Comprehensive, Quantitative, Intact Proteoform Measurements of Patient-Derived Breast Tumor Xenografts Using an Improved Top-Down Proteomics Pipeline

摘要

Our top-down proteomics pipeline provided significant improvement in proteome coverage, precision of the quantification, and the ability to identify statistically significant changes on proteoform abundances, in comparison to another recent report that analyzed proteoforms in the same PDX samples. Although still relatively limited in coverage compared to the conventional bottom-up approach, top-down analysis provides a complementary view of the proteome (e.g., truncated and/or post-translationally modified proteoforms, variants, additional protein identifications). The top-down, bottom-up, and peptidomics analysis of the same PDX samples showed the same degree of changes in protein/peptide abundances between the two subtypes. The top-down measurements provided unique information on up-regulation of many proteoforms of histones and 60S ribosomal proteins as well as key pathway level changes (e.g., glycolysis) in the luminal subtype. This holds great promise in providing new insights into cancer biology. Fractionation and new technologies (e.g., SLIM IMS) will greatly improve proteome coverage.