Data‐Independent Acquisition and Label‐Free Quantification for Quantitative Proteomics Analysis of Human Cerebrospinal Fluid

Abstract This article presents a practical guide to mass spectrometry–based data‐independent acquisition and label‐free quantification for proteomics analysis applied to cerebrospinal fluid, offering a robust and scalable approach to probing the proteomic composition of the central nervous system. © 2024 Wiley Periodicals LLC. Basic Protocol 1 : Cerebrospinal fluid sample collection and preparation for mass spectrometry analysis Basic Protocol 2 : Mass spectrometry sample analysis with data‐independent acquisition Support Protocol : Data‐dependent mass spectrometry and spectral library construction Basic Protocol 3 : Analysis of mass spectrometry data