Characterization of cerebrospinal fluid via data-independent acquisition mass spectrometry

Cerebrospinal fluid (CSF) is in direct contact with the brain and serves as a valuable specimen to examine neurodegenerative diseases in order to identify suitable diagnostic biomarkers. In the field of neuroproteomics the most popular mass spectrometry-based strategy for biomarker discovery studies is data-dependent acquisition (DDA). Drawbacks of this method are stochastic and irreproducible precursor ion selection. Recently, data-independent acquisition (DIA) emerged as an alternative method. In this study we evaluate the use of DIA for native CSF analytics with particular focus on spectral library generation for data analysis, DIA data reproducibility and identification of brain specific proteins.

脑脊液（Cerebrospinal fluid, CSF）与大脑直接接触，是研究神经退行性疾病、筛选适配诊断生物标志物的优质样本。在神经蛋白质组学领域，用于生物标志物发现研究的主流基于质谱的策略为数据依赖型采集（data-dependent acquisition, DDA）。该方法的缺陷在于前体离子选择具有随机性且无法重现。近年来，数据非依赖型采集（data-independent acquisition, DIA）作为替代方法应运而生。本研究评估了DIA在天然脑脊液分析中的应用，重点关注数据分析所需的谱库构建、DIA数据的重现性以及脑特异性蛋白的鉴定。