A comprehensive map and functional annotation of the normal human cerebrospinal fluid proteome

• This study identified the largest high-precision dataset of the CSF proteome.
• The absolute amounts of some CSF proteins are quantified.
• A high proportion of the CSF proteins are microenvironment components of CNS cells.
• A high proportion of the CSF proteins participate in neurocyte connectivity.
• A large part of CSF proteins are biomarker candidates of neurological diseases.

Knowledge about the normal human cerebrospinal fluid (CSF) proteome serves as a baseline reference for CSF biomarker discovery and provides insight into CSF physiology. In this study, high-pH reverse-phase liquid chromatography (hp-RPLC) was first integrated with a TripleTOF 5600 mass spectrometer to comprehensively profile the normal CSF proteome. A total of 49,836 unique peptides and 3256 non-redundant proteins were identified. To obtain high-confidence results, 2513 proteins with at least 2 unique peptides were further selected as bona fide CSF proteins. Nearly 30% of the identified CSF proteins have not been previously reported in the normal CSF proteome. More than 25% of the CSF proteins were components of CNS cell microenvironments, and network analyses indicated their roles in the pathogenesis of neurological diseases. The top canonical pathway in which the CSF proteins participated was axon guidance signaling. More than one third of the CSF proteins (788 proteins) were related to neurological diseases, and these proteins constitute potential CSF biomarker candidates. The mapping results can be freely downloaded at http://122.70.220.102:8088/csf/, which can be used to navigate the CSF proteome.Biological significanceThis study identified and functionally annotated the largest high-precision dataset of the CSF proteome, which offers a baseline reference for CSF biomarker discovery and reveals insight into CSF physiology.

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