Utility of high resolution accurate mass spectrometry (HRMS) in the mass isotopomer distribution analysis (MIDA) of CSF proteins modified by stable isotope labeling in mammals (SILAM) methodology applied to neurodegenerative diseases

The research on neurodegenerative diseases is challenged by accurate disease diagnosis and evaluation of treatment response, thus there is a need for indicators at the molecular level, specifically biomarkers, that reliably provide disease diagnostic, progression, and prognostic information. The parenchyma of the brain is immersed in the interstitial fluid (ISF), which is in equilibrium with the cerebrospinal fluid (CSF) allowing for ex vivo sample analysis of potential endogenous in vivo biomarkers. Details on the kinetic parameters of these analytes may provide a more sensitive, specific and accurate measure of disease pathology, biological physiology, and pharmacodynamic response of therapeutics. To study the differential changes in the de novo biosynthesis as well as the clearance of proteinaceous/peptidic biomarkers, a mass spectrometric detectable label is introduced via stable isotope labeling in mammals (SILAM) methodology. Proteolytic processing of the proteins generates surrogate proteotypic peptides. The mass isotopomer distribution analysis (MIDA) of these proxy reporters via high resolution accurate mass spectrometry (HRMS) provides kinetic profiles of the proteins. Presented here is the conceptual methodology of applying LC-HRMS analysis to obtain MIDA data of CSF proteins which were modified by SILAM methodology utilizing D-labeled water ((H2O)-H-2, D2O).