LC–MS-Based Proteomics for Protein Biomarker Quantification for Both Prognosis and Diagnosis in the Clinical Setting

Biomarkers play a significant role in evaluating disease risk and treatment by acting as indicators of biological processes as well as pharmacological reactions to therapy. Candidate protein biomarkers are highly promising, specific biomarkers. These provide more functional information and reflect a more precise physiological cellular state. However, reliable and robust measurement of low-abundance protein biomarkers remains a challenge, primarily because of the presence of an array of post-translational modifications (PTMs). In recent years, advances in protein quantification technologies that provide higher sensitivity and specificity are expected to accelerate protein biomarker discovery and verification. In this column, we discuss the label-free and stable isotope labeling proteomics approaches that help in biomarker discovery. We also discuss the different enrichment techniques, such as stable isotope labeling by amino acid in cell culture (SILAC), isobaric tags for relative and absolute quantitation (iTRAQ), and tandem mass tags (TMT, that help in measuring low-abundance protein biomarkers.