Julia Ruta

The paper maps the spatial and structural proteome architecture of HEK293 cells using subcellular fractionation and cross-linking mass spectrometry, identifying residue-level protein interactions and expanding the human cell interactome.

This study maps HSV-1 virion-wide protein interactions, revealing maturation-driven network remodeling and conserved organizational principles across herpesviruses.

The paper integrates structural and proteomic methods to characterize the protein organization of a giant virus, identifying sub-compartments and membrane protein topologies.

This study introduces SHVIP, a method to identify virus-host PPIs in intact infected cells, revealing 739 PPIs and validating their biological relevance through disruption experiments.

The paper audits error control in twelve crosslinking mass spectrometry pipelines using ground-truth designs, finding some pipelines exceed false discovery rates by up to 29-fold.

This study uses cryo-electron tomography to describe the molecular architecture and structural heterogeneity of individual synaptic vesicles in mouse brains and cultured neurons.

The paper develops recombinant protein standards and a search engine for XL-MS, showing Scout outperforms existing tools in speed, sensitivity, and false-discovery rate control.

This paper introduces CLASP, a cross-link assisted spatial proteomics method, to map sub-organelle proteomes and membrane protein topology in human mitochondria.

This study identifies Rtc5 and Oxr1 as TLDc domain-containing proteins that regulate V-ATPase assembly and subcellular localization in yeast.

The paper improves inter-link detection in cross-linking mass spectrometry by using a fused database and context-sensitive subgrouping, increasing coverage by 30-75% while maintaining low error rates.