🎓 PhD Defense at BayBioMS - Congratulations to Dr. Miriam Abele! We bid farewell to October 2025 - what a month it has been! And what better way to start November than with great news from our first PhD defense!

✨ A decade of science, collaboration, and innovation – celebrating 10 years of #BayBioMS at @tum.de School of Life Sciences! What an incredible day at the 10-Year Anniversary Symposium 🎉

It was such a pleasure to participate in such a diverse symposium with high quality contributions. And ended perfect with joint bike ride around Freising. Thank you @baybioms.bsky.social

✨ Honored to present my #plant #peptidomics research at the Elite Network of Bavaria on-site project review - in the presence of eminent professors, representatives of the Bavarian State Ministry of Science and the Arts, colleagues, and friends.

Grateful for the inspiring discussions and the opportunity to share how we explore plant peptide dynamics through #mass #spectrometry within our doctoral program “The Proteomes That Feed the World”. #Peptidomics #MassSpectrometry #PhD #Research #TeamMassSpec

🎉 #BayBioMS turns 10! 🎉 Next week, we’re celebrating #10years! A decade of cutting-edge #MassSpectrometry. It’s an occasion not to be missed! We look forward to celebrating with you! 🧪🎈 #TeamMassSpec #Proteomics #Metabolomics #Bioinformatics

🧵(1/7) 🎉 #BayBioMS turns 10! 🎉 2025 marks our 10th anniversary of Mapping Molecular Mountains. (Final reminder for next week's big anniversary & many thanks to the extended list of new sponsors.)

🌄 The tradition continues! 🎉 This year’s #BrixenProteomics #SummerSchool once again exceeded expectations. We welcomed passionate young talents and leading experts from academia and industry for a week filled with science, inspiration, and collaboration. 🔬✨

🎉 BayBioMS turns 10! 🎉 2025 marks our 10th anniversary of Mapping Molecular Mountains. Thus, we’re excited to invite you to the 10 Years of #BayBioMS #Symposium – a celebration of a decade of accelerating #MassSpectrometry research at the @tum.de! 🧵(1/6)

🔬 The next BayBioMS Advanced Mass Spectrometry Seminar is happening this Wednesday! 🧪 Doors open at 4:45 PM — free drinks and snacks will be served! This time, we will highlight cutting-edge work in: #Phosphoproteomics (Targeted) #peptidomics #PTM analysis (#citrullination)

Excited our paper is out in Cell @cp-cell.bsky.social! 🧬⚡ DNA photo-crosslinking proteomics in living cells 🎯 Pinpoints protein-DNA interactions to single amino acids 🌎 Globally quantifies DNA binding for >1800 proteins at a timescale of minutes 🔗 www.cell.com/cell/fulltex... 🧵

UV crosslinking works great for protein-RNA complexes, but DNA is much less photo-reactive and photo-crosslinking not commonly used. Analogous, we find that the photo-activatable nucleotide 4ST (DNA) is about ten times less reactive than the commonly used 4SU (RNA). (1/n)

Unlike natural DNA, 4ST can be activated by wavelengths far outside the absorption range of most natural biomolecules. This avoids photodamage, allowing us to use high-power LEDs, with ~1000-fold higher intensity than conventional bulbs, for activating 4ST in living cells (www.uven.org). (2/n)

To analyze protein photo-crosslinked to DNA by proteomics, we develop XDNAX: protein-crosslinked DNA extraction. (3/n)

XDNAX extracts are very clean and we discover previously elusive peptide-DNA crosslinks within them. They pinpoint protein-DNA interaction sites to individual amino acids. (4/n)

In contrast to formaldehyde crosslinking, photo-crosslinking only captures direct interactions (‘zero-distance’). The proteins we find in close proximity to DNA show very high degrees of intrinsic disorder. In fact, intrinsic disorder rises the closer proteins localize to DNA. (5/n)

To identify transcription factors or chromatin modifiers responding to changes in a cell, DNA interactomes can be compared between conditions. Treating breast cancer cells with increasing estrogen doses, we find the estrogen receptor and other regulators recruited to DNA dose-dependently. (6/n)

This also works in primary cells, where we see recruitment of inflammation-associated transcription factors to DNA in macrophages challenged with LPS. (7/n)

We use these quantitative powers to profile three genotoxic drugs and find very distinct reactions in the DNA interactome of cancer cells. This reveals drug-specific vulnerabilities that can be exploited for combination treatments. (8/n)

DNA photo-crosslinking takes 1 minute on ice, while formaldehyde requires 10 minutes at room temperature. We record a time series of photo-crosslinked DNA interactomes during acute BAF inhibition and identify fast-acting restrictors of chromatin accessibility missed by conventional methods. (9/n)

Overall, we present a resource of nearly 50 photo-crosslinked, i.e. direct physical, DNA interactomes and identify 688 peptide-DNA crosslinks. These crosslinks mark known but also unknown protein-DNA interaction sites, some overlapping with variant sites linked to genetic or somatic disease. (10/n)

Very happy we pushed this across the finish line. Huge thanks to all the co-authors: Simon, Shuyao @shashuyao.bsky.social, the Greulich lab @franzigmuc.bsky.social, Susi, Karin @baybioms.bsky.social, Sandra, the Kubicek lab, the Uhlenhaut lab, and especially Bernhard @kusterlab.bsky.social. (11/11)

We were present at #InPPO2025 in beautiful Banff, Alberta, 🇨🇦!

Thank you / Merci, Canada! 🇨🇦 Grateful to have participated for the first time at the ‘6th International Plant Proteomics Organization Conference (InPPO2025)’ - an exciting and dynamic event & community!

It was a true pleasure and privilege to share the progress of my Doctorate research project and the community effort to build a Crop Proteome Atlas of the Elite Network Bavaria supported project ‘Proteomes that Feed the World’, all the way to this part of the globe.

From giving a flash talk and presenting a poster, to the honor of (co-)chairing the ‘Early Career Researcher’ session, it was a rewarding opportunity to engage in conversations across academia, industry, and government of both Canada and the U.S. representatives.

“Cultivating Innovation through the Integration of Plant Science and Proteomics” - a theme that resonates more than ever. #InPPO2025 #PlantProteomics #ECR #ScienceOutreach #Proteomics #TeamMassSpec #Bioinformatics #MassSpec

#MCP News | Miriam Abele, Armin Soleymaniniya & colleagues at @tum.de (@baybioms.bsky.social) developed MS2Bac, a software system that enables bacterial identification from protein data. They published their resource in Molecular & Cellular Proteomics. ow.ly/tooX50VLZcA #TeamMassSpec #ASBMBJournals

That title really undersells it: “we present the most extensive bacterial proteomic resource to date, covering 303 species, 119 genera, and five phyla with over 636,000 unique expressed proteins, confirming the existence of over 38,700 hypothetical proteins.”

Proteomic Diversity in Bacteria: Insights and Implications for Bacterial Identification www.mcponline.org/ar... --- #proteomics #prot-paper

Hey #TeamMassSpec, exciting news to end the week! 🔬✨ We are announcing our next seminar! Join us for the Advanced Mass Spectrometry Seminar with special guest Brendan MacLean, the #PI behind #Skyline — the leading open-source tool for targeted proteomics and metabolomics. 🧪💻

Thrilled to see our work highlighted by @us-hupo.org as Data of the Month! 🧬🔬

Abele et al. developed a comprehensive proteomics workflow, analyzing the proteomes of over 300 diverse bacterial species. The dataset (www.proteomicsdb.org/) enables quantitative comparisons leading to the creation of a new bacterial identification algorithm, MS2Bac. ow.ly/Y8Fc50VlVWc

Our teaching activities are in full swing! This time, our Metabolomics Leader, Dr. Karin Kleigrewe, delivered the lecture series #Metabolomics – An Introduction.

The past week it’s been busy for our Proteomics Leader, Dr. Christina Ludwig, who has been actively engaged in teaching!

It's been a busy and wonderful week of learning and fun at #EMBOQuantPro 👩‍🏫 👏 As the course comes to an end, we would like to say a big thank you to our participants, trainers, and organisers for making this an unforgettable experience! See you at our other events ➡️ https://embl.org/events

Shout out to the organisers @jesperolsenlab.bsky.social, (Tina Ludwig) @baybioms.bsky.social kathrynslilley.bsky.social, Caroline May and Britta Eggers and the speakers @bonalditiziana.bsky.social, @coscialab.bsky.social, @kusterlab.bsky.social, @anamdv.bsky.social, @jsandow.bsky.social

🔬 Wrapping up #DGMS2025 on a high note! 🎉 The final day of DGMS 2025 is in ongoing, and we’re still here, actively engaging with the community! Today, our Metabolomics Leader, Dr. Karin Kleigrewe, delivered an inspiring keynote talk on #metabolomics and its integration with #multiomics studies.

🚀 #DGMS2025 is in full swing! 🎉 We are present at the 56th Annual Meeting of the German Society for #MassSpectrometry, and we hope you're enjoying it as much as we are!

🔔 Award alert! 🚨 💭 Mentorship is more than guidance—it’s about fostering growth, curiosity, and collaboration. Here to prove that the first two months of 2025 were a perfect start for our team. 🎉

A great initiative by @eupaproteomics.bsky.social. @baybioms.bsky.social cannot miss. Check the link below if you want to find us, or any proteomics-related lab in Europe.

Hey #TeamMassSpec & #Proteomics Just like the past years, we, led by Dr. Christina Ludwig, are part of the organization of the amazing Brixen Proteomics Summer School. The first announcement is going on since a couple of days and many more exciting news will follow again soon.

The Brixen Summer School is back and is, as usual, building up a strong speaker list. Thank you @eupaproteomics.bsky.social @ukbspr.bsky.social @msaid-de.bsky.social @thermofishersci.bsky.social @biognosys.bsky.social @ionopticks.bsky.social @evosep.bsky.social for support!

🧵(1/7) Our first 🦋 post is nothing less than: 🚀 New Research Paper Alert! 🚀 🦠 Big news for #Bacterial #MassSpec #Proteomics! 2025 has started properly for our team. 🥳