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Varjosalo_Lab

@varjosal.bsky.social
722 followers 728 following 88 posts

Unveiling the secrets of life through proteomics @helsinkiuni, @HiLIFE_helsinki, @BIOTECH_UH, Proteomics, Genomics, Systems biology 🇫🇮🇨🇳🇧🇩🇭🇷🇮🇳🇮🇹🇹🇷

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Reposted by Varjosalo_Lab
Marco Hein @marco.heinlab.org · 29/06/2026
How do you indicate in a slide deck that an image is AI-generated (and not real data or human-made artwork) in a clear yet unobtrusive way? Today I saw a great solution: a small astroid (the geometric shape, not an asteroid), similar to the Gemini logo. Simple, subtle, and easily recognizable.
An astroid: a pinched, concave diamond-shaped geometric object.
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Reese Richardson @reeserichardson.bsky.social · 05/06/2026
The Thermo Fisher situation keeps getting worse. We've now collected 450+ problematic images presented as verification data in TF's antibody catalog. This includes: 🖌️ Dozens more images with duplications or painting 🖨️ Hundreds of blots that all share the same background (behold slideshow below)
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Oded Rechavi @odedrechavi.bsky.social · 06/05/2026
Submitting a grant with q.e.d
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Varjosalo_Lab @varjosal.bsky.social · 20/04/2026
Elected as an ordinary member of the Finnish Academy of Science and Letters (founded 1908) at its Spring Meeting on 17 April. This honor came considerably earlier than I had expected. Thanks to my group, colleagues, and collaborators. And to my family. The work continues.
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Nature Portfolio @natureportfolio.nature.com · 18/01/2026
Millions of people worldwide carry genetic mutations that weaken their immune system. A feature in Nature reports on the research to find ways to treat and prevent severe infections in those people. #medsky 🧪
go.nature.com
The infection enigma: why some people die from typically harmless germs
Millions of people worldwide carry genetic mutations that weaken their immune system.
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Henna Virkkunen @hennavirkkunen.wsocial.eu · 15/01/2026
Over €307 million in funding are now available for #AI and related technologies. Two new calls have just been launched under the Horizon Europe Work Programme, mobilising €307.3M to strengthen Europe’s digital innovation & competitiveness.
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Varjosalo_Lab @varjosal.bsky.social · 22/12/2025
New paper out in J Proteome Res! 🧬 We automated plasma proteomics with Mag-Net enrichment on Biomek i5—achieving deep coverage at just a few dollars per sample. 🔗 pubs.acs.org/doi/10.1021/acs.jproteome.5c00420 @hilife-helsinki.bsky.social @resynbio.bsky.social @evosep.bsky.social
pubs.acs.org
Automated Mag-Net Enrichment Unlocks Deep and Cost-Effective LC–MS Plasma Proteomics
Plasma is an ideal material for proteomics due to its diverse protein content reflecting physiological and pathological states and its compatibility with minimally invasive sampling. Deep proteomic pr...
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Reposted by Varjosalo_Lab
Kris Willis @kawillis.bsky.social · 29/12/2025
PubMed wrapped: categorizing the top 5 high-level topics of papers published in 2025. LLM-based classification of 1,783,299 documents in total 1/3
Treemap showing the proportion of papers published in 2025 that can be classified into one of the 5 largest high-level topics in the PubMed database: (1) health care systems, care providers, health policy, interventions; (2) algorithms, statistical modeling, image analysis, analytics; (3) hospitalization, critical care, mortality, patient outcomes, general surgery; (4) mental health, depression, psychological stress, social support; (5) biomedical engineering, nanoparticles, drug delivery. Together these 5 categories represent 37% of 2025 papers indexed in PubMed.
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ReSyn Biosciences @resynbio.bsky.social · 22/12/2025
📢Publication Alert🌶️! Congratulations HiLIFE Helsinki for selecting #Mag_Net from #TeamReSynBio for your automated HT platform for deep proteomics profiling of plasma: pubs.acs.org/doi/10.1021/...
pubs.acs.org
Automated Mag-Net Enrichment Unlocks Deep and Cost-Effective LC–MS Plasma Proteomics
Plasma is an ideal material for proteomics due to its diverse protein content reflecting physiological and pathological states and its compatibility with minimally invasive sampling. Deep proteomic pr...
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Reposted by Varjosalo_Lab
Biognosys @biognosys.bsky.social · 22/12/2025
🎉Congratulations to the team from the @helsinki.fi! In their recent study, the authors report preliminary data showing that the P2 and P2-iST Plasma kits delivered the highest plasma proteome coverage compared with other enrichment approaches. Read the publication: pubs.acs.org/doi/10.1021/...
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Varjosalo_Lab @varjosal.bsky.social · 22/12/2025
New paper out in J Proteome Res! 🧬 We automated plasma proteomics with Mag-Net enrichment on Biomek i5—achieving deep coverage at just a few dollars per sample. 🔗 pubs.acs.org/doi/10.1021/acs.jproteome.5c00420 @hilife-helsinki.bsky.social @resynbio.bsky.social @evosep.bsky.social
pubs.acs.org
Automated Mag-Net Enrichment Unlocks Deep and Cost-Effective LC–MS Plasma Proteomics
Plasma is an ideal material for proteomics due to its diverse protein content reflecting physiological and pathological states and its compatibility with minimally invasive sampling. Deep proteomic pr...
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Varjosalo_Lab @varjosal.bsky.social · 15/12/2025
🧬 New paper in Nature Communications! We found that POLE2,part of DNA polymerase ε,moonlights as a receptor for NPF motifs, binding 70+ proteins across replication, transcription & repair. The interactome is more interconnected than thought. @teamgogl.bsky.social 🇫🇮🇫🇷🇭🇺🇬🇧 www.nature.com/articles/s41...
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Chris Ashwood @cashwood.proteaglyco.com · 04/12/2025
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...
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Brett Phinney @ucdproteomics.bsky.social · 02/12/2025
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)
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Sophien Kamoun @kamounlab.bsky.social · 03/12/2025
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...
medium.com
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…
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Magdalena Skipper @magdalenaskipper.bsky.social · 03/12/2025
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...
nature.com
AI reviewers are here — we are not ready
Artificial intelligence promises rapid and polite feedback on papers — but we must first review the reviewer.
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Ernst Schmid @ernstschmid.bsky.social · 26/02/2025
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...
cell.com
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...
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Ludwig Lautenbacher @llautenbacher.bsky.social · 11/11/2025
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...
nature.com
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...
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Biognosys @biognosys.bsky.social · 10/11/2025
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
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Brett Phinney @ucdproteomics.bsky.social · 03/11/2025
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
youtu.be
We try the new DIA-NN 2.3 (November 2025)
YouTube video by Brett Phinney
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Scientific Today @scitoday.bsky.social · 18/10/2025
Science HR in 2026: Smarter, Flexible, and Affordable Job Posting for Scientists and Employers #science #jobs #recruiting www.scientific.today/news/1275/sc...
scientific.today
Science HR in 2026: Smarter, Flexible, and Affordable Job Posting for Scientists and Employers
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Oded Rechavi @odedrechavi.bsky.social · 15/10/2025
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 👇)
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Nature @nature.com · 06/10/2025
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
A photo of a Nobel medal
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Riley Research Group @riley-research.bsky.social · 27/09/2025
Awesome to see GlyCounter at work! www.biorxiv.org/content/10.1...
biorxiv.org
Extracting informative glycan-specific ions from glycopeptide MS/MS spectra with GlyCounter
Glycopeptide tandem mass spectra typically contain numerous glycan-specific fragments that can inform several features of glycan modifications, including glycan class, composition, and structure. Whil...
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ypic.bsky.social @ypic.bsky.social · 15/09/2025
Final countdown! Only 3 days to go until the YPIC Webinar #19: Transition from Academia to Start-Up. #YPIC #Proteomics #StartUpScience #ScienceCareers #AcademicToIndustry
us06web.zoom.us
Welcome! You are invited to join a meeting: 19th YPIC Webinar: Panel Discussion - Transition from Academia to Your Own Start-Up. After registering, you will receive a confirmation email about joining ...
Join us for our 19th YPIC Webinar – “Transition from Academia to Start-Up” From pipettes to pitches: how four brilliant scientists turned their academic ideas into successful start-ups! Are you curi...
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Varjosalo_Lab @varjosal.bsky.social · 05/09/2025
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...
mcponline.org
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...
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Varjosalo_Lab @varjosal.bsky.social · 26/08/2025
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
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Reposted by Varjosalo_Lab
Javi Ibarrondo @jibarrondo.bsky.social · 26/06/2025
www.nature.com/articles/s41... 🧪
nature.com
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...
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Prof Sam Illingworth @samillingworth.com · 16/06/2025
🐧📉 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 🧪
nature.com
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...
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Stratocore @stratocore.bsky.social · 10/06/2025
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
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Varjosalo_Lab @varjosal.bsky.social · 08/06/2025
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
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Reposted by Varjosalo_Lab
Adam Gilbert @adammgilbert65.bsky.social · 04/06/2025
A potentially very useful tool to assess Cys ligandability on proteins www.sciencedirect.com/science/arti...
sciencedirect.com
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…
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Vadim Demichev @vadim-demichev.bsky.social · 30/05/2025
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...
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Varjosalo_Lab @varjosal.bsky.social · 30/05/2025
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!
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PastelBio @pastelbio.bsky.social · 19/05/2025
MultiStageSearch: An Iterative Workflow for Unbiased Taxonomic Analysis of Pathogens Using Proteogenomics pubs.acs.org/doi/10.... --- #proteomics #prot-paper
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Evangelia Petsalaki @epetsalaki.bsky.social · 16/05/2025
We present SELPHI 2.0 a machine learning model integrating >40 sequence, omics and structural features to predict kinase-substrate interactions between 420 kinases and 240K phosphosites and improve interpretation of global phosphoproteomics data www.sciencedirect.com/science/arti...
sciencedirect.com
Data-driven extraction of human kinase-substrate relationships from omics datasets
Phosphorylation forms an important part of the signalling system that cells use for decision making and regulation of processes such as cell division …
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Evosep @evosep.bsky.social · 14/05/2025
University of Helsinki have developed a fully automated #plasma #proteomics workflow—from sample prep to Evotip loading. Achieving >4,200 proteins/sample with high reproducibility and low cost, this workflow is a game-changer for large-scale clinical studies.
evosep.com
Blog post I Automated Plasma Proteomics from Sample to Evotip
New study shows how combining the Evosep One with automated Evotip sample preparation enables scalable, high-throughput plasma proteomics.
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Juha Hulmi @juhahulmi.bsky.social · 13/05/2025
Happy that our article is Editor´s choice in the May issue of 2025 in @jphysiol.bsky.social. physoc.onlinelibrary.wiley.com/doi/10.1113/...
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Evosep @evosep.bsky.social · 13/05/2025
Heading to #ASMS2025 in Baltimore? Join us May 31 for the Evosep User Meeting! Markku Varjosalo shares insights on automated plasma workflows. Connect, learn, and network—refreshments included! Register here: www.evosep.com/asms2025/ #teammassspec #proteomics #lcms
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PastelBio @pastelbio.bsky.social · 12/05/2025
Automated MagNet Enrichment Unlocks Deep and Cost-Effective LC-MS Plasma Proteomics www.biorxiv.org/cont... --- #proteomics #prot-preprint
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Varjosalo_Lab @varjosal.bsky.social · 12/05/2025
Happy to host good candidates! DM for more info.
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Varjosalo_Lab @varjosal.bsky.social · 11/05/2025
New preprint out! We benchmarked five plasma enrichment methods and developed an automated, cost-effective MagNet workflow. Up to 4,200 proteins/sample identified using DIA on timsTOF Pro 2 with, at just a few dollars/sample. doi.org/10.1101/2025... #PlasmaProteomics #DIA #timsTOF #Evosep
doi.org
Automated MagNet Enrichment Unlocks Deep and Cost-Effective LC-MS Plasma Proteomics
Plasma is an ideal material for proteomics due to its diverse protein content reflecting physiological and pathological states, and its compatibility with minimally invasive sampling. Deep proteomic p...
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Varjosalo_Lab @varjosal.bsky.social · 06/05/2025
Finland 🇫🇮 has moved to Astral times! The first of the three Astral instruments for the Helsinki Proteomics Center has arrived at the Viikki Proteomics Unit! The long wait is over – and amazing science is just around the corner! Big thank to Biocenter Finland & Research Council of Finland 🙏
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Alexey Nesvizhskii @nesvilab.bsky.social · 05/05/2025
Exciting news: We have released #FragPipe 23, and it's one of our biggest updates ever. Windows installer, support for TMT on Astral and timsTOF, TMT35, PTM site reports for DIA, improved Astral data handling in #MSFragger, improved diaTracer for diaPASEF data, better Skyline integration, and more!
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EMBO @embo.org · 30/04/2025
The FEBS | EMBO Women in Science Award aims to highlight the major contributions made by female scientists to #LifeSciences research. Winners of the award are inspiring role models for future generations of #WomenInScience Nominate a scientist by 15 May: www.embo.org/the-embo-com... 🧪
embo.org
FEBS|EMBO Women in Science Awardees – Nominate for the Women in Science Award – EMBO
Nominees should be female scientists working in an EMBC Member State or FEBS member country, who have made outstanding contributions to life sciences research and significantly advanced our…
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Yasset Perez-Riverol @ypriverol.bsky.social · 25/04/2025
ibaqpy: A scalable #Python package for baseline quantification in proteomics leveraging #SDRF metadata www.sciencedirect.com/science/arti.... We continue our effort to provide tools and algorithms that leverage SDRF metadata to perform quantitative proteomics analysis.
sciencedirect.com
Ibaqpy: A scalable Python package for baseline quantification in proteomics leveraging SDRF metadata
Intensity-based absolute quantification (iBAQ) is essential in proteomics as it allows for the assessment of a protein's absolute abundance in various…
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Ylva Ivarsson @ivarssonlab.bsky.social · 25/04/2025
Happy to announce the 2025 Tiselius symposium in Uppsala, August 28. Excellent line up of speakers including Lori Passmore @lapassmore.bsky.social, Katja Luck @katjaluck.bsky.social, Markku Varjosalo @varjosal.bsky.social and Arne Elofsson. No fee & short talk slots available tiseliussymposium.org
tiseliussymposium.org
Tiselius Symposium
28 August 2025, Uppsala
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Varjosalo_Lab @varjosal.bsky.social · 20/04/2025
Short interview hupo.org/Humans-of-HUPO
hupo.org
Human Proteome Organization (HUPO) - Humans of HUPO
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Varjosalo_Lab @varjosal.bsky.social · 19/04/2025
Ok. What the easiest (best) way to develop and maintain lab web pages?
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Albert and Mary Lasker Foundation @laskerfdn.bsky.social · 11/04/2025
A recent study constructed a protein and RNA distribution atlas from 21 tissues and 8 cell types to study plasma proteome dynamics. The atlas enables enhanced quantification of organ-enriched protein panels during disease. www.cell.com/cell/fulltex... 🧪
cell.com
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