Jack Freestone

This paper evaluates FDR control in mass spectrometry proteomics tools, finding that none consistently control FDR at the peptide level in DIA data, especially for single-cell datasets.

The paper introduces Percolator-RESET, a post-processor for tandem mass spectrometry proteomics that better controls the false discovery rate than Percolator.

The paper investigates FDR control in proteomics MS/MS database searches, finding no strong evidence of issues in open modification or narrow window approaches after accounting for chimeric spectra and candidate differences.

The paper introduces CONGA, a method that combines narrow and open modification searches to improve detection of post-translational modifications while maintaining statistical power.

Group-walk improves FDR control in grouped data by incorporating group structure, achieving power gains in peptide discovery across different groups.