Harrison Specht
@harrisons.bsky.social
Exploring biology with mass spectrometry
Reposted by Harrison Specht
Spatial Proteomics Workshop for Protists
(see more in thread below)
Registration
Early Bird Monday 22nd June 2026.
Regular Monday 10th August 2026.
There will be a conference dinner on day 1. To register visit protistology.org.uk/autumn-meeti...
(see more in thread below)
Registration
Early Bird Monday 22nd June 2026.
Regular Monday 10th August 2026.
There will be a conference dinner on day 1. To register visit protistology.org.uk/autumn-meeti...
February 6, 2026 at 6:11 PM
Spatial Proteomics Workshop for Protists
(see more in thread below)
Registration
Early Bird Monday 22nd June 2026.
Regular Monday 10th August 2026.
There will be a conference dinner on day 1. To register visit protistology.org.uk/autumn-meeti...
(see more in thread below)
Registration
Early Bird Monday 22nd June 2026.
Regular Monday 10th August 2026.
There will be a conference dinner on day 1. To register visit protistology.org.uk/autumn-meeti...
Reposted by Harrison Specht
Aside from the whisper network, how are #teammassspec finding out how much certain instrument models are down for (service delays, backordered parts, things breaking all the time, etc)?
February 3, 2026 at 8:46 AM
Aside from the whisper network, how are #teammassspec finding out how much certain instrument models are down for (service delays, backordered parts, things breaking all the time, etc)?
Reposted by Harrison Specht
Applications are now open for @olgavitek.bsky.social 's May Intitute on computation and statistics for mass spectrometry and proteomics at @northeasternu.bsky.social !
--> computationalproteomics.khoury.northeastern.edu
--> computationalproteomics.khoury.northeastern.edu
May Institute – Computation and statistics for mass spectrometry and proteomics
computationalproteomics.khoury.northeastern.edu
January 20, 2026 at 11:26 PM
Applications are now open for @olgavitek.bsky.social 's May Intitute on computation and statistics for mass spectrometry and proteomics at @northeasternu.bsky.social !
--> computationalproteomics.khoury.northeastern.edu
--> computationalproteomics.khoury.northeastern.edu
Reposted by Harrison Specht
#AminoAcidAdvent Day 6: Cysteine (Cys; C)
Like Mork & Mindy, these stinky residues love to bond! Jerks like us break these bonds, with chemoproteomics trying to map, probe, and manipulate them. Leftovers stuck to S-S is a fun field but I love them for their antioxidant and metal binding abilities.
Like Mork & Mindy, these stinky residues love to bond! Jerks like us break these bonds, with chemoproteomics trying to map, probe, and manipulate them. Leftovers stuck to S-S is a fun field but I love them for their antioxidant and metal binding abilities.
December 9, 2025 at 1:41 PM
#AminoAcidAdvent Day 6: Cysteine (Cys; C)
Like Mork & Mindy, these stinky residues love to bond! Jerks like us break these bonds, with chemoproteomics trying to map, probe, and manipulate them. Leftovers stuck to S-S is a fun field but I love them for their antioxidant and metal binding abilities.
Like Mork & Mindy, these stinky residues love to bond! Jerks like us break these bonds, with chemoproteomics trying to map, probe, and manipulate them. Leftovers stuck to S-S is a fun field but I love them for their antioxidant and metal binding abilities.
Reposted by Harrison Specht
Exciting new #Zebrafish research from the #WeinsteinLab, led by Jong Park!
“Specialized gas-exchange endothelium of the zebrafish gill” —
www.biorxiv.org/content/10.6...
Amazing to see red blood cells moving through the gills! Don’t forget to check out the supplemental movies ;-)
“Specialized gas-exchange endothelium of the zebrafish gill” —
www.biorxiv.org/content/10.6...
Amazing to see red blood cells moving through the gills! Don’t forget to check out the supplemental movies ;-)
December 2, 2025 at 10:48 PM
Exciting new #Zebrafish research from the #WeinsteinLab, led by Jong Park!
“Specialized gas-exchange endothelium of the zebrafish gill” —
www.biorxiv.org/content/10.6...
Amazing to see red blood cells moving through the gills! Don’t forget to check out the supplemental movies ;-)
“Specialized gas-exchange endothelium of the zebrafish gill” —
www.biorxiv.org/content/10.6...
Amazing to see red blood cells moving through the gills! Don’t forget to check out the supplemental movies ;-)
Reposted by Harrison Specht
The 2026 Chemistry Faculty Jobs List has 330 tenure-track positions and 47 teaching-only positions: docs.google.com/spreadsheets... #facultychemjobs #chemsky #chemchat ⚗️🧪
The 2026 Chemistry Faculty Jobs List
docs.google.com
November 25, 2025 at 7:56 PM
The 2026 Chemistry Faculty Jobs List has 330 tenure-track positions and 47 teaching-only positions: docs.google.com/spreadsheets... #facultychemjobs #chemsky #chemchat ⚗️🧪
Reposted by Harrison Specht
one of the coolest things about ChatGPT is how you can actually just never use it. you can fill your whole entire life with simply not once using it. it's incredible.
November 25, 2025 at 4:15 PM
one of the coolest things about ChatGPT is how you can actually just never use it. you can fill your whole entire life with simply not once using it. it's incredible.
So which AI peer review tool can tell me authors gave all the Code to make their Figures? 🧪
✅ Code uses right functions for plot type in Figure?
✅ Is there a 1:1 correspondence between Code and Figures?
❌ Automated reanalysis --> IMO this requires expert knowledge to know the data wasn't hacked
✅ Code uses right functions for plot type in Figure?
✅ Is there a 1:1 correspondence between Code and Figures?
❌ Automated reanalysis --> IMO this requires expert knowledge to know the data wasn't hacked
November 21, 2025 at 3:29 PM
So which AI peer review tool can tell me authors gave all the Code to make their Figures? 🧪
✅ Code uses right functions for plot type in Figure?
✅ Is there a 1:1 correspondence between Code and Figures?
❌ Automated reanalysis --> IMO this requires expert knowledge to know the data wasn't hacked
✅ Code uses right functions for plot type in Figure?
✅ Is there a 1:1 correspondence between Code and Figures?
❌ Automated reanalysis --> IMO this requires expert knowledge to know the data wasn't hacked
Proteomics + an elegant mechanism! I cannot wait to read in full! #proteomics #TeamMassSpec 🧪
Great to see Brenda Schulman’s team post their new bioRxiv paper. MS-based proteomics helped uncover a beautifully simple mechanism: cysteine levels tune metabolism by flipping the inverse stability of LRRC58 and its substrate CDO1.
www.biorxiv.org/content/bior...
www.biorxiv.org/content/bior...
www.biorxiv.org
November 17, 2025 at 2:54 PM
Proteomics + an elegant mechanism! I cannot wait to read in full! #proteomics #TeamMassSpec 🧪
Reposted by Harrison Specht
No one is immune to aging but what exactly happens to our immune system as it ages? @thibaultcolombani.bsky.social takes a molecular dive into the immune system and talks about understanding age-induced immune altercations through single-cell proteomics.
www.youtube.com/watch?v=WUU1...
www.youtube.com/watch?v=WUU1...
November 13, 2025 at 7:02 PM
No one is immune to aging but what exactly happens to our immune system as it ages? @thibaultcolombani.bsky.social takes a molecular dive into the immune system and talks about understanding age-induced immune altercations through single-cell proteomics.
www.youtube.com/watch?v=WUU1...
www.youtube.com/watch?v=WUU1...
Check out our new blog post on barcodes and the future of quickly measuring proteins for biomedical research! 🧪
www.parallelsq.org/blog/barcode...
www.parallelsq.org/blog/barcode...
Barcodes and the future of measuring proteins - PTI - Parallel Squared Technology Institute
Increasing the rate at which we measure proteins increases the rate at which we can discover new biology and solve disease.
www.parallelsq.org
November 12, 2025 at 3:14 PM
Check out our new blog post on barcodes and the future of quickly measuring proteins for biomedical research! 🧪
www.parallelsq.org/blog/barcode...
www.parallelsq.org/blog/barcode...
Reposted by Harrison Specht
Exited to share our latest work! Out now in @natcomms.nature.com
Koina aims to transform how #proteomics uses machine learning. You no longer need to be a tech wizard to use ML and now can easily run #ML models. Integrated with FragPipe, Skyline and EncyclopeDIA!
www.nature.com/articles/s41...
Koina aims to transform how #proteomics uses machine learning. You no longer need to be a tech wizard to use ML and now can easily run #ML models. Integrated with FragPipe, Skyline and EncyclopeDIA!
www.nature.com/articles/s41...
Koina: Democratizing machine learning for proteomics research - Nature Communications
Koina is an open-source, online platform that simplifies access to machine learning models in proteomics, enabling easier integration into analysis tools and helping researchers adopt and reuse ML mod...
www.nature.com
November 11, 2025 at 8:06 PM
Exited to share our latest work! Out now in @natcomms.nature.com
Koina aims to transform how #proteomics uses machine learning. You no longer need to be a tech wizard to use ML and now can easily run #ML models. Integrated with FragPipe, Skyline and EncyclopeDIA!
www.nature.com/articles/s41...
Koina aims to transform how #proteomics uses machine learning. You no longer need to be a tech wizard to use ML and now can easily run #ML models. Integrated with FragPipe, Skyline and EncyclopeDIA!
www.nature.com/articles/s41...
Reposted by Harrison Specht
May Institute on Computation & Statistics for MS and Proteomics is taking great shape. Fantastic new and repeat instructors and lots of new content. We are grateful to our sponsors Fragmatics and Biognosys. Keep an eye on the website computationalproteomics.khoury.northeastern.edu
November 10, 2025 at 4:39 PM
May Institute on Computation & Statistics for MS and Proteomics is taking great shape. Fantastic new and repeat instructors and lots of new content. We are grateful to our sponsors Fragmatics and Biognosys. Keep an eye on the website computationalproteomics.khoury.northeastern.edu
🧪 Two of my favorite sci-things!
Already run q.e.d on my latest bioRxiv submissions :)
Already run q.e.d on my latest bioRxiv submissions :)
Excited to launch an openRxiv partnership with the scientist-run AI review service qed (@qedscience.bsky.social), the brainchild of @odedrechavi.bsky.social 1/n
openrxiv.org/enabling-rev...
openrxiv.org/enabling-rev...
Enabling options for review: from training and transparency to author-centered AI tools - openRxiv
Peer review is widely viewed as a critical aspect of biomedical communication. Ideally, it provides authors with feedback so they can improve manuscripts and gives readers, particularly nonspecialists...
openrxiv.org
November 7, 2025 at 12:57 PM
🧪 Two of my favorite sci-things!
Already run q.e.d on my latest bioRxiv submissions :)
Already run q.e.d on my latest bioRxiv submissions :)
Reposted by Harrison Specht
🎓 Upcoming Online Course: R/Bioconductor for Mass Spectrometry & Proteomics
📅 November 17–19, 2025
Join Dr Laurent Gatto for a hands-on course on mass spectrometry–based proteomics analysis using R and Bioconductor.
👉 Register & learn more: www.physalia-courses.org/courses-work...
📅 November 17–19, 2025
Join Dr Laurent Gatto for a hands-on course on mass spectrometry–based proteomics analysis using R and Bioconductor.
👉 Register & learn more: www.physalia-courses.org/courses-work...
R/Bioconductor for Mass Spectrometry and Proteomics
Dates 17-19 November 2025 To foster international participation, this course will be held online
www.physalia-courses.org
November 6, 2025 at 10:00 AM
🎓 Upcoming Online Course: R/Bioconductor for Mass Spectrometry & Proteomics
📅 November 17–19, 2025
Join Dr Laurent Gatto for a hands-on course on mass spectrometry–based proteomics analysis using R and Bioconductor.
👉 Register & learn more: www.physalia-courses.org/courses-work...
📅 November 17–19, 2025
Join Dr Laurent Gatto for a hands-on course on mass spectrometry–based proteomics analysis using R and Bioconductor.
👉 Register & learn more: www.physalia-courses.org/courses-work...
Thanks!
Not yet, but I wouldn't expect huge benefits over the default LF models unless you are trying some exotic chromatography, collision energies or additives.
Not yet, but I wouldn't expect huge benefits over the default LF models unless you are trying some exotic chromatography, collision energies or additives.
November 4, 2025 at 6:37 PM
Thanks!
Not yet, but I wouldn't expect huge benefits over the default LF models unless you are trying some exotic chromatography, collision energies or additives.
Not yet, but I wouldn't expect huge benefits over the default LF models unless you are trying some exotic chromatography, collision energies or additives.
#Proteomics Tutorial drop!
Had fun writing this, ping me if interested in other search engines. #TeamMassSpec
www.parallelsq.org/blog/fantast...
Had fun writing this, ping me if interested in other search engines. #TeamMassSpec
www.parallelsq.org/blog/fantast...
Fantastic Proteins and Where to Find Them - PTI - Parallel Squared Technology Institute
Here, we will offer a tutorial for how to build instrument-specific spectral library predictions for PSMtag modified peptides using DIA-NN 2.3.0. This will allow users to do more accurate proteome-wid...
www.parallelsq.org
November 4, 2025 at 4:47 PM
#Proteomics Tutorial drop!
Had fun writing this, ping me if interested in other search engines. #TeamMassSpec
www.parallelsq.org/blog/fantast...
Had fun writing this, ping me if interested in other search engines. #TeamMassSpec
www.parallelsq.org/blog/fantast...
A bit dense, but the important message is dead simple:
We got to cite the E = mc² paper!
Kidding :)
The important part is that combinations of isotopes unlock 100-1000x gains in protein measurement speed.
Here's how: www.biorxiv.org/content/10.1...
#TeamMassSpec #Proteomics 🧪
We got to cite the E = mc² paper!
Kidding :)
The important part is that combinations of isotopes unlock 100-1000x gains in protein measurement speed.
Here's how: www.biorxiv.org/content/10.1...
#TeamMassSpec #Proteomics 🧪
How to design 1000-plex mass tags using the differential mass defect
Multiplexing samples in mass spectrometry-based proteomics has long been accomplished by isotopologues of small molecules. These chemically-identical "mass tags" conjugate to peptides to encode sample...
www.biorxiv.org
October 24, 2025 at 2:08 PM
A bit dense, but the important message is dead simple:
We got to cite the E = mc² paper!
Kidding :)
The important part is that combinations of isotopes unlock 100-1000x gains in protein measurement speed.
Here's how: www.biorxiv.org/content/10.1...
#TeamMassSpec #Proteomics 🧪
We got to cite the E = mc² paper!
Kidding :)
The important part is that combinations of isotopes unlock 100-1000x gains in protein measurement speed.
Here's how: www.biorxiv.org/content/10.1...
#TeamMassSpec #Proteomics 🧪
🧪🔥🔥🔥
Some researchers get their boost from papers or grants.
My adrenaline rush comes from pull requests and seeing others use our tools.
I got two happiness shots today:
- www.nature.com/articles/s41... using #quantms
- github.com/PRIDE-Archiv... new PR to #pridepy tool
☕🔥
My adrenaline rush comes from pull requests and seeing others use our tools.
I got two happiness shots today:
- www.nature.com/articles/s41... using #quantms
- github.com/PRIDE-Archiv... new PR to #pridepy tool
☕🔥
Activity-targeted metaproteomics uncovers rare syntrophic bacteria central to anaerobic community metabolism - Nature Microbiology
An approach combining BONCAT, stable isotope probing and metaproteomics showcases the hidden metabolic interconnectivity of microorganisms within an anaerobic digestion community.
www.nature.com
October 22, 2025 at 6:56 PM
🧪🔥🔥🔥
Reposted by Harrison Specht
AlphaDIA enables DIA transfer learning for feature-free proteomics - @mannlab.bsky.social @jalew188.bsky.social go.nature.com/4qmEQMM
AlphaDIA enables DIA transfer learning for feature-free proteomics - Nature Biotechnology
An open-source platform for data-independent acquisition proteomics adapts predicted libraries to experimental settings.
go.nature.com
October 21, 2025 at 4:53 PM
AlphaDIA enables DIA transfer learning for feature-free proteomics - @mannlab.bsky.social @jalew188.bsky.social go.nature.com/4qmEQMM
🧪 I tried it and I'm happily surprised!
As long as it doesn't boil the oceans, I would run it on all new papers I read for:
🌎 Mapping the interrelatedness of claims -- papers are so complex now!
🔬 Calling out potential gaps -- so that I can know the experiments were properly controlled.
As long as it doesn't boil the oceans, I would run it on all new papers I read for:
🌎 Mapping the interrelatedness of claims -- papers are so complex now!
🔬 Calling out potential gaps -- so that I can know the experiments were properly controlled.
October 20, 2025 at 9:37 PM
🧪 I tried it and I'm happily surprised!
As long as it doesn't boil the oceans, I would run it on all new papers I read for:
🌎 Mapping the interrelatedness of claims -- papers are so complex now!
🔬 Calling out potential gaps -- so that I can know the experiments were properly controlled.
As long as it doesn't boil the oceans, I would run it on all new papers I read for:
🌎 Mapping the interrelatedness of claims -- papers are so complex now!
🔬 Calling out potential gaps -- so that I can know the experiments were properly controlled.
Reposted by Harrison Specht
And, we are back with another presentation from this year's Research Fest. PTI's Senior Computational Scientist, Kevin McDonnell, talks about developing joint modeling (aka JMod) of mass spectra for empowering multiplexed DIA proteomics.
www.youtube.com/watch?v=plK4...
www.youtube.com/watch?v=plK4...
Jmod: Joint modeling of mass spectra for empowering mulitplexed DIA proteomics | Kevin McDonnell
YouTube video by Parallel Squared Technology Institute
youtu.be
October 16, 2025 at 6:49 PM
And, we are back with another presentation from this year's Research Fest. PTI's Senior Computational Scientist, Kevin McDonnell, talks about developing joint modeling (aka JMod) of mass spectra for empowering multiplexed DIA proteomics.
www.youtube.com/watch?v=plK4...
www.youtube.com/watch?v=plK4...
Yes! This 100x over.
October 15, 2025 at 6:57 PM
Yes! This 100x over.
Well color me curious... and perfect choice of portrait 😂
October 15, 2025 at 1:47 PM
Well color me curious... and perfect choice of portrait 😂