)
Not one of the classic 20 but U love it! Fenyo and @ronbeavis.bsky.social showed you need to think about its alkylation (Unimod #1008). Pro tip 2: check that the MS1 agrees with Se-78 and Se-80 abundance (it might not).
pubs.acs.org/doi/10.1021/...
Not one of the classic 20 but U love it! Fenyo and @ronbeavis.bsky.social showed you need to think about its alkylation (Unimod #1008). Pro tip 2: check that the MS1 agrees with Se-78 and Se-80 abundance (it might not).
pubs.acs.org/doi/10.1021/...