Opinion Article - Journal of Systems Biology & Proteome Research (2022) Volume 3, Issue 6

PROTEOME DYNAMICS IN VIVO FROM LC-MS AND HEAVY WATER METABOLIC LABELING

A dynamic equilibrium between protein synthesis and degradation leads to protein homeostasis. It is crucial for the proper operation of all organs and is frequently linked to illnesses like nonalcoholic fatty liver disease and neurodegenerative diseases. Using liquid chromatography, mass spectrometry, and heavy water metabolic labelling together provides a potent method for studying proteostasis in vivo with high throughput. In time-course investigations, stable isotope incorporation is often estimated using intact peptide signals. The protein decay rate constant is derived from the time-course of label incorporation. A reliable estimate of label incorporation is often provided by intact peptide signals, which are computed from integration in chromatographic time and mass-to-charge ratio domains. The peptide signals could be negatively impacted by sample complexity, a small dynamic range, and a low signal-to-noise ratio, though. By altering peak shape in the chromatographic time and m/z domains, these artefacts make the DRC estimations more difficult. On the other hand, fragment ions are less susceptible to these distortions and may be an excellent tool for supporting DRC estimations. Here, we demonstrate that the isotope enrichment during metabolic labelling with heavy water is reflected in the label incorporation encoded into the isotope distributions of fragment ions. In order to create useful methods for DRC estimations, we investigate the label incorporation statistics.

Author(s): Chantal Alharbi

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