Deep proteomic profiling of matched CSF and plasma samples for aging biomarker discovery beyond protein

Aging is the leading risk factor for many neurodegenerative disorders. However, the transition between healthy and diseased state in advanced age is poorly understood. To elucidate potential early signs of degeneration-related changes in healthy aging, we aimed to find differential cleavage, alternative splicing and phosphorylation events in aging cerebrospinal fluid (CSF) and plasma of cognitively normal adults. To this end, we applied data-independent acquisition mass spectrometry (DIA-MS) with Biognosys’ TrueDiscovery^® platform to profile both sample types and analysed MS data using Spectronaut^® software.

We quantified 5,599 and 3,112 protein groups, and 127,560 and 94,415 peptides in CSF and plasma respectively. Then we focused on the peptide differential abundance to perform proteome-wide analysis of endogenous cleavage, splicing and phosphorylation changes in aging. We found differential cleavage, potential alternative splicing and phosphorylation from both known aging and neurodegeneration associated genes (including APOE, APP and APLP1) as well as novel genes for which association with aging and neurodegeneration has not yet been established.