Proteostasis Modelling using Deuterated Water Metabolic Labeling and Data-Independent Acquisition Mass Spectrometry

We present the first application of a deuterated water metabolic labeling workflow coupled with data-independent acquisition (DIA) tandem mass spectrometry (MS/MS) for quantifying label enrichment in MS/MS to study protein turnover. The approach automates the turnover rate determination from combined precursor and fragment ions. The truncation of the observed isotope distributions of fragments is overcome by implementing an approach to determining the label enrichment from two mass isotopomers. The high redundancy of fragment ions provides a confident assessment for deuterium enrichment. The DIA approach provides increased proteome coverage and depth for quantifying protein turnover rates compared to the traditional data-dependent (DDA) approach. This novel approach is validated in a murine myotube model of muscle hypertrophy and atrophy through the treatment with insulin-like growth factor 1 (IGF-1) and dexamethasone (Dex), respectively.