Julia Ruta
@juliaruta.bsky.social
PhD student at FMP Berlin in Fan Liu Lab | Cross-linking Mass Spectrometry | Bioinformatician | Structural Interactomics and modeling
Reposted by 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
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#proteomics #prot-paper
November 11, 2025 at 6:40 PM
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
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#proteomics #prot-paper
Reposted by Julia Ruta
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...
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...
August 15, 2025 at 1:26 PM
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...
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...
Reposted by Julia Ruta
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
📄 www.nature.com/articles/s41...
#LoveVirology #TeamMassSpec
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...
www.nature.com
July 22, 2025 at 8:15 AM
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
📄 www.nature.com/articles/s41...
#LoveVirology #TeamMassSpec
Happy to have been able to contribute to Lars‘ work!
Integrative structural interactomics reveals protein organization and structure in a giant virus https://www.biorxiv.org/content/10.1101/2025.06.16.659922v1
June 19, 2025 at 10:02 AM
Happy to have been able to contribute to Lars‘ work!
Reposted by Julia Ruta
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...
www.nature.com/articles/s41...
February 7, 2025 at 3:16 PM
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...
www.nature.com/articles/s41...
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....
#Proteomics #TeamMassSpec
www.embopress.org/doi/full/10....
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...
www.embopress.org
December 16, 2024 at 1:32 PM
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....
#Proteomics #TeamMassSpec
www.embopress.org/doi/full/10....
Reposted by Julia Ruta
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...
Software: github.com/KosinskiLab/...
Preprint: biorxiv.org/content/10.1...
December 4, 2024 at 10:02 AM
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...
Software: github.com/KosinskiLab/...
Preprint: biorxiv.org/content/10.1...
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...
#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 - 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...
www.nature.com
November 8, 2024 at 9:01 PM
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...
#XLMS #Massspec #Proteomics
www.nature.com/articles/s41...
Reposted by Julia Ruta
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
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
www.biorxiv.org
December 3, 2023 at 4:51 AM
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.
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.
December 4, 2023 at 9:04 AM
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.
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.