Abstract: Methods disclosed herein concern cancer proteogenomics, which integrates genomics, transcriptomics and mass spectrometry (MS)-based proteomics to gain insights into cancer biology and treatment efficacy. To promote clinical utility of embodiments herein, proteogenomics approaches were developed for frozen core needle biopsies using tissue-sparing specimen processing with or without a microscaled proteomics workflow.

Abstract: The present disclosure provides for compositions and methods of treating cancer. In some embodiments, PTPN11 is targeted with and anti-PTPN11 drug, such as a Shp2 inhibitor (e.g., SHP099). In some embodiments, other upregulated, hyperphosphorylated, or hyperacetylated target proteins are inhibited or targeted.