Over the past decade, liquid chromatography tandem mass spectrometry (LC MS/MS)-based workflows become standard for biomarker discovery in proteomics. These medium- to high-throughput (in terms of protein content) profiling approaches have been applied to clinical research. As a result, human proteomes have been characterized to a greater extent than ever before. However, proteomics in clinical research and biomarker discovery studies has generally been performed with small cohorts of subjects (or pooled samples from larger cohorts). This is problematic, as when aiming to identify novel biomarkers, small studies suffer from inherent and important limitations, as a result of the reduced biological diversity and representativity of human populations. Consequently, larger-scale proteomics will be key to delivering robust biomarker candidates and enabling translation to clinical practice.Cerebrospinal fluid (CSF) is a highly clinically relevant body fluid, and an important source of potential biomarkers for brain-associated damage, such as that induced by traumatic brain injury and stroke, and brain diseases, such as Alzheimer's disease and Parkinson's disease. We have developed a scalable automated proteomic pipeline (ASAP) for biomarker discovery. This workflow is compatible with larger clinical research studies in terms of sample size, while still allowing several hundred proteins to be measured in CSF by MS. In this chapter, we describe the whole proteomic workflow to analyze human CSF. We further illustrate our protocol with some examples from an analysis of hundreds of human CSF samples, in the specific context of biomarker discovery to characterize central nervous system disorders.