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
#AminoAcidAdvent Day 5: Threonine (Thr; T)
This essential amino acid was the last of "the 20" discovered, with no relation to the number 3 (sorry Jack White), but 1 of our 3 phosphomusketeers (TM). Dayhoff gave it the honors of T cause it was more frequent than the other T's... take that Y and W!
This essential amino acid was the last of "the 20" discovered, with no relation to the number 3 (sorry Jack White), but 1 of our 3 phosphomusketeers (TM). Dayhoff gave it the honors of T cause it was more frequent than the other T's... take that Y and W!
December 8, 2025 at 1:09 PM
#AminoAcidAdvent Day 5: Threonine (Thr; T)
This essential amino acid was the last of "the 20" discovered, with no relation to the number 3 (sorry Jack White), but 1 of our 3 phosphomusketeers (TM). Dayhoff gave it the honors of T cause it was more frequent than the other T's... take that Y and W!
This essential amino acid was the last of "the 20" discovered, with no relation to the number 3 (sorry Jack White), but 1 of our 3 phosphomusketeers (TM). Dayhoff gave it the honors of T cause it was more frequent than the other T's... take that Y and W!
#AminoAcidAdvent Day 4: Methionine (Met; M)
Arguably the bane of mass spectrometrists, always oxidizing and throwing off your mass. This easily remembered (1 of the 6 unique first letters) stinky essential amino acid is also often overlooked as a common off-target reaction of alkylation reagents. 😱
Arguably the bane of mass spectrometrists, always oxidizing and throwing off your mass. This easily remembered (1 of the 6 unique first letters) stinky essential amino acid is also often overlooked as a common off-target reaction of alkylation reagents. 😱
December 7, 2025 at 12:41 PM
#AminoAcidAdvent Day 4: Methionine (Met; M)
Arguably the bane of mass spectrometrists, always oxidizing and throwing off your mass. This easily remembered (1 of the 6 unique first letters) stinky essential amino acid is also often overlooked as a common off-target reaction of alkylation reagents. 😱
Arguably the bane of mass spectrometrists, always oxidizing and throwing off your mass. This easily remembered (1 of the 6 unique first letters) stinky essential amino acid is also often overlooked as a common off-target reaction of alkylation reagents. 😱
#AminoAcidAdvent Day 3: Tryptophan (Trp; W)
An essential amino acid in foods like turkey, used for notable compounds like serotonin and melatonin.
I remember W because it is weird and the backbone looks like a W. But no, it was called W because “tWiptophan (or, contains Double ring)”. Dayhoff!
An essential amino acid in foods like turkey, used for notable compounds like serotonin and melatonin.
I remember W because it is weird and the backbone looks like a W. But no, it was called W because “tWiptophan (or, contains Double ring)”. Dayhoff!
December 6, 2025 at 12:56 PM
#AminoAcidAdvent Day 3: Tryptophan (Trp; W)
An essential amino acid in foods like turkey, used for notable compounds like serotonin and melatonin.
I remember W because it is weird and the backbone looks like a W. But no, it was called W because “tWiptophan (or, contains Double ring)”. Dayhoff!
An essential amino acid in foods like turkey, used for notable compounds like serotonin and melatonin.
I remember W because it is weird and the backbone looks like a W. But no, it was called W because “tWiptophan (or, contains Double ring)”. Dayhoff!
#AminoAcidAdvent Day 2: Serine (Ser; S)
Is one of 6 where the first letter is unique, and one of two with hydroxyl side chains... so it is polar. Some people love it as one of the phospho musketeers.
I didn't know it was first described in silk protein:
babel.hathitrust.org/cgi/pt?id=hv...
Is one of 6 where the first letter is unique, and one of two with hydroxyl side chains... so it is polar. Some people love it as one of the phospho musketeers.
I didn't know it was first described in silk protein:
babel.hathitrust.org/cgi/pt?id=hv...
December 5, 2025 at 12:45 PM
#AminoAcidAdvent Day 2: Serine (Ser; S)
Is one of 6 where the first letter is unique, and one of two with hydroxyl side chains... so it is polar. Some people love it as one of the phospho musketeers.
I didn't know it was first described in silk protein:
babel.hathitrust.org/cgi/pt?id=hv...
Is one of 6 where the first letter is unique, and one of two with hydroxyl side chains... so it is polar. Some people love it as one of the phospho musketeers.
I didn't know it was first described in silk protein:
babel.hathitrust.org/cgi/pt?id=hv...
#AminoAcidAdvent Day 1: Proline
The kinkiest of amino acids (NSFW!), synthesized from glutamic acid, and some even call it the simplest "enzyme". Regardless, its a pro move to include the hydroxyproline variable mod if your abundant proteins have collagen domains... really, do this.
The kinkiest of amino acids (NSFW!), synthesized from glutamic acid, and some even call it the simplest "enzyme". Regardless, its a pro move to include the hydroxyproline variable mod if your abundant proteins have collagen domains... really, do this.
December 4, 2025 at 12:50 PM
#AminoAcidAdvent Day 1: Proline
The kinkiest of amino acids (NSFW!), synthesized from glutamic acid, and some even call it the simplest "enzyme". Regardless, its a pro move to include the hydroxyproline variable mod if your abundant proteins have collagen domains... really, do this.
The kinkiest of amino acids (NSFW!), synthesized from glutamic acid, and some even call it the simplest "enzyme". Regardless, its a pro move to include the hydroxyproline variable mod if your abundant proteins have collagen domains... really, do this.
Really not science: so I adored prairie home companion but had never seen anything like it live. Until right now.
www.shortwavekitsch.com
www.shortwavekitsch.com
November 30, 2025 at 10:18 PM
Really not science: so I adored prairie home companion but had never seen anything like it live. Until right now.
www.shortwavekitsch.com
www.shortwavekitsch.com
Not science: after months of not really reading (aka stress), I am late to the Dungeon Crawler Carl series and loving it. Squid Games + Hunger Games + Hitchhiker's Guide + DnD + who knows what else = this LitRPG masterpiece, and I can't put it down (read book 1 on trip). Lotsa stars/thumbs from me.
November 13, 2025 at 1:40 PM
Not science: after months of not really reading (aka stress), I am late to the Dungeon Crawler Carl series and loving it. Squid Games + Hunger Games + Hitchhiker's Guide + DnD + who knows what else = this LitRPG masterpiece, and I can't put it down (read book 1 on trip). Lotsa stars/thumbs from me.
Good news: only 370 emails made it through to my inbox. That is still alot of emails.
Bad news: if it is important, I hope they write me again, cause I am not going through 370 emails anytime soon, if at all.
Bad news: if it is important, I hope they write me again, cause I am not going through 370 emails anytime soon, if at all.
![alot [of emails] monster](https://cdn.bsky.app/img/feed_thumbnail/plain/did:plc:gl7bvz3uo4ym2fnmvgkjzeb3/bafkreiafi3qk6gq7kociv7fxixq4rrbbzozfuleihj3kmm7ighpbxucxty@jpeg)
November 13, 2025 at 12:54 PM
Good news: only 370 emails made it through to my inbox. That is still alot of emails.
Bad news: if it is important, I hope they write me again, cause I am not going through 370 emails anytime soon, if at all.
Bad news: if it is important, I hope they write me again, cause I am not going through 370 emails anytime soon, if at all.
Not science: after 2 weeks home I can confirm my dogs do a lot of sleeping during the day.
October 15, 2025 at 3:10 PM
Not science: after 2 weeks home I can confirm my dogs do a lot of sleeping during the day.
To round out this chapter, something funny was when 4 of the candidates snagged a pic together… and I think we might be a boy band now?
October 14, 2025 at 10:48 PM
To round out this chapter, something funny was when 4 of the candidates snagged a pic together… and I think we might be a boy band now?
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
synthetic-theatre.ai
October 5, 2025 at 1:03 PM
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
synthetic-theatre.ai
Continuing our highlight of the upcoming #HUPO2025 in TO, we had @mlaval6.bsky.social on #THEProteomicsShow with me and Ben @proteomicsnews.bsky.social. We don’t know hockey, but we still talked cool bioinformatics stuff. Find it wherever you find fine podcasts or here anchor.fm/theproteomic...
September 25, 2025 at 6:59 PM
Continuing our highlight of the upcoming #HUPO2025 in TO, we had @mlaval6.bsky.social on #THEProteomicsShow with me and Ben @proteomicsnews.bsky.social. We don’t know hockey, but we still talked cool bioinformatics stuff. Find it wherever you find fine podcasts or here anchor.fm/theproteomic...
I am gonna follow the way of Puddin'. Actually, I don't know what I would do, but having a garage would be cool, mostly cause I don't have one on my house.
September 24, 2025 at 7:35 PM
I am gonna follow the way of Puddin'. Actually, I don't know what I would do, but having a garage would be cool, mostly cause I don't have one on my house.
Btw, for anyone wondering if I am planning a move to Portugal, the answer is no. You might have seen me talking in Oeiras last May as I interviewed for a job at NIMSB (which was great btw), but alas, sticking around in Charleston for now. "What" am I doing in Charleston still seems pretty open.
September 24, 2025 at 12:29 PM
Btw, for anyone wondering if I am planning a move to Portugal, the answer is no. You might have seen me talking in Oeiras last May as I interviewed for a job at NIMSB (which was great btw), but alas, sticking around in Charleston for now. "What" am I doing in Charleston still seems pretty open.
We recently got to have Jennifer Geddes-McAlister on #THEProteomicsShow to chat with me and Ben @proteomicsnews.bsky.social about #HUPO2025, T-O and her research. Super fun and definitely check it out. Find it wherever you find fine podcasts, or here anchor.fm/theproteomic...
September 21, 2025 at 7:10 PM
We recently got to have Jennifer Geddes-McAlister on #THEProteomicsShow to chat with me and Ben @proteomicsnews.bsky.social about #HUPO2025, T-O and her research. Super fun and definitely check it out. Find it wherever you find fine podcasts, or here anchor.fm/theproteomic...
The promise of AI searching is huge, but sometimes it’s laughable. Ex. From the basic AI gen answer to me clicking dive deeper and the answer is the opposite.
I enjoy benign examples, but this can and does play out in very important questions.
Also, I still don’t know if Slo Mo dies.
I enjoy benign examples, but this can and does play out in very important questions.
Also, I still don’t know if Slo Mo dies.
September 9, 2025 at 12:51 AM
The promise of AI searching is huge, but sometimes it’s laughable. Ex. From the basic AI gen answer to me clicking dive deeper and the answer is the opposite.
I enjoy benign examples, but this can and does play out in very important questions.
Also, I still don’t know if Slo Mo dies.
I enjoy benign examples, but this can and does play out in very important questions.
Also, I still don’t know if Slo Mo dies.
Maybe today’s #THEProtemicsShow with me and Ben @proteomicsnews.bsky.social should be called the Genomics Show, but it’s great, for real. Olga Dudchenko from THE DNA zoo sat down with us and let us ask all sorts of dumb questions. Maybe we understand structural genomics now? Find it wherever!
September 5, 2025 at 11:44 AM
Maybe today’s #THEProtemicsShow with me and Ben @proteomicsnews.bsky.social should be called the Genomics Show, but it’s great, for real. Olga Dudchenko from THE DNA zoo sat down with us and let us ask all sorts of dumb questions. Maybe we understand structural genomics now? Find it wherever!
I am *very* belatedly finalizing my COMPARE Phase 1 analysis, and was looking for these 8 species I swear we ran. Whelp, found the SST raws on 2020-3-2, but no actual runs of my samples. What happened... oh yeah.
So that is why compare phase 1 is 31 species and not 39. whomp whomp COVID.
So that is why compare phase 1 is 31 species and not 39. whomp whomp COVID.
September 4, 2025 at 12:52 PM
I am *very* belatedly finalizing my COMPARE Phase 1 analysis, and was looking for these 8 species I swear we ran. Whelp, found the SST raws on 2020-3-2, but no actual runs of my samples. What happened... oh yeah.
So that is why compare phase 1 is 31 species and not 39. whomp whomp COVID.
So that is why compare phase 1 is 31 species and not 39. whomp whomp COVID.
I had trouble with that link so I’ll post here. (I miss far side. Feel like it used to be a constant desk calendar in my world.)
August 30, 2025 at 2:20 AM
I had trouble with that link so I’ll post here. (I miss far side. Feel like it used to be a constant desk calendar in my world.)
From chefs to forensic scientists, #THEProteomicsShow is coming at you hard. This week of Alt Proteomics had Ben @proteomicsnews.bsky.social and I talking to Ashley Spicer about proteomics in wildlife forensics… and rhino capers. Find it wherever you find fine podcast or anchor.fm/theproteomic...
August 29, 2025 at 10:41 AM
From chefs to forensic scientists, #THEProteomicsShow is coming at you hard. This week of Alt Proteomics had Ben @proteomicsnews.bsky.social and I talking to Ashley Spicer about proteomics in wildlife forensics… and rhino capers. Find it wherever you find fine podcast or anchor.fm/theproteomic...
Easy, The Expanse S04E08 around 29 minutes they put a sample in THE MACHINE (notice it wasn't an instrument) and it spits this out right away. Not as glamorous as other instances, but totally spot on with bonus points for UniProt IDs. (h/t to @alexhgo.bsky.social, right?)
August 28, 2025 at 6:26 PM
Easy, The Expanse S04E08 around 29 minutes they put a sample in THE MACHINE (notice it wasn't an instrument) and it spits this out right away. Not as glamorous as other instances, but totally spot on with bonus points for UniProt IDs. (h/t to @alexhgo.bsky.social, right?)
Today’s episode of #THEProteomicsShow with me and Ben @proteomicsnews.bsky.social had on Chef Michael Toscano, cause you know, protein. Actually had a ton more overlap with science than you might expect. 100% worth a listen. Find it wherever you find fine podcasts.
August 22, 2025 at 10:33 AM
Today’s episode of #THEProteomicsShow with me and Ben @proteomicsnews.bsky.social had on Chef Michael Toscano, cause you know, protein. Actually had a ton more overlap with science than you might expect. 100% worth a listen. Find it wherever you find fine podcasts.
“Larry, cancel my meetings for the week, we’ve got a fistful of barrels showing up.”
* we have two pods this week and I’m keeping those on schedule. Larry is my fictitious admin assistant, also know for brothers Daryl.
* we have two pods this week and I’m keeping those on schedule. Larry is my fictitious admin assistant, also know for brothers Daryl.
August 18, 2025 at 12:52 PM
“Larry, cancel my meetings for the week, we’ve got a fistful of barrels showing up.”
* we have two pods this week and I’m keeping those on schedule. Larry is my fictitious admin assistant, also know for brothers Daryl.
* we have two pods this week and I’m keeping those on schedule. Larry is my fictitious admin assistant, also know for brothers Daryl.
This week’s #THEProteomicsShow continues to explore #AltProteomics, but this time more about the data. Ben @proteomicsnews.bsky.social and I sat down with Yasset @ypriverol.bsky.social and talked about non-mass spec data and related aspects. Find it wherever you find fine podcasts and enjoy!
August 15, 2025 at 10:21 AM
This week’s #THEProteomicsShow continues to explore #AltProteomics, but this time more about the data. Ben @proteomicsnews.bsky.social and I sat down with Yasset @ypriverol.bsky.social and talked about non-mass spec data and related aspects. Find it wherever you find fine podcasts and enjoy!
Since maybe you don’t have or hate FB: a story in pictures. But yeah, it was a solid summer storm.
August 14, 2025 at 12:01 AM
Since maybe you don’t have or hate FB: a story in pictures. But yeah, it was a solid summer storm.