Cardiovascular Proteomics Primer: Managing Expectations and Setting Yourself up for Success

To fully understand cardiovascular physiological and pathophysiological mechanisms, there is a need to know not only which proteins are present but also where they are localized, their proteoforms, and how these properties change as a result of pathogenesis. The scientific discipline of proteomics broadly includes applying research methods to determine the identification, abundance, localization, structure, function (physiological and pathophysiological), and interactions of proteins. Mass spectrometry-based proteomics can be applied to identify, characterize, and quantify thousands of proteins in a single experiment or used to perform targeted analyses of a single or few specific proteins to assess a wide variety of properties. Given the breadth of applications, one-sizefits- all approaches do not exist. Rather, the appropriate experimental design needs to be tailored to address specific biological questions. In this chapter, we introduce the reader to general concepts of proteomic analysis, emphasize keys to success associated with each aspect of the proteomic workflow, and describe reasonable expectations so readers are primed to discuss their research goals with mass spectrometry practitioners and develop a plan most suited to address their research question. This chapter is targeted to readers without prior proteomics experience and focuses on those applications we expect to be particularly interesting to clinician scientists who want to apply proteomic approaches to the analysis of human biological specimens. While many of the key points are generally applicable to any cell or tissue type, we include specific considerations that are relevant to unique challenges faced in cardiovascular research.