Improvements in mass spectrometry (MS)-based peptide sequencing provide a new
opportunity to determine whether polymorphisms, mutations, and splice variants identified in
cancer cells are translated. Herein, we apply a proteogenomic data integration tool
(QUILTS) to illustrate protein variant discovery using whole genome, whole transcriptome,
and global proteome datasets generated from a pair of luminal and basal-like breast-cancer-
patient-derived xenografts (PDX). The sensitivity of proteogenomic analysis for singe …