Table II. Highly confident SNV peptides.

Variant peptides identified by MS which were found to be somatic, with 10 or more peptide spectral matches (PSMs), variant expression at the RNA level, and evidence for protein expression in the associated gene (100+ PSMs across the gene). Includes associated gene name, chromosome, genomic start and end, genomic variant location, Ensembl protein identifier, original and variant amino acids, and the method it was identified in (iTRAQ, Label Free Low Resolution (LF-LR) or Label Free High Resolution (LF-HR)). All highly confident variants were found to be somatic in the luminal tumor only.