I have been using SAINT for #interactome/ #apms analysis forever but always found it cumbersome to pipe into workflows especially on macOS/unix env. But no mas! We made a full Python port of SAINTexpress (spc only for now) github.com/FossatiLab/s...

Our new review paper about Pathway-Centric PTM Data Analysis is out this week in #Proteomics! We cover databases, enrichment tools, software for pathway reconstruction, and full-fledged platforms that help to interpret high-throughput PTM datasets. Check it out here: doi.org/10.1002/pmic...

The big picture: Tracing the arc of conceptual milestones in life sciences over the past century, centered around major discoveries driven by evolving technologies. We are excited about the progress & the research enabled by tech from @ParallelSqTech. youtu.be/SrzoLGBVTsY?...

What an excellent opportunity with so many great labs and interesting projects. Planed lab rotations inside the network to connect and learn from others. And you can go "all in on AI" as Mr. Mann called for in last years HUPO.

How much hands-on lab expertise gets lost? We developed a multimodal AI agent that turns videos into protocols and detects procedural errors. Making science accessible. Great collaboration with #Google. Preprint: www.biorxiv.org/content/10.1... @patiskowronek.bsky.social explains👇

🚀 Excited to share our new preprint: msBayesImpute - A Versatile Framework for Addressing Missing Values in Biomedical Mass Spectrometry Proteomics Data 👉 Improves imputation accuracy, normalization, and differential expression detection 📝https://www.biorxiv.org/content/10.1101/2025.10.02.679746v1

Predicting protein-protein interactions. They '...systematically screened 200 million human protein pairs and predicted 17,849 interactions with anexpected precision of 90%, of which 3,631 interactions were not identified in previous experimental screens.' www.science.org/doi/epdf/10....

🥁 Check out our new preprint on OmniPath, the prior knowledge resource for #SystemsBiology, and its brand-new OmniPath Explorer web app! 🥳 📖 Preprint: www.biorxiv.org/content/10.1... 🔍 Explorer: explore.omnipathdb.org OmniPath integrates 160+ resources for multi-omics analysis & modeling. 🧶⬇️

Abuse of power at universities is a problem in many countries. Unfortunately, the open to read book is just available in German language.

If you are a #PhD candidate or #student in the fields of #Biochemistry or #ChemBio and would like to go to the #Biochemistry2026 conference in Würzburg, consider applying for the brand new @gdchbiochem.bsky.social Meeting #Award! en.gdch.de/network-stru... #ChemSky #ECR #EarlyCareerResearcher

Major part of my PhD thesis is finally online! Thanks to everyone involved 🙏 @walterwchen.bsky.social @rjdlab.bsky.social @tmoeckli.bsky.social @hirakdas.bsky.social and the entire @warscheidlab.bsky.social #peroxisomes #Massspec #proteomics

Excited to share our latest work published in #ScienceSignaling! 🚀 www.science.org/doi/10.1126/... (1/4)

When analysing peptides from in-gel digests by LC-MS/MS, has anyone noticed a 1+ ion of m/z 1342.93 after washing the column with 80% ACN? We are leaving the pump at 80% ACN at 1uL/min for 5 mins after our usual 0-40% ACN gradient. Doesn't correspond to any contaminants. #massspechelp

PepMapViz: A Versatile Toolkit for Peptide Mapping, Visualization, and Comparative Exploration academic.oup.com/bio... --- #proteomics #prot-paper

Jesper Olsen Lab (Guzman et al) independently reproduces MAP-MS (eDR) proteome depth and compares Astral Zoom MS to the older model. "...yielding ~15,000 and ~30,000 additional precursors..." eDR: www.biorxiv.org/content/10.1... MAP-MS: www.biorxiv.org/content/10.1...

As Requested - A Starter Pack of PIs in Biology (or adjacent) fields who are recruiting POSTDOCS! Please don't hesitate to reach out if you wish to be added! go.bsky.app/4gbXXR3

▶️▶️ To all mass spec enthusiasts: A postdoc position (three years) is available in our international group. Please apply if you are interested in structural MS and in developing novel cross-link ing MS workflows!🧪 Thanks @diegofgar.bsky.social for sharing! #teammassspec #AcademicSky #ChemSky

Check out our newest paper (tinyurl.com/scp-ms) straight from the lab of @erwinschoof.bsky.social. If you are considering to FAIMS or not to FAIMS and whether wide or narrow window DIA is better, you might find some answers you are looking for. #proteomics

🚀 Attention DIA/DDA proteomics users! Whether you're using #DIA-NN, #MaxQuant, #quantms, or any tool that outputs mzIdentML and mzML, the NEW pmultiqc v0.0.29 is here! 💡 Create stunning, shareable HTML reports for your collaborators in seconds. ✨ Try pmultiqc.quantms.org Examples👇 #Proteomics #QC

📣📣It is great to finally welcome @cnicproteomics.bsky.social to Bluesky 🎊 Follow them if you want to learn about the latest development in PTM research applied to cardiovascular diseases! 🫀🧪🧫🖥️🛠️

DIA, DOA, DUI, DDA, etc. Here is a comparisons of some quantitative proteomics methods from a POV you might not have seen before: github.com/pwilmart/qua...

Are you interested in #proteomics and #skeletalmuscle? It can be a real pain to get deep reproducible coverage. Check out our review with @adeshmukh.bsky.social We analyse some considerations including current limitations and how to potentially overcome them #myoblue @unimelbcmr.bsky.social

🚀🚀 🚀 Exciting News! 🚀 🚀 🚀 After more than 4.5 fantastic years at @embl.org, I am excited to announce that from 1 August 2025, I’ll be starting my own research group at Physikalisch-Technische Bundesanstalt (PTB) in Braunschweig, Germany — as part of the Biochemistry Department [1/n]

⏳ Just 1 week left to register for MaxQuant Summer School 2025! 📅 Registration closes: July 7 📍 Utrecht, July 21–25 💻 Hands-on training in MaxQuant, Perseus & mass-spectrometry-based proteomics 🔗 Sign up now: eventbrite.de/e/maxquant-s... 🌐 Details: maxquant.org/summer_school/ #TeamMassSpec

Anyone interested in using mass spectrometry to identify and quantify peptides and proteins in plasma, tissue and organoid cell systems? I have a Research Assistant position in my lab at the Institute of Metabolic Science - Metabolic Research Laboratories. Apply here: lnkd.in/dCxhS3GN

Update of our protein outlier caller PROTRIDER. We now handle missing values, a widespread issue for mass spec where missing values are not a random -- and this improves outlier detection on non-missing data! Thumbs up to Daniela and George for the great work. doi.org/10.1101/2025...

🚀 We're launching quantms.org — new hub for all #quantms related projects. Explore its components #pmultiqc & #ibaqpy, and check all reanalysis we're sharing with the community: quantms.org/datasets Meet the Team and Labs behind the project 👉 quantms.org/about #OpenSource #Proteomics #ASMS2025

Almost intentionally, looks like all of the new Thermo instrument pages are up (Astral Zoom, Excedion Pro, Optispray). Overall vibes? Excedion is the bigger upgrade, almost 2x faster and can now do ETD. Astral Zoom improvements are more incremental. No change to instrument sensitivity specs.

Very excited that another chapter of my PhD is finally out! 🎉 We compared methods to infer kinase activities from #phosphoproteomics data so check it out if that sounds interesting to you. More details in the thread below 🧵👇🏼

🚨Our new paper is online🚨 We use zero-distance⚡photo-crosslinking⚡to reveal direct protein-DNA interactions in living cells, enabling quantitative analysis of the DNA-interacting proteome on a timescale of minutes. #DNA #Chromatin #Proteomics www.cell.com/cell/fulltex...

🧵5 Top Free Alternatives to BioRender for Scientific Illustrations! These five websites offer free scientific illustrations for biologists. Great for presentations, research papers and other research communication needs. Save and share the post!

This is the way we recommend everyone make targeted proteomics assays. We've been doing it this way for 6-7 years now but only recently got around to putting a manuscript together. We use it for everything from SRM to PRM. Great work by @deannaplubell.bsky.social

Phosphorylation depends both on the sequence and on spatial proximity in vivo between kinases and their substrates. Both of these factors are accounted for in this preprint 1/2

New Paper from the Lab 🎉If you are interested in USP30, protein engineering and targeting DUBs with small molecules I can wholeheartedly recommend this Paper 😊

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.

🚨 New in @naturemethods.bsky.social #CHIMERYS has already transformed #proteomics since 2022, powering DDA, DIA & PRM analysis in a single workflow. Wanna know how CHIMERYS works? 👉 www.nature.com/articles/s41... #TeamMassSpec #NatureMethods #ASMS2025 🧪🔬 1/7

In the meantime, if anybody needs any assistance currently with their mass spec proteomics project design, method review, data analysis, or result interpretation, please feel free to reach out.. It would be my pleasure to be of assistance.. I am also available for consulting/freelancing.. 5/6

"Science of a coffee cup: A physicist walks into a bar and annoys everyone with unsolicited experiments." A good read for a cloudy Sunday. Now I can annoy my labmates with this knowledge. pubs.aip.org/aip/pof/arti...

#teammassspec does anyone use 96-well plates from Macherey-Nagel with the HR-X material? Either the 85 or 45μm format? If not, can one recommend another plate for C18 based desalting? Ideally something suitable for small amounts of peptides.

A basic solution to a very common problem. collab with @kusterlab.bsky.social and @bendavisgroup.bsky.social www.mcponline.org/article/S153...

Big news: we are setting up a new non-profit organization to run bioRxiv and medRxiv. It's called openRxiv [no it's not a new preprint server; it's dedicated organization to oversee the servers] openrxiv.org 1/n

Happy to meet at my poster P01-6 at the @DGMS in Göttingen to discuss the effect of mechanical stress signalling and different mass spec methods for analysis.

One of the most significant and challenging projects of my career so far. PepCentric: a scalable computational platform utilizing novel 2-D fragment indexing for rapid peptide-centric searches, enabling proteogenomics searches against billions of spectra in seconds. www.biorxiv.org/content/10.1...

Happy @warscheidlab.bsky.social Team after three days training on the Thermo #Astral. Many thanks to Michal Nadler Holly for such a great course! #TeamMassSpec #proteomics #PhDlife @lakshitaaa.bsky.social @johannes-uni-wue.bsky.social @hirakdas.bsky.social

@warscheidlab.bsky.social is finally also on bluesky. We are a Würzburg-based proteomics lab with research interests in peroxisomes, mitochondrial import stress or mechanical stress in skeletal muscle cells.

Job alert 🧪 ‼️ Hi #teammassspec: In our #RTG2467 @unihalle.bsky.social we have a job opening for a PhD student in my group! 🎉 If you want to do cool stuff in cross-linking mass spectrometry of the tumor suppressor p53, please take a look: personal.verwaltung.uni-halle.de/jobs/wissmi/ Please RT!

Applying LLMs to biomedical research today can go one of two ways: we either use a closed-source web app, or we get coding ourselves. Many researchers lack training for the latter, so their only choice is the former. We want to change that. www.nature.com/articles/s41...

Hello #proteomics and #science World! Short intro to myself: End of last year I finished my PhD at the @cecad.bsky.social in the KruegerLab and started now my postdoc in @jesperolsenlab.bsky.social, where I continue working on spatial proteomics! @ypic.bsky.social member with the full heart❤️

Reminder that @europepmc.org is a mirror of Pubmed with better search and that it indexes *all* bioRxiv preprints (as well as ResearchSquare), not just the ones funded by NIH like chauvinist Pubmed

Where do you prefer to input across samples in MS-proteomics? 1- In match-between-runs - considering MBR as some kind of imputation. 2- peptide level 3- protein level 4- All levels.