Vagisha Sharma

This paper enhances the Comet search engine with fragment-ion indexing, improving peptide spectral matching speeds by up to 94% while maintaining accuracy in proteomics applications.

The paper introduces a framework for quality control in quantitative proteomics, combining internal and external QC measures with tools for data analysis and deposition.

The paper creates a proteomic resource profiling 90 drugs in six cell lines, revealing cell-specific responses and enabling integration with transcriptional data to identify therapeutic opportunities.