Reposted by Varjosalo_LabMarco Hein @marco.heinlab.org · 29/06/2026How 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. 142
Reposted by Varjosalo_LabReese Richardson @reeserichardson.bsky.social · 05/06/2026The 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) 18590366
Reposted by Varjosalo_LabOded Rechavi @odedrechavi.bsky.social · 06/05/2026Submitting a grant with q.e.d 1301
Varjosalo_Lab @varjosal.bsky.social · 20/04/2026Elected 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. 090
Reposted by Varjosalo_LabNature Portfolio @natureportfolio.nature.com · 18/01/2026Millions 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.comThe infection enigma: why some people die from typically harmless germsMillions of people worldwide carry genetic mutations that weaken their immune system. 11910
Reposted by Varjosalo_LabHenna Virkkunen @hennavirkkunen.wsocial.eu · 15/01/2026Over €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. 2115
Reposted by Varjosalo_LabVarjosalo_Lab @varjosal.bsky.social · 22/12/2025New 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.socialpubs.acs.orgAutomated Mag-Net Enrichment Unlocks Deep and Cost-Effective LC–MS Plasma ProteomicsPlasma 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... 092
Reposted by Varjosalo_LabKris Willis @kawillis.bsky.social · 29/12/2025PubMed wrapped: categorizing the top 5 high-level topics of papers published in 2025. LLM-based classification of 1,783,299 documents in total 1/3 155
Reposted by Varjosalo_LabReSyn 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.orgAutomated Mag-Net Enrichment Unlocks Deep and Cost-Effective LC–MS Plasma ProteomicsPlasma 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... 021
Reposted by Varjosalo_LabBiognosys @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/... 021
Varjosalo_Lab @varjosal.bsky.social · 22/12/2025New 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.socialpubs.acs.orgAutomated Mag-Net Enrichment Unlocks Deep and Cost-Effective LC–MS Plasma ProteomicsPlasma 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... 092
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... 082
Reposted by Varjosalo_LabChris Ashwood @cashwood.proteaglyco.com · 04/12/2025Astral 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... 061
Reposted by Varjosalo_LabBrett Phinney @ucdproteomics.bsky.social · 02/12/2025This 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) 6274
Reposted by Varjosalo_LabSophien Kamoun @kamounlab.bsky.social · 03/12/2025I 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.comERC-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… 69961
Reposted by Varjosalo_LabMagdalena Skipper @magdalenaskipper.bsky.social · 03/12/2025Artificial 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.comAI reviewers are here — we are not readyArtificial intelligence promises rapid and polite feedback on papers — but we must first review the reviewer. 2189
Reposted by Varjosalo_LabErnst Schmid @ernstschmid.bsky.social · 26/02/2025Very 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.comPredictomes, a classifier-curated database of AlphaFold-modeled protein-protein interactionsSchmid 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... 32911
Reposted by Varjosalo_LabLudwig Lautenbacher @llautenbacher.bsky.social · 11/11/2025Exited 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.comKoina: Democratizing machine learning for proteomics research - Nature CommunicationsKoina 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... 04116
Reposted by Varjosalo_LabBiognosys @biognosys.bsky.social · 10/11/2025A 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 052
Reposted by Varjosalo_LabBrett Phinney @ucdproteomics.bsky.social · 03/11/2025I 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/MIMnDw0loCkyoutu.beWe try the new DIA-NN 2.3 (November 2025)YouTube video by Brett Phinney 0143
Reposted by Varjosalo_LabScientific Today @scitoday.bsky.social · 18/10/2025Science HR in 2026: Smarter, Flexible, and Affordable Job Posting for Scientists and Employers #science #jobs #recruiting www.scientific.today/news/1275/sc...scientific.todayScience HR in 2026: Smarter, Flexible, and Affordable Job Posting for Scientists and Employers 2218
Reposted by Varjosalo_LabOded Rechavi @odedrechavi.bsky.social · 15/10/2025BIG 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 👇) 56495185
Reposted by Varjosalo_LabNature @nature.com · 06/10/2025BREAKING: 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 122395
Reposted by Varjosalo_LabRiley Research Group @riley-research.bsky.social · 27/09/2025Awesome to see GlyCounter at work! www.biorxiv.org/content/10.1...biorxiv.orgExtracting informative glycan-specific ions from glycopeptide MS/MS spectra with GlyCounterGlycopeptide tandem mass spectra typically contain numerous glycan-specific fragments that can inform several features of glycan modifications, including glycan class, composition, and structure. Whil... 074
Reposted by Varjosalo_Labypic.bsky.social @ypic.bsky.social · 15/09/2025Final countdown! Only 3 days to go until the YPIC Webinar #19: Transition from Academia to Start-Up. #YPIC #Proteomics #StartUpScience #ScienceCareers #AcademicToIndustryus06web.zoom.usWelcome! 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... 195
Varjosalo_Lab @varjosal.bsky.social · 05/09/2025New 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.orgState-of-the-Art and Future Directions in Structural ProteomicsStructural proteomics has undergone a profound transformation, driven by the convergence of advanced experimental methodologies and computational innovations. Cutting-edge mass spectrometry (MS)-based... 041
Varjosalo_Lab @varjosal.bsky.social · 26/08/2025Thrilled 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 0100
Reposted by Varjosalo_LabJavi Ibarrondo @jibarrondo.bsky.social · 26/06/2025www.nature.com/articles/s41... 🧪nature.comThe pivot penalty in research - NatureAn 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... 012
Reposted by Varjosalo_LabProf 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.comRegional emperor penguin population declines exceed modelled projections - Communications Earth & EnvironmentThe 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... 04122
Reposted by Varjosalo_LabStratocore @stratocore.bsky.social · 10/06/2025Luke 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 022
Varjosalo_Lab @varjosal.bsky.social · 08/06/2025Back 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 050
Reposted by Varjosalo_LabAdam Gilbert @adammgilbert65.bsky.social · 04/06/2025A potentially very useful tool to assess Cys ligandability on proteins www.sciencedirect.com/science/arti...sciencedirect.comTopCysteineDB: A Cysteinome-wide Database Integrating Structural and Chemoproteomics Data for Cysteine Ligandability PredictionDevelopment of targeted covalent inhibitors and covalent ligand-first approaches have emerged as a powerful strategy in drug design, with cysteines be… 074
Reposted by Varjosalo_LabVadim Demichev @vadim-demichev.bsky.social · 30/05/2025DIA-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... 1328
Varjosalo_Lab @varjosal.bsky.social · 30/05/2025This 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! 020
Reposted by Varjosalo_LabPastelBio @pastelbio.bsky.social · 19/05/2025MultiStageSearch: An Iterative Workflow for Unbiased Taxonomic Analysis of Pathogens Using Proteogenomics pubs.acs.org/doi/10.... --- #proteomics #prot-paper 032
Reposted by Varjosalo_LabEvangelia Petsalaki @epetsalaki.bsky.social · 16/05/2025We 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.comData-driven extraction of human kinase-substrate relationships from omics datasetsPhosphorylation forms an important part of the signalling system that cells use for decision making and regulation of processes such as cell division … 12413
Reposted by Varjosalo_LabEvosep @evosep.bsky.social · 14/05/2025University 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.comBlog post I Automated Plasma Proteomics from Sample to EvotipNew study shows how combining the Evosep One with automated Evotip sample preparation enables scalable, high-throughput plasma proteomics. 051
Reposted by Varjosalo_LabJuha Hulmi @juhahulmi.bsky.social · 13/05/2025Happy that our article is Editor´s choice in the May issue of 2025 in @jphysiol.bsky.social. physoc.onlinelibrary.wiley.com/doi/10.1113/... 042
Reposted by Varjosalo_LabEvosep @evosep.bsky.social · 13/05/2025Heading 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 041
Reposted by Varjosalo_LabPastelBio @pastelbio.bsky.social · 12/05/2025Automated MagNet Enrichment Unlocks Deep and Cost-Effective LC-MS Plasma Proteomics www.biorxiv.org/cont... --- #proteomics #prot-preprint 093
Varjosalo_Lab @varjosal.bsky.social · 11/05/2025New 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 #Evosepdoi.orgAutomated MagNet Enrichment Unlocks Deep and Cost-Effective LC-MS Plasma ProteomicsPlasma 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... 0193
Varjosalo_Lab @varjosal.bsky.social · 06/05/2025Finland 🇫🇮 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 🙏 4130
Reposted by Varjosalo_LabAlexey Nesvizhskii @nesvilab.bsky.social · 05/05/2025Exciting 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! 48015
Reposted by Varjosalo_LabEMBO @embo.org · 30/04/2025The 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.orgFEBS|EMBO Women in Science Awardees – Nominate for the Women in Science Award – EMBONominees 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… 13424
Reposted by Varjosalo_LabYasset Perez-Riverol @ypriverol.bsky.social · 25/04/2025ibaqpy: 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.comIbaqpy: A scalable Python package for baseline quantification in proteomics leveraging SDRF metadataIntensity-based absolute quantification (iBAQ) is essential in proteomics as it allows for the assessment of a protein's absolute abundance in various… 1129
Reposted by Varjosalo_LabYlva Ivarsson @ivarssonlab.bsky.social · 25/04/2025Happy 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.orgtiseliussymposium.orgTiselius Symposium28 August 2025, Uppsala 0127
Varjosalo_Lab @varjosal.bsky.social · 20/04/2025Short interview hupo.org/Humans-of-HUPOhupo.orgHuman Proteome Organization (HUPO) - Humans of HUPO 031
Varjosalo_Lab @varjosal.bsky.social · 19/04/2025Ok. What the easiest (best) way to develop and maintain lab web pages? 100
Reposted by Varjosalo_LabAlbert and Mary Lasker Foundation @laskerfdn.bsky.social · 11/04/2025A 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 053