Important groundwork from the Picotti lab. A deep dive into in-source fragmentation.

The next iteration of O-MAP targeting genomic loci is now at eLife!! DNA O-MAP enables proximity labeling at specific DNA loci took a ton of work from many lab members and collaborators, so it's really exciting to wrap up this paper with @oligopain.bsky.social! elifesciences.org/articles/102...

This is so, so well-articulated.

AITHYRA is recruiting a LIFE SCIENCE PI We are interested in research questions related to one of our four core disease areas: cancer research, immunological disorders, infectious diseases, neurodevelopment disorders. Job Ad: aithyra.at/fileadmin/do... Apply by 30.4.2026 #StartingPI #LS #AITHYRA

AITHYRA is recruiting an AI/ML STARTING PI Generative Models, Large Language Models, Agentic AI, Active & Reinforcement Learning, AI-driven Scientific Discovery & Lab Automation, ML-driven molecular simulations... Job Ad: aithyra.at/fileadmin/do... Apply by 30.4.2026 #StartingPI #AI/ML #AITHYRA

Acquisition news for bottom up and top down proteomics with Thermo acquiring Proteinaceous and MSAID. Proteinaceous was founded in 2016 (possibly earlier) as a spin out from Neil Kelleher’s lab at Northwestern. MSAID was spun out from Mathias Wilhelm and Bernhardt Kuster’s labs in 2019.

Wonderful (and fun!) read from @mastroianni.bsky.social which finishes with a clear answer on how to solve the collective action problem of dismantling scientific publishing

Really happy to see this one out: www.sciencedirect.com/science/arti... Alibek's drive & great coll w/ friends @gekaragoz.bsky.social & E. Hallacli resulted in a cool story that starts with our beloved #Marchantia and ends with iPSC-derived neurons 🤩🤪 A short 🧵

So 2025 turned out to be a big year for de novo antibody design! Here are thoughts and predictions on the state of de novo antibody design heading into 2026 🧵

Thread: Multi-omics sounds cool—until you actually try it. Here's are the nuances. 1/ You’ve got RNA-seq. Methylation. Proteomics. Time to “integrate” the data. But how? And why? Let’s break it down.

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...

Unexpectedly, @jurgjn.bsky.social found that running Alphafold3 predictions for protein interactions can yield ipTM scores that are more predictive of true interactions when run in pools of proteins instead of pairwise predictions. Presumably, this reflects some sort of "competition effect".

New preprint: We isolate peptide–RNA photo-crosslinks with tunable RNA chains from living cells for mass spec. This maps over 4,700 crosslinking sites across 744 proteins and offers the first glimpse into the RNA sequences in crosslinks by MS. Read here: doi.org/10.1101/2025...

"Many scholars, including us, have highlighted the threat posed by techno-solutionism in education: Rather than expanding our intellectual horizons, these technologies undermine the very conditions that allow us to think for ourselves." 1/n www.project-syndicate.org/commentary/a...

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...

🎉 Exciting opportunity for students in proteomics! 🎉 The Student Proteomics Fund (SPF) is back! 📅 Key dates: Call opens: October 1, 2025 Submission deadline: November 30, 2025 Don’t miss your chance to bring your research idea to life! New boost #SPF #YPIC #Proteomics

Just one more week left to get an application in! Starting my lab at the Perutz and the @viennabiocenter.bsky.social has been a fantastic opportunity that shaped me as a scientist!

The Vienna BioCenter PhD program in Molecular BioSciences will offer 20+ fully-funded positions in the Autumn Call which is now open. Have a look at what our campus has to offer: www.vbcphd.at

Do you or your lab use the Skyline software for #MassSpectrometry #proteomics? I'm looking for instructors to help with this year's Skyline Online, a virtual workshop/crash-course for all things Skyline! I'm especially looking for early career researchers for this opportunity. Please DM!

Academic authors, here's a peek into the black box of journal publishing from an journal editor if you can bear it:

Impressive work from great colleagues at RKI. Ultra-fast virus 🦠 diagnostics with mass spec. Original publication on vPro-MS here: www.nature.com/articles/s41...

After the DVP symposium now begins the start of the European Symposium on Single Cell Proteomics #ECSP25 A quick intro from @kmechtler.bsky.social and we kick off two days of exciting science starting with SCP of neutrophils in glioblastoma

A really nice example on how to visually communicate the text contents of a paper on mobile phones

I am excited to announce that the position of a senior postdoc (3 +3 years) in the field of theoretical biology is available in my group. The position provides the opportunity to closely interact with experimentalists and develop own research projects. Please RT. Details 👇: shorturl.at/iiiOv

▶️▶️ 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

‼️ Job alert 🚨: I have an open 3-year postdoc position in my lab to develop novel crosslinking mass spectrometry workflows. 🧪🧪 So if you want to do cool stuff in protein MS, please apply ! ⬇️ Please RT www.verwaltung.uni-halle.de/dezern3/Auss... #Academicsky #Chemsky #teammassspec

A few months ago, Nature published how-to guide for using ChatGPT to write your peer reviews in 30 minutes. This is, of course, a horrible idea. Here’s my response with @jbakcoleman.bsky.social .

Excited to see this published! It is a good step in the process for people to assess their FDR control in proteomics experiments. Great work from @bo-wen.bsky.social and @urikeich.bsky.social in particular who drove this.

12/ Bioinformatics isn't just code. It's skepticism. It’s pattern recognition. It’s noticing when something feels off. Your instincts matter. Listen to them. Then verify with data.

Love today’s #xkcd comic on #MassSpec 🤣

🚨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...

If there any #Sciex decision makers here on Bluesky - I urge you to reconsider. Skyline/Proteowizard support is not only important for your customers using these tools, but it also benefits other bioinformatics efforts that depend on these tools.

Please apply for this open position for a senior scientist at our faculty. It is the head of the mass spec center and you will be my close colleague! Application Deadline:8.5.2025 jobs.univie.ac.at/job/Senior-S...

DIA-MS and targeted #proteomics workshop May 19, 2025, Masaryk University, Brno CZ Organized by CZproteo keynote by Alexey Nesvizhskii @nesvilab.bsky.social Program & Registration: czproteo.cz/workshop-cur...

Aithyra is hiring! We are looking for multiple starting PIs in life sciences and AI/ML. We offer highly competitive packages and salaries among the highest in Europe. www.oeaw.ac.at/aithyra/news...

I wrote a very long blog post about AI writing. I hope you'll read it. meresophistry.substack.com/p/the-mental...

Super excited to share our latest work on deciphering the #Ubiquitin Code “𝗨𝗯𝗶𝗥𝗘𝗔𝗗 𝗱𝗲𝗰𝗶𝗽𝗵𝗲𝗿𝘀 𝗽𝗿𝗼𝘁𝗲𝗮𝘀𝗼𝗺𝗮𝗹 𝗱𝗲𝗴𝗿𝗮𝗱𝗮𝘁𝗶𝗼𝗻 𝗰𝗼𝗱𝗲 𝗼𝗳 𝗵𝗼𝗺𝗼𝘁𝘆𝗽𝗶𝗰 𝗮𝗻𝗱 𝗯𝗿𝗮𝗻𝗰𝗵𝗲𝗱 𝗞48 𝗮𝗻𝗱 𝗞63 𝘂𝗯𝗶𝗾𝘂𝗶𝘁𝗶𝗻 𝗰𝗵𝗮𝗶𝗻𝘀” @cp-molcell.bsky.social 1/8 www.cell.com/molecular-ce...

2025 Quantitative Proteomics Course in Seattle WA. Space is limited, register now! This is the 11th year of offering this weeklong course. skyline.ms/project/home... #proteomicsky #massspecsky #massspec

We are expanding our team and looking for a postdoc in Davos! Are you passionate about combining cutting-edge proteomics and immunology to unravel the mechanisms behind human diseases? Join our collaborative and supportive environment in beautiful Davos.

Time to share our organelle proteome paper out in @cellcellpress.bsky.social: doi.org/nzwz We created a spatial map of human cells using organelle immunoprecipitation at scale. Locate your fav protein among the 7,600 we mapped across 19 subcellular compartments: organelles.sf.czbiohub.org/ 1/3 🧪

Finally, an experienced MS group performed a proper comparison of MS plasma proteomics vs. Olink! Kudos to the Coon lab! Cannot wait to read all the details!

🚨 Out now! @marcoyannic.bsky.social and his former colleagues at the Chan Zuckerberg Biohub have unveiled a new study in Cell. The team led by Manuel Leonetti mapped the subcellular distribution of thousands of proteins to create an atlas of the human proteome ➡️ tinyurl.com/ypn65duk @univie.ac.at

I’ve reported on infectious diseases for 15 years, but during the covid-19 pandemic and even more during the global outbreak of mpox clade IIb, I was shocked by the amount of misinformation I was seeing. Misinfo had always been part of any outbreak, but this felt different. 🧪

Now this is a paper I had long been waiting for! NanoSPLITS is out! Parallel single cell proteomic and transcriptomic measurements from the same cell! Great work from @cajunscience.bsky.social and @nanopots.bsky.social www.nature.com/articles/s41...

The strain on scientific publishing: we set out to characterise the remarkable growth of the scientific literature in the last few years, in spite of declining growth in total scientists. What is going on? direct.mit.edu/qss/article/... A 🧵 1/n #AcademicSky #PhDchat #ScientificPublishing #SciPub

It gives me great pleasure to announce our next European Single Cell Proteomics Conference www.apma.at/6thescp/ We would be delighted to receive many abstracts from students so that they have the opportunity to give their first presentation. On behalf of: Erwin, Fabian, Manuel, Fabian and Karl

My perspective on CVs for DIA-based #proteomics is out in JPR It explores how normalisation, the CV formula and software parameters affect the outputs. It suggests parameters to use for biological and technical studies and provides an R package to calculate CVs. doi.org/10.1021/acs....

I spend a bit of time talking to folk with plasma cohorts about MS vs affinity approaches for discovery. Thought it was worth a thread. Most love the marketing. 5,000 proteins? 10,000 proteins? OLink was used in UK Biobank? Wow, mass spec is sooooo last year. Except life is not that simple.

Few quick notes for new followers 🦋 Please add some bio ✍️ before starting to follow. I still have time to go through new followers and skip those without bio just as a precaution. If you add it later, I (and others) may not return to follow back and I would hate to miss out on great scientists👩‍🔬🧑‍🔬!

Welcome @kmechtler.bsky.social to Bluesky! Very glad you join the conversation. Here is Alejandro's starter pack to get started. go.bsky.app/HH7kqEh