Cerebrospinal fluid (CSF) proteins and their chemical states have been implicated repeatedly in aging and neurodegenerative diseases. To screen for novel aging-associated changes in CSF protein abundances and chemical states, we performed limited proteolysis-mass spectrometry (LiP-MS) on CSF from young and old mice. Several proteins change in abundance with aging, especially immunoglobulins and IgM in particular. In analyses of chemical states in data acquired in data-dependent acquisition (DDA) and data-independent acquisition (DIA) modes, comparisons revealed protein grouping to be a key factor in accurate structural analysis. We implemented a new protein grouping method designed to improve LiP-MS accuracy and tested for structural changes at the protein rather than peptide level. We discovered six high-confidence hits that appeared to change in chemical state with aging, including Kng1, Itih2, Lp-PLA<sub>2</sub>, and 14-3-3 proteins, all of which have binding partners or proteoforms that are known to change in the brain and/or CSF with Alzheimer’s disease. Cd5l, a binding partner of IgM, was a LiP-MS hit, and we discovered that the covalent Cd5l-IgM immunocomplex exists in CSF and that its abundance increases with aging.

Limited Proteolysis-mass spectrometry screening platform reveals aging-associated changes in cerebrospinal fluid protein abundances and chemical states

ACS Spring Meeting 2021

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