Pioneer and Altimeter: Fast Analysis of DIA Proteomics Data Optimized for Narrow Isolation Windows www.biorxiv.org/cont...

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#proteomics #prot-preprint

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...

Agreed on both.

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)?

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

#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.

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 ;-)

The 2026 Chemistry Faculty Jobs List

The 2026 Chemistry Faculty Jobs List has 330 tenure-track positions and 47 teaching-only positions: docs.google.com/spreadsheets... #facultychemjobs #chemsky #chemchat ⚗️🧪

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

Proteomics + an elegant mechanism! I cannot wait to read in full! #proteomics #TeamMassSpec 🧪

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...

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.

Check out our new blog post on barcodes and the future of quickly measuring proteins for biomedical research! 🧪

www.parallelsq.org/blog/barcode...

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...

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...

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 :)

R/Bioconductor for Mass Spectrometry and Proteomics Dates 17-19 November 2025 To foster international participation, this course will be held online

🎓 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...

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.

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...

#Proteomics Tutorial drop!

Had fun writing this, ping me if interested in other search engines. #TeamMassSpec

www.parallelsq.org/blog/fantast...

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...

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 🧪

🧪🔥🔥🔥

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.

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.

Jmod: Joint modeling of mass spectra for empowering mulitplexed DIA proteomics | Kevin McDonnell YouTube video by Parallel Squared Technology Institute

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...

Yes! This 100x over.

Well color me curious... and perfect choice of portrait 😂

Good read, I learned a few new facts!

Where's the paragraph explaining WHY AI will not replace scientists ? 🧪

The general audience would benefit from this.

🧪

a teddy bear is standing in front of a blue door ALT: a teddy bear is standing in front of a blue door

Increasingly in favour of the Marie Kondo approach to collaborations in science. Does your collaborator spark joy? If not ➡️♻️🗑️

No one's skills or knowledge are so unique or indispensable that they get to make your day miserable with every interaction. 🧪🔭

Parquet fans unite!