Individualized or personalized medicine entails a vision that allows doctors, patients and researchers to access billions of molecular data points with high temporal resolution. The investigation of the blood plasma and its molecular composition (proteins, metabolites, etc) provides easy access to information about the state of an individuals body and thus potential insight into health and disease. Quantitative proteomic measurements have the potential to uncover novel biomarker for disease. Recent methodological developments using SWATH MS have allowed the proteomic profiling of hundreds of samples in high throughput. The talk will discuss these recent methodological developments and the remaining challenges in data analysis. SWATH MS has been used in recent longitudinal profiling studies and the talk will discuss an ongoing study of diabetes progression and introduce some of the challenges of integrating multi-omics datasets.