Micha Birklbauer

⏱️ Ten days left. Time flies, so apply now 👉 www.protaiomics.eu
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#ResearchCareers #Proteomics #ArtificialIntelligence #MSCA #PhDOpportunities #FullyFundedPhD

Breaking barriers in crosslinking mass spectrometry with enhanced throughput and sensitivity using Orbitrap Astral - Nature Communications Mapping protein interactions requires sensitive mass spectrometry. Here, the authors show that the Orbitrap Astral, combined with optimized chromatography, improves detection of low-abundance crosslin...

Congratulations to my research partners at the Proteomics Tech Hub at the @impvienna.bsky.social on their newest publication on the optimization of crosslinking on the Orbitrap Astral! Happy that I was able to contribute! 🥳
www.nature.com/articles/s41...

New paper alert! Researchers at the Proteomics Tech Hub at the @viennabiocenter.bsky.social have developed a new cross-linking mass spectrometry workflow that allows scientists to more easily detect and study protein interactions that were previously undetectable. More: bit.ly/4nV5n1w

GitHub - hadley/genzplyr: dplyr but make it bussin fr fr no cap dplyr but make it bussin fr fr no cap. Contribute to hadley/genzplyr development by creating an account on GitHub.

Do you teach #rstats? Do your students complain about how lame and old-fashioned dplyr is? Don't worry: I have the solution for you: github.com/hadley/genzp....

genzplyr is dplyr, but bussin fr fr no cap.

Register now! Five days of keynotes, workshops, flash talks, posters, and more on computational mass spectrometry Confirmed keynote speakers Armin Soleymaniniya · Arthur Declercq · Claire Koenig · Hannah Boekweg · Jonas Scheid · Karel Berka · Matthias Anagho-Mattanovich · Roman Bushuiev · Valdemaras Petrosius 📆 19-23 January 2026 📍 Harrachov, Czechia

Registration is now open for the EuBIC-MS Winter School 2026!

Join us in Harrachov, Czechia for a week of keynotes, workshops, and networking on computational MS.

Info and registration: eubic-ms.org/events/2026-...

#EuBIC2026 #MassSpectrometry #MassSpec #Bioinformatics #Proteomics #Metabolomics

Last week we had our yearly organizational meeting, this time in Vienna, Austria. We had 3 great days discussing the activities of the past year and planning the upcoming ones. Thanks to everyone who joined and contributed to a great meeting!

The 6th European Symposium on Single Cell Proteomics took place on Campus this week, once again drawing a big international crowd eager to experience interesting talks, poster presentations, networking & knowledge exchange!

Enjoy these snapshots and make sure to sign up next year!
#viennabiocenter

Also, I know that in DIA-NN there is a "threads" parameter that can be set, for the i9 that should be at least at 24 (and the OS hopefully schedules that to be each on separate cores). Maybe that helps :)

Haha pretty sure they'd be happy to hear about it though. As a dev I can confirm that it's hard to keep track of all the changes in the hardware world ;)

Might be because the software maybe isn't adapted to properly use all the cores in the new Intel CPUs yet? E.g. no more hyper threading on Intel CPUs and if it only uses performance cores there will be a huge performance loss compared to Ryzen CPUs. Probably worth asking the devs.

In vivo crosslinking and effective 2D enrichment for proteome wide interactome studies Communications Chemistry, Published online: 13 August 2025; doi:10.1038/s42004-025-01644-6Cross-linking mass spectrometry faces challenges due to low reaction efficiencies and complex matrices in protein–protein interaction (PPI) studies. Here, the authors enhance an Azide-A-DSBSO-based in vivo crosslinking workflow with affinity enrichment and size exclusion chromatography, yielding over 5000 crosslinks from K562 cells and generating a comprehensive PPI network.

Just out: In vivo crosslinking and effective 2D enrichment for proteome wide interactome studies

Excited to share our latest in vivo crosslinking workflow using a dual enrichment strategy: Over 5000 crosslinks and 56 novel PPls- Huge thanks to the amazing team: Philipp Bräuer, Laszlo Tirian, Fränze Müller, Karl Mechtler at the Vienna BioCenter who made this possible! doi.org/10.1038/s420...

In vivo crosslinking and effective 2D enrichment for proteome wide interactome studies www.nature.com/artic...

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#proteomics #prot-paper

The deadline to submit abstracts and register for this years symposium on single cell proteomics #ESCP25 in Vienna is approaching this Sunday! This year we additionally host a workshop for deep visual proteomics and a Thermo User Meeting.

Time to get signed up for the Symposium on Structural Proteomics! This time at @humantechnopole.bsky.social in Milan 6th-8th October Full speaker lineup announced. Thanks to @thermofishersci.bsky.social @brukercorporation.bsky.social, Affipro and MSVision for support
Info
ssp2025.squarespace.com

I would like to inform you that the registration deadline for our ESCP25 conference is July 27th.
We are looking forward to interesting scientific contributions.

An honest description of a new type of in-cell enrichable lysine crosslinker! Crosslinking proteomics is not really my thing. I've done it a few times over the years and I've personally had success with in vitro expe...

Cool science - better writing - 100% recommend this new paper. proteomicsnews.blogspot.com/2025/06/an-h...

‼️ 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

Developing a new cleavable crosslinker reagent for in-cell crosslinking Communications Chemistry, Published online: 23 June 2025; doi:10.1038/s42004-025-01568-1Crosslinking mass spectrometry (XL-MS) has become a crucial tool for studying protein structures and interactions in their native environments, however, the current cleavable linkers are fraught with practical limitations. Here, the authors synthesize and characterize DiSPASO, a novel lysine-reactive, MS-cleavable, and membrane-permeable crosslinker with an alkyne-based click chemistry handle for affinity enrichment, showing potential for improving protein-protein interaction mapping.

Just out: Developing a new cleavable crosslinker reagent for in-cell crosslinking

Redox proteomics in lung cancer patients reveals that there is a higher oxidation of the cysteines of glycolytic and methylglyoxal metabolism enzymes. doi.org/10.1038/s414...

Conference stage with Marie Locard-Paulet, the chairs, and the opening slide in the background.

Marie Locard-Paulet presenting the EuBIC-MS #ProteoBench project at the #EuPA2025 conference.

👉 Learn more about our open proteomics software benchmarking platform at proteobench.readthedocs.io.

#Proteomics #Bioinformatics #Benchmarking

DeepLC introduces transfer learning for accurate LC retention time prediction and adaptation to substantially different modifications and setups While LC retention time prediction of peptides and their modifications has proven useful, widespread adoption and optimal performance are hindered by variations in experimental parameters. These varia...

New in DeepLC! Ability to deal with wild, weird, and wobbly LC setups or peptide modifications. This ability is possible with transfer learning; where only a minimal amount of training peptides are needed for accurate retention time predictions.

www.biorxiv.org/content/10.1...

🚧 Refactored lesSDRF; feedback welcome!

I’ve pushed a new version of lesSDRF to make high-throughput SDRF annotation faster and more intuitive.

Github issue: github.com/CompOmics/le...
Temporary app: refactorlessdrf.streamlit.app

I could use some feedback before making this the new lesSDRF 🙏

And big thanks also to the @eubic-ms.org hackathon team contributing to our #SpectriPy package github.com/RforMassSpec... !

Next on the list submission of the package to 👉 @bioconductor.bsky.social

Proteome-wide non-cleavable crosslink identification with MS Annika 3.0 reveals the structure of the C. elegans Box C/D complex - Communications Chemistry Crosslinking mass spectrometry enables the structural analysis of proteins and protein complexes and serves as a powerful tool in protein-protein interaction studies, however, the data analysis of lar...

PS: If you haven't read our paper on the initial release of MS Annika 3.0 which supports proteome-wide non-cleavable crosslink identification yet, check it out here 😉
www.nature.com/articles/s42...

GitHub - hgb-bin-proteomics/MSAnnika: MS Annika is a crosslink search engine based on MS Amanda, aimed at identifying crosslinks of cleavable and non-cleavable crosslinkers from MS2 and MS3 spectra. MS Annika is a crosslink search engine based on MS Amanda, aimed at identifying crosslinks of cleavable and non-cleavable crosslinkers from MS2 and MS3 spectra. - hgb-bin-proteomics/MSAnnika

Newest version of our crosslink search engine MS Annika is out! Version 3.0.7 features performance improvements for searching Astral data, a new parameter for custom and multi-enzyme digestion, and support for Proteome Discoverer 3.2. More here: github.com/hgb-bin-prot...

Screenshot of the new Altmetric Explorer integration of Thoughts. #AcademicSky #HigherEd #PsySky #Brain #Machine #Interfaces

THREAD

Today Altmetric is announcing a major development in collaboration with the Brain Occipital Lobe Learning Observation Centre Kalhausen-Strasbourg.

From today Altmetric will be able to determine what research paper you're thinking of, regardless of what you're actually writing/saying.
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