Update 🙋 V2 Guide to tuning spectral libraries using DIA-NN. --> Geared to proteomics nerds and newbies, alike! dx.doi.org/10.17504/pro...

Fine-tuning tagged spectral libraries in DIA-NN V.2

Fine-tuning tagged spectral libraries in DIA-NN. TL;DR: We have made some models so now you can predic. Read full protocol, steps, and materials on protocols.io

dx.doi.org

For those wanting the key insights without the deep methods dive, we published a research briefing in @NatureCVR nature.com/articles/s44... #SpatialProteomics #CardiovascularResearch

Deciphering molecular heterogeneity of carotid plaques using spatial proteomics - Nature Cardiovascular Research

We applied an ultra-sensitive, histomorphology-guided spatial proteomics workflow to advanced atherosclerotic carotid plaques to define molecular changes associated with minimum fibrous-cap thickness....

nature.com

Mann Lab@mannlab.bsky.social · last mo.

Our proteomics study of carotid plaque vulnerability is out in @natcardiovascres.nature.com — with Ankit Sinha & Lars Maegdefessel @tum.de. Our unique methodologies and integrative analysis highlight molecular and spatial diversity present in plaque tissues. www.nature.com/articles/s44...

A rare, new org. with a vision for public goods and a rapid path to impact! And they use mass spectrometry! #TeamMassSpec take note.

The Deliverome Project@deliverome.org · 2mo ago

Join us: deliverome.org/careers More on the Deliverome Project: ifp.org/the-delivero... Follow along: deliverome.org

Our machine learning driven quantification algorithm for proteomics now published in Nature Biotechnology. Optimal protein quantification and, for the first time, error estimates for individual quantities. Paper link in comments below.

my views on drug discovery: 1. American/global life sciences academia does a fantastic job of doing basic biological target discovery and disease understanding 2. American/global pharma companies take those discoveries and actually make viable drugs out of them

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

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 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

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 🧪

Mann Lab@mannlab.bsky.social · 9mo ago

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...

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...

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

parallelsq.org

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: 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...

nature.com

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

NU Barnett Institute @barnettinstitute.bsky.social · 9mo ago

Applications for the 2026 May Institute at the Barnett Institute will open soon! This two-week program offers hands-on training, lectures, and networking, a great opportunity to learn from and connect with leaders in the field. Sign up for our mailing list to stay updated: lnkd.in/eu4q2pEb

🧪 Two of my favorite sci-things! Already run q.e.d on my latest bioRxiv submissions :)

Richard Sever@richardsever.bsky.social · 9mo ago

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...

🎓 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...

R/Bioconductor for Mass Spectrometry and Proteomics

Dates 17-19 November 2025 To foster international participation, this course will be held online

physalia-courses.org

#Proteomics Tutorial drop! 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...

parallelsq.org

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 🧪

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...

biorxiv.org

🧪🔥🔥🔥

Yasset Perez-Riverol@ypriverol.bsky.social · 10mo ago

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 ☕🔥

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

🧪 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.

Oded Rechavi@odedrechavi.bsky.social · 10mo ago

Here's the link to the system, try it! qedscience.com @qedscience.bsky.social

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...

Jmod: Joint modeling of mass spectra for empowering mulitplexed DIA proteomics | Kevin McDonnell

YouTube video by Parallel Squared Technology Institute

youtu.be

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

Oded Rechavi@odedrechavi.bsky.social · 10mo ago

Here's the link to the system, try it! qedscience.com @qedscience.bsky.social

🧪

Altmetric@altmetric.com · 10mo ago

2025 isn't over yet but it's unlikely that Twitter will see a resurgence of research discussions.

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. 🧪🔭

a teddy bear is standing in front of a blue door

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

media.tenor.com