Michael R. Shortreed

This paper develops a proteomics strategy for detecting viral mutations and variants in saliva by prioritizing high-prevalence peptides and using G-PTM-D for sensitive variant discovery.

The paper introduces PIP-ECHO, a method to control false discovery rate in peptide-identity-propagation, showing it outperforms existing tools in FDR control and differential protein abundance detection.

This study identifies dehydroamino acids and their crosslinks in Alzheimer's disease brain proteome, showing increased prevalence in AD compared to controls.

IsoBayes infers protein isoform presence and abundance using Bayesian methods integrating proteomics and transcriptomics data, showing good sensitivity and specificity in simulations and real datasets.

O-Pair Search identifies O-glycopeptides and localizes O-glycosites using collision- and electron-based dissociation spectra, improving speed and identification rates.

Spritz generates sample-specific proteogenomic databases annotated with sequence variations and PTMs from RNA-seq data, enabling improved identification of proteoforms in mass spectrometry analyses.

The paper evaluates and implements two label-free quantification tools in the Galaxy platform for proteomics and multi-omics analysis.