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INNOVATIVE METHODOLOGY

Determination of protein synthesis in vivo using labeling from deuterated water and analysis of MALDI-TOF spectrum

¹Department of Pediatrics, Division of Endocrinology, Los Angeles Biomedical Research Institute at Harbor-University of California Los Angeles Medical Center; and ²Department of Medicine, Division of Gastroenterology, David Geffen School of Medicine, Los Angeles, California

Submitted 14 September 2007 ; accepted in final form 12 December 2007

This paper describes a method of determining protein synthesis and turnover using in vivo labeling of protein with deuterated water and analysis of matrix-assisted laser desorption time-of-flight mass spectrometer (MALDI-TOF) spectrum. Protein synthesis is calculated using mass isotopomer distribution analysis instead of precursor to product amino acid enrichment ratio. During protein synthesis, the incorporation of deuterium from water changes the mass isotopomer distribution (isotope envelop) according to the number of deuterium atoms (0, 1, 2, 3, etc.) incorporated, and the distribution of the protein with 0, 1, 2, 3,... atoms of deuterium follows a binomial distribution. A mathematical algorithm by which the distribution of deuterium isotopomers can be extracted from the observed MALDI-TOF spectrum is presented. Since deuterium isotopomers are unique to newly synthesized proteins, the quantitation of their distribution provides a method for the quantitation of newly synthesized proteins. The combined use of postsource decay sequence identification and mass isotopomer distribution analysis makes the use of in vivo labeling with deuterated water a precise method to determine specific protein synthesis.

mass isotopomer distribution analysis; isotopomer; spectral analysis; peptide sequence identification; matrix-assisted laser desorption time-of-flight mass spectrometer

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