Applications for Mass Spectrometry-based Proteomics and Phosphoproteomics in Precision Medicine

Proteins are the main effectors of cellular phenotypes. Aberrant protein functions dictate disease onset and progression. The precise and reproducible quantification of proteins and posttranslational modifications (PTMs), such as phosphorylation, remains a challenge. A number of mass spectrometry (MS) methods allow the high-throughput characterization of the proteome and phosphoproteome in normal and disease patient samples with unprecedented depth, thus showing promise for precision medicine. This chapter reviews currently available MS technologies for protein and PTM quantification and discusses improvements in the preparation of human biological samples for MS analysis. Key publications that advanced the utilization of MS for the molecular profiling of cancer patients' samples are also highlighted. Finally, remaining challenges for integrating MS-based proteomics and phosphoproteomics with other omics, clinical and imaging data to improve precision medicine approaches are discussed.