Cerebrospinal fluid (CSF) has been considered the key source for the search of biomarkers, in particular for neurological diseases, such as Alzheimer's and Parkinson's disease, since it reflects the state of the central nervous system (CNS). Finding biomarkers in the earliest stages of neurodegenerative diseases has become imperative, since, at the moment, there are no drugs that can reverse these pathological processes. Untargeted metabolomics analysis by liquid chromatography combined with SWATH-MS relative quantification is an emerging approach to search for potential biomarkers. In this chapter, we describe a method for untargeted metabolomics analysis of CSF samples that can also be used in parallel to a proteomics approach. The analysis is focused on the SWATH acquisition mode, where beyond precursor's relative quantification, the information of the MS/MS relative quantification is also used to help in the search of new potential biomarkers.
Keywords: Cerebrospinal fluid; Potential biomarkers; SWATH-MS relative quantification; Untargeted metabolomics.