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By Sameh Magdeldin

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Therefore, the successful implementation of the heavy water labeling experiment, in addition to improvements in mass spectrometry, sample preparation, and fractionation, depends on the efficiency of robust software for data processing. It is also preferable that the software could handle the data generated by different high-resolution instruments. Recently, several highresolution mass spectrometer platforms have been used to study protein turnover using stable isotopes, including 2H2O. Q-TOF mass spectrometer (Agilent) was applied to assess the proteome dynamics in plasma and different tissues [25].

These stringent selection criteria combined with precise isotope distribution analysis results in accurate quantification of protein synthesis rates. 5. Biological application of heavy water-based proteome turnover studies Recent technological advancements in bioanalytical instrumentation and their application to systems biology are starting to significantly advance our understanding of integrative physiology. These achievements would not be possible without progresses made in genomics, proteomics, and metabolomics, that is, “omics” technologies that enable comprehensive screening of the genome, proteome, and metabolome [70, 71], respectively.

The short-term heavy water protocol for protein synthesis The short-term protocol requires the bolus load of heavy water and the measurement of peptide enrichment during the semilinear increase segment of 2H-labeling time-course curve [15, 22]. The optimal design for the short-term heavy water protocol requires multiple time points in the early period of protein synthesis, although a single time-point sampling after 2 H2O administration is also possible [47]. For the kinetic calculations, we assume that protein levels do not change during the 2H2O-metabolic labeling study period, and that there is a steady-state flux of all proteins.

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