Diogo Borges Lima

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.

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.

The paper introduces real-time library search (RTLS) to improve cross-link identification in XL-MS by leveraging intensity ratios of diagnostic peaks, enhancing identification depth in complex samples.

XlinkCyNET is a Cytoscape plugin for visualizing protein interaction networks derived from cross-linking mass spectrometry data.