Varjosalo_Lab

Astral users, if you're getting sequence interruptions in Xcalibur/Chromeleon, it's time to update your software:
- LC–MS sequences may be interrupted due to an MS
response timeout
- full resolution of this defect has now been achieved with AST 2.0 SP1 QF
thermo.flexnetoperations.com/control/thmo...

This is our loading buffer on our Exploris 480 /U3000 system today. Coming to Nature Methods ASAP: The Proteomics S.P.I.D.E.R. Method (Suitability Protocol Integrating Dead Eight-legged Reference)

ERC-Plus: jackpot science or missed chance to fix academia? My reflections on ERC-Plus, Europe’s newest ultra-competitive research grant and what it tells us about the academic culture we’re…

I just published: ERC-Plus: jackpot science or missed chance to fix academia?

My reflections on ERC-Plus, Europe’s newest ultra-competitive research grant and what it tells us about the academic culture we’re building.

medium.com/p/erc-plus-j...

AI reviewers are here — we are not ready Artificial intelligence promises rapid and polite feedback on papers — but we must first review the reviewer.

Artificial intelligence promises rapid and polite feedback on papers — but we must first review the reviewer. This stand first says it all…
A timely World View Colin in our pages by Giorgio Gilestro

🧪 #academicSky
@nature.com

www.nature.com/articles/d41...

Predictomes, a classifier-curated database of AlphaFold-modeled protein-protein interactions Schmid and Walter train a classifier that discerns functionally relevant structure predictions in proteome-wide protein-protein interaction (PPI) screens using AlphaFold-Multimer, and they use this co...

Very excited to share that my thesis work is out in Molecular Cell! We trained a Structure and Omics informed Classifier (SPOC) to score binary AlphaFold multimer (AF-M) predictions by structural quality and consistency with experimental omics datasets. www.cell.com/molecular-ce...

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...

A new era for plasma proteomics is on the horizon. 🌅

Get ready for next-generation performance, precision, and simplicity — brought to you by PreOmics® and Biognosys.

✨ www.preomics.com/products/p2-...

#plasmaprep #proteomics #iST #sampleprep #P2-iST

YouTube video by Brett Phinney We try the new DIA-NN 2.3 (November 2025)

I try the newest version of DIA-NN, version 2.3 and its new Infini search approach on some Lumos and tismTOF HT datasets. If you're new to DIA-NN this might be a good video to watch. youtu.be/MIMnDw0loCk

Science HR in 2026: Smarter, Flexible, and Affordable Job Posting for Scientists and Employers

Science HR in 2026: Smarter, Flexible, and Affordable Job Posting for Scientists and Employers

#science #jobs #recruiting

www.scientific.today/news/1275/sc...

BIG ANNOUNCEMENT📣: I haven’t been this excited to be part of something new in 15 years… Thrilled to reveal the passion project I’ve been working on for the past year and a half!🙀🥳 (thread 👇)

A photo of a Nobel medal

BREAKING: The Nobel Prize in Physiology or Medicine has been awarded jointly to Mary E. Brunkow, Fred Ramsdell, and Shimon Sakaguchi "for their discoveries concerning peripheral immune tolerance"

Stay tuned for more.
#NobelPrize

Awesome to see GlyCounter at work!

www.biorxiv.org/content/10.1...

Final countdown! Only 3 days to go until the YPIC Webinar #19: Transition from Academia to Start-Up.

#YPIC #Proteomics #StartUpScience #ScienceCareers #AcademicToIndustry

State-of-the-Art and Future Directions in Structural Proteomics Structural proteomics has undergone a profound transformation, driven by the convergence of advanced experimental methodologies and computational innovations. Cutting-edge mass spectrometry (MS)-based...

New review w/ Lotta J. Happonen (MCP): “State-of-the-Art and Future Directions in Structural Proteomics.” Integrating XL-MS/HDX-MS/LiP-MS with cryo-EM, NMR, X-ray, SAXS/SANS, native & top-down MS + AI.
Full text: www.mcponline.org/article/S153...

Thrilled to share: Helsinki Proteomics Center is installing 3 Thermo Scientific Orbitrap Astral/Astral Zoom mass spectrometers. First Astral Zoom arrived in early Aug—among the first worldwide. Rollout by end of summer 2025. Read more: lnkd.in/d76vpMf6 #proteomics #massspectrometry

The pivot penalty in research - Nature An analysis of millions of scientific papers and patents reveals a ‘pivot penalty’ when researchers shift direction, with the impact of studies decreasing rapidly the further they move from their prev...

www.nature.com/articles/s41... 🧪

1️⃣ 🇿🇦🏴‍☠️ spotted!

Cool pic! Can you Photoshop you holding a helm?

Regional emperor penguin population declines exceed modelled projections - Communications Earth & Environment The number of emperor penguins in the Bellingshausen and Weddell Sea declined by 22% over the period 2009–2023, a reduction of 1.6% per year, exceeding predictions from population models based on high...

🐧📉 Emperor penguin decline worse than predicted

A new study finds a 22% drop in emperor penguins (2020–2023) in part of Antarctica – far steeper than climate models expected.

This highlights urgent risks from sea ice loss

🔗 www.nature.com/articles/s43...

#SciComm #ClimateChange #Penguins 🧪

Works for me 🤔

Luke Brzozowski of ‪@uhn.ca showed how 20+ core facilities are driving hospital-based innovation at #CTLS2025, from genomics to theranostics.

💡 Techna team
🧪 Biobanks & imaging
🏥 Research meets care

#CTLSBrno #CoreFacilities #TranslationalResearch #Stratocore @ctlslifescience.bsky.social

Back from ASMS 2025 — what a ride!
Tech 💥 Science 🧬 Pirates 🏴‍☠️ Crabs 🦀 and great conversations with old and new friends.
Grateful for the laughs, the inspiration, and the community.
Already missing Baltimore a bit.

See you next year at ASMS in San Diego! 🌞🌊

#ASMS2025 #massspec #blueskyscience

TopCysteineDB: A Cysteinome-wide Database Integrating Structural and Chemoproteomics Data for Cysteine Ligandability Prediction Development of targeted covalent inhibitors and covalent ligand-first approaches have emerged as a powerful strategy in drug design, with cysteines be…

A potentially very useful tool to assess Cys ligandability on proteins
www.sciencedirect.com/science/arti...

Feels like 1/3 less than last year. And maybe also add location to the list? My bet is that San Diego will be HUGE.

Well, there is some turbulence...

DIA-NN 2.2.0 is released! The new DIA-NN 2.2.0 Enterprise achieves up to ~1.6x median speedup on 64-cores under Windows (please see benchmark below). Release notes: github.com/vdemichev/Di..., download (Academia): github.com/vdemichev/Di...

This year’s #ASMS2025 is already off to an unexpected start. Helsinki-Vantaa airport on strike (again).
Luckily, I am ✈️ Icelandair—thanks to @evosep.bsky.social for scheduling me for Saturday🙏

Let’s see how this adventure unfolds. Wish me luck—and hope to see many of you in Baltimore!

Cannot agree more 😄
And also some additional pics/video of robots ☝️

Sequencing?