Frontiers in mass spectrometry–based clinical proteomics for cancer diagnosis and treatment

Abstract

Numerous omics studies, primarily genomics analyses, have been conducted to fully understand the molecular biological characteristics of cancer. In recent years, the depth of proteomic analysis, which comprehensively analyzes proteins and molecules that function directly in vivo, has increased dramatically. Proteomics using mass spectrometry (MS) is a promising technology to directly examine proteoforms, including post‐translational modifications and variants originating from genomic aberrations. Recent advances in MS‐based proteomics have enabled direct, in depth, and quantitative analysis of the expression levels of various cancer‐related proteins, as well as their cancer‐specific proteoforms, and proteins that fluctuate with cancer initiation and progression in cell lines and tissue samples. Additionally, the integration of proteomic data with genomic, epigenomic, and transcriptomic data has formed the growing field of proteogenomics, which is already yielding new biological and diagnostic knowledge. Deep proteomic profiling provides clinically useful information in various aspects, including understanding the mechanisms of cancer development and progression and discovering targets for diagnosis and drug development. Furthermore, it is expected to make a significant contribution to the promotion of personalized medicine. In this review, recent advances and impacts in MS‐based clinical proteomics are highlighted with a focus on oncology.

Abstract

Clinical proteomics has become increasingly important in recent years. In this review, we provide an overview of state‐of‐the‐art mass spectrometry techniques in cancer research and describe our targeted glycoform analysis for the development of specific cancer biomarkers and our immunopeptidomics studies for the identification of tumor‐specific immunopeptides.