Daniel Geiszler

This paper explores designing high-plex mass tags using differential mass defect to enable large-scale multiplexing in proteomics.

JMod improves sequence identification and quantification in multiplexed DIA proteomics by jointly modeling overlapping mass spectra, enabling higher throughput with maintained accuracy.

MSFragger-Labile improves the analysis of labile post-translational modifications by incorporating modification-specific fragment ions into mass spectrometry searches.

The paper develops a method to automatically detect diagnostic spectral features for post-translational modifications in mass spectrometry data, improving PTM identification and localization rates.

The paper introduces a method to accurately identify glycan compositions in glycopeptide spectra and control false discovery rates, integrating it into a computational pipeline for glycoproteomics analysis.

PTM-Shepherd automates analysis of post-translational modifications from open search proteomics data, improving detection of artifacts and biases across experiments.