James E. Bruce

Mitochondrial respiratory capacity in kidney podocytes is high, age-dependent, and sexually dimorphic.

This study isolates podocyte mitochondria from mice to show they have higher respiratory capacity than tubule mitochondria, with age- and sex-dependent differences.

A community audit of error control in crosslinking mass spectrometry

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.

Large-Scale Quantitative Cross-Linking and Mass Spectrometry Provides New Insight on Protein Conformational Plasticity within Organelles, Cells, and Tissues

The paper uses quantitative cross-linking and mass spectrometry data to cluster cross-links by their conformational state preferences, providing insights into protein conformational plasticity across different biological contexts.

Combining quantitative proteomics and interactomics for a deeper insight into molecular differences between human cell lines

This study combines quantitative proteomics and interactomics to analyze molecular differences between three human cell lines, revealing cell-type-specific changes in protein interactions and conformations.

Interactome dynamics during heat stress signal transmission and reception

The paper uses qXL-MS to study interactome changes during heat stress, finding RNA-binding proteins show significant interactome shifts, suggesting RNA acts as a temperature sensor.

Integrated Analysis of Cross-Links and Deadend Peptides for Enhanced Interpretation ofQuantitative XL-MS

The paper analyzes cross-links and dead-end peptides from XL-MS data to infer conformational changes in proteins between different conditions.

Mitochondrial interactome remodeling in aging mouse skeletal muscle associated with functional decline.

The paper uses cross-linking to study mitochondrial interactome changes in aging mouse muscle, finding age-related shifts in protein interactions linked to functional decline.

Towards a structurally resolved human protein interaction network

The paper uses AlphaFold2 to predict structures for 65,484 human protein interactions, identifying high confidence models and disease-related mutations.

Mitochondrial interactome quantitation reveals structural changes in metabolic machinery in failing murine heart

The paper uses XL-MS and iqPIR to compare mitochondrial protein interactions in healthy and failing murine hearts, identifying structural changes in metabolic machinery.

Quantitative isotope-labeled crosslinker proteomics reveals developmental variation in protein interactions and posttranslational modifications in Diaphorina citri, the citrus greening insect vector

The paper uses isotope-labeled crosslinkers to analyze protein interactions and posttranslational modifications in Diaphorina citri across life stages, revealing developmental changes in chromatin structure.

Mitochondrial protein interaction landscape of SS-31

This study identifies SS-31 interacting proteins in mitochondria using chemical cross-linking and mass spectrometry, revealing their roles in ATP production and 2-oxoglutarate metabolism.

Cross-linking/Mass Spectrometry: A Community-Wide, Comparative Study Towards Establishing Best Practice Guidelines

This paper summarizes current XL-MS practices, compares strategies, and proposes common protocols to establish best practice guidelines for accurate and reproducible results.

Integrating cross-linking experiments with ab initio protein-protein docking

The paper improves protein-protein docking by integrating cross-linking data, enhancing prediction accuracy and reducing false positives.