Global cardiac myofilament protein phosphorylation levels, and their site-specific stoichiometry, are physiologically and clinically relevant for heart function. Unlike myofilament phosphorylation, other PTMs such as O-GlcNAcylation are just beginning to gain attention due to their potential physiological and clinical implications. This review will focus on what is currently known about cardiac troponin I phosphorylation, and on the potential physiological and clinical impact of targeted proteomics including new findings on cardiac troponin I sites and stoichiometry. We will then discuss the increasing recognition of other myofilament PTMs functional relevance and the potential of targeted MS approaches, particularly MRM, for accelerating their systematic characterization. In addition, we will broadly discuss the development and application of MRM to quantitatively assess site-specific PTMs. Finally, we will give an overview of expert's consensus on MRM methods design/validation and best practices to develop MRM assays intended to reach clinical application. The unique ability of MRM and similar methods to identify and quantify cardiac myofilament PTMs is likely to become central in answering important biological questions in the field of cardiac integrative physiology.