Alzheimer's disease (AD) is the most common cause of dementia, and it is currently estimated to afflict 5 million people in the United States. Several therapeutic targets have been identified as contributors to Alzheimer's disease pathophysiology such as Aβ, tau, inflammation, and other disease-causing mechanisms, but highly effective therapies and accurate diagnostic tests are still currently unavailable. Most current therapeutic approaches target Aβ, and the treatment of Alzheimer's disease is often initiated during the mild-to-moderate stage of dementia, which may be too late as 50% of hippocampal neurons are typically dead at this point. Initially, in order to understand Aβ kinetics in the pathophysiology of Alzheimer's disease, we developed a novel method to metabolically label central nervous system (CNS) proteins during protein translation and sample labeled proteins from cerebrospinal fluid (CSF) during and after labeling to measure the kinetics of proteins in the CNS. We have utilized this technique of stable isotope labeling kinetics (SILK) to successfully measure the production and clearance of Aβ in the human CNS and have since translated this approach to other model systems including in vitro cell culture and animal models and to other proteins and diseases such as apolipoprotein E, soluble amyloid precursor proteins, tau, superoxide dismutase-1 (SOD1) in amyotrophic lateral sclerosis, and alpha-synuclein in Parkinson's disease. This chapter will review recent advancements in the development and application of SILK for measuring the pathophysiology and drug development for CNS diseases. SILK has provided important insights into Alzheimer's disease pathophysiology with altered synthesis and clearance of amyloid-beta, and drug effects on amyloid-beta. Further, the risk factors of AD, including aging, the largest AD risk factor, reveal profound slowing of amyloid-beta clearance, and the most prevalent genetic risk factor, apolipoprotein E, is being assessed. The initial work in AD has been expanded to specific proteins involved in the pathogenesis of other CNS disorders including amyotrophic lateral sclerosis (i.e., SOD) and Parkinson's disease (i.e., alpha-synuclein). The use of SILK technology with specific disease-causing proteins has been generalized using SILAV to expand its application to addressing questions in proteomics and the peripheral compartments outside of the CNS.