Julia Ruta

Breaking barriers in crosslinking mass spectrometry with enhanced throughput and sensitivity using Orbitrap Astral www.nature.com/artic...

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#proteomics #prot-paper

RosettaFold 3 is here! 🧬🚀

AtomWorks (the foundational data pipeline powering it) is perhaps the really most exciting part of this release!

Congratulations @simonmathis.bsky.social and team!!! ❤️

bioRxiv preprint: www.biorxiv.org/content/10.1...

Structural host-virus interactome profiling of intact infected cells - Nature Communications Virus-host protein-protein interactions are fundamental to viral pathogenesis, yet few are structurally resolved. Here, the authors combine cross-linking mass spectrometry, bio-orthogonal labeling and...

Check out Structural Host–Virus Interactome Profiling (SHVIP) in intact cells infected with Herpes Simplex Virus type 1 (HSV-1)! Now published!

📄 www.nature.com/articles/s41...
#LoveVirology #TeamMassSpec

Happy to have been able to contribute to Lars‘ work!

Foldseek-Multimer is a strategy for complex-to-complex protein structure alignment to quickly perform large-scale structural comparisons between complexes. @martinsteinegger.bsky.social

www.nature.com/articles/s41...

Redesigning error control in cross-linking mass spectrometry enables more robust and sensitive protein-protein interaction studies | Molecular Systems Biology imageimageThe authors introduce a fused target-decoy strategy and a context-sensitive data subgrouping scheme for cross-linking MS. This strategy allows for the identification of inter-protein links w...

It was nice to be able to contribute to Boris’ study on improving error control in XL-MS!
#Proteomics #TeamMassSpec

www.embopress.org/doi/full/10....

We have released version 2 of AlphaPulldown - a general pipeline for high-throughput structural modeling!
Software: github.com/KosinskiLab/...
Preprint: biorxiv.org/content/10.1...

Proteome-scale recombinant standards and a robust high-speed search engine to advance cross-linking MS-based interactomics - Nature Methods This Article reports cross-linking mass spectrometry (XL-MS) standard datasets with fully controlled protein interactions that are an order of magnitude more complex than existing ones. These datasets...

Scout, our high speed search engine, is finally published. Additionally, we developed a standard, ground truth dataset for cross-linking Mass Spectrometry which guided the development of Scout.
#XLMS #Massspec #Proteomics

www.nature.com/articles/s41...

PROTEOME-SCALE RECOMBINANT STANDARDS AND A ROBUST HIGH-SPEED SEARCH ENGINE TO ADVANCE CROSS-LINKING MS-BASED INTERACTOMICS https://www.biorxiv.org/content/10.1101/2023.11.30.569448v1 Advancing data analysis tools for proteome-wide cross-linking mass spectrometry (XL-MS) requires gro

PROTEOME-SCALE RECOMBINANT STANDARDS AND A ROBUST HIGH-SPEED SEARCH ENGINE TO ADVANCE CROSS-LINKING MS-BASED INTERACTOMICS https://www.biorxiv.org/content/10.1101/2023.11.30.569448v1

Cross-linking goes bioorthogonal!
In our new preprint, we achieve higher coverage virus-host crosslinks than traditional interaction proteomics approaches by specifically labeling viral proteins, and can characterize new interaction sites in disordered regions via AF-multimer.