Label-Free Quantifi cation by Data Independent Acquisition Mass Spectrometry to Map Cardiovascular Proteomes

The large-scale identification and quantification of proteins by liquid chromatography mass spectrometry (LC MS) can be achieved by at least three general methods, categorized into targeted, data independent (DIA), and data dependent (DDA) acquisition modes. Each acquisition strategy has its own set of benefits and drawbacks, and the methods serve complementary purposes for the study of protein quantification in biological samples. While not specific to research in cardiovascular physiology, a long-standing but recently popularized proteomic approach, termed Data Independent Acquisition Mass Spectrometry (DIA-MS), promises unique strengths to complement and extend the existing capabilities of traditional “discovery” proteomic profiling by combining development of a peptide library and DIA-MS. In this chapter we will provide background on the DIA-MS technique, highlighting its fundamental differences relative to other mass spectrometry methods, and discuss important considerations for researchers interested in implementing this technique for their proteomic experiments.