Bottom-up proteomics relies on the use of proteases and is the method of choice for
identifying thousands of protein groups in complex samples. Top-down proteomics has been
shown to be robust for direct analysis of small proteins and offers a solution to the" peptide-
to-protein" inference problem inherent with bottom-up approaches. Here, we describe the
first large-scale integration of genomic, bottom-up and top-down proteomic data for the
comparative analysis of patient-derived mouse xenograft models of basal and luminal B …