Recent developments in mass spectrometry data acquisition paralleled by advancements in bioinformatics offer a framework for comprehensive analysis of proteomes and discovery of credible biomarkers. Specifically, SWATH (Sequential Window Acquisition of all THeoretical fragment ion spectra) has been validated for measuring the abundance of hundreds to thousands of proteins across large sets of samples. However, a lack of generic sample preparation platform to tackle heterogeneity of biological material can be a limiting factor to a broader application of SWATH. Here we present the development of universal and fully automated sample preparation workflows that utilize liquid handling robot for building comprehensive pan-species spectral repositories and for quantitative profiling of proteins in a 96-sample format. A molecular weight cut-off filter plate enables efficient protein digestion using FASP approach. Within the same deck layout, peptide desalting and fractionation are achieved using 3D-printed adapter filled with StageTips packed with SCX or SDB-XC membrane. Samples are dried using automated nitrogen blowdown. We leveraged the improved throughput to create a compendium of quantitative assays for 28 bovine tissues and body fluids and demonstrated highly reproducible quantitation of over 6,500 proteins using SWATH across all sample types (median CV ≤ 10%). When applied to an ovine model of myocardial infarction, the automated workflows allowed clear differentiation between damaged and healthy tissue resulting in 300 significantly regulated proteins. A significant correlation between protein, mRNA and miRNA data was achieved thus validating the workflows for clinical applications and allowing prediction of markers diagnostic for myocardial injury.