The discovery proteomics approach is largely limited by the scan speed as peptides are selected for fragmentation based on abundance. This stochastic process results in a bias towards the more abundant proteins.62 In contrast to discovery proteomics, targeted proteomics focuses on a predetermined group of proteins of interest (e.g. ECM proteins). Proteotypic peptides unique to these proteins are quantified in what is known as selected reaction monitoring (SRM) or multiple reaction monitoring (MRM).76 The targeted approach increases selectivity, sensitivity, and accuracy and enables simultaneous measurement of hundreds of transitions in a single LC-MS/MS run.76 The transitions for proteotypic peptides will be interrogated as a surrogate of total protein levels, but peptides not included in the search (e.g. non-annotated PTMs) are not detected.55 This approach is particularly useful to detect CVD biomarkers, as Domanski et al.77 demonstrated in a study that also included ECM biomarkers of fibrosis. Moreover, targeted proteomics constitutes a robust method to validate findings obtained from discovery experiments (Figure 4).3 Figure 4MS strategies for ECM characterisation. Untargeted proteomics is appropriate for discovery experiments where no a priori information is available. When a delimited number of targets of interest are known a priori, targeted proteomics offers a robust method for detection and quantification. Novel MS methods such as a combination of higher energy collision dissociation (HCD) and electron transfer dissociation (ETD) allow for characterisation of complex PTMs including glycosylation. ZIC-HILIC, zwitterionic hydrophilic interaction LC; Pd, product-dependent; Alt, alternating.