Labeling and Label-Free Shotgun Proteomics Quantification in the Research of Cardiovascular Diseases

Shotgun proteomics, comprising of labeling and label-free strategies, have expanded rapidly in the past decade and substantially advanced cardiovascular research. Employing liquid chromatography coupled to tandem mass spectrometry as the tool, shotgun proteomics enables unbiased, high-throughput quantitative analysis of proteome-wide alterations in protein abundance, and therefore contributes significantly to the elucidation of the mechanisms underlying cardiovascular diseases (CVD) and the discovery of potential cardiac biomarker candidates. Promising though, further technical improvements are desirable for overcoming technical challenges and ensuring successful application in cardiovascular medicine. Here we elaborate technical aspects of both labeling and label-free shotgun proteomics, including fundamental rationales, limitations, and considerations in CVD proteomics research. Several major challenges and corresponding solutions are also discussed regarding the application of shotgun proteomics in CVD research. Furthermore, we illustrate the applications of shotgun proteomics in cardiovascular research with the emphasis on disease biomarker discovery and mechanism investigation on both subcellular and whole tissue levels, post-translational modification (PTM) characterization.