Flexible Quality Control for Protein Turnover Rates Using d2ome

Deberneh, Henock M.; Sadygov, Rovshan G.

doi:10.3390/ijms242115553

Cited by 1 publication

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References 29 publications

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“…The two-parameter data modeling simultaneously determines the turnover rate ( k ) and asymptotic RIA ( I 0 asymp ) for a peptide by fitting the time series of the monoisotopic RIA to the exponential decaying model, eq , using nonlinear least-squares regression . The N EH for a peptide at the plateau of labeling is then determined from eq , as N EH = ln false( italicI 0 normalasymp false) − ln false( italicI 0 ( 0 ) false) ln false( 1 − italicp normalW / ( 1 − p H ) false) …”

Section: Methodsmentioning

confidence: 99%

Numbers of Exchangeable Hydrogens from LC–MS Data of Heavy Water Metabolically Labeled Samples

Deberneh,

Taylor,

Borowik

et al. 2024

J. Am. Soc. Mass Spectrom.

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Labeling with deuterium oxide (D 2 O) has emerged as one of the preferred approaches for measuring the synthesis of individual proteins in vivo. In these experiments, the synthesis rates of proteins are determined by modeling mass shifts in peptides during the labeling period. This modeling depends on a theoretical maximum enrichment determined by the number of labeling sites (N EH ) of each amino acid in the peptide sequence. Currently, N EH is determined from one set of published values. However, it has been demonstrated that N EH can differ between species and potentially tissues. The goal of this work was to determine the number of N EH for each amino acid within a given experiment to capture the conditions unique to that experiment. We used four methods to compute the N EH values. To test these approaches, we used two publicly available data sets. In a de novo approach, we compute N EH values and the label enrichment from the abundances of three mass isotopomers. The other three methods use the complete isotope profiles and body water enrichment in deuterium as an input parameter. They determine the N EH values by (1) minimizing the residual sum of squares, (2) from the mole percent excess of labeling, and (3) the time course profile of the depletion of the relative isotope abundance of monoisotope. In the test samples, the method using residual sum of squares performed the best. The methods are implemented in a tool for determining the N EH for each amino acid within a given experiment to use in the determination of protein synthesis rates using D 2 O.

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