Stable isotope metabolic labeling suggests differential turnover of the DPYSL protein family.

Abstract

In this work, we discuss how in vivo 15 N metabolic labeling in combination with MS simultaneously provides information on protein expression and protein turnover. We metabolically labeled mice with the stable nitrogen isotope 15 N using a 15 N-enriched diet and analyzed unlabeled (14 N) versus 15 N-labeled brain tissue with LC-MS/MS. We then compared the 14 N versus 15 N peptide isotopologue clusters of 14 N and 15 N-labeled dihydropyrimidinase-related (DPYSL) proteins. We present a workflow assessing protein expression and turnover at different time points of mouse brain development. Our data demonstrate distinct protein turnover patterns of DPYSL3 and DPYSL5 compared to other quantified proteins. We report the presence of two DPYSL3 and DPYSL5 populations with different 15 N incorporation rates, indicating altered protein turnover during development. In vivo 15 N metabolic labeling allows the simultaneous investigation of protein expression and turnover, enabling detailed protein dynamics studies. We report for the first time protein turnover data for the DPYSL2, DPYSL3, and DPYSL5 protein family members. As DPYSL proteins have important functions for nervous system maturation, our data provide useful information on their molecular fate during brain development.