Reliability of Protein Abundance and Synthesis Measurements in Human Skeletal Muscle.

We investigated the repeatability of dynamic proteome profiling (DPP), which is a novel technique for measuring the relative abundance (ABD) and fractional synthesis rate (FSR) of proteins in humans. LC-MS analysis was performed on muscle samples taken from male participants (n = 4) that consumed 4 × 50 ml doses of deuterium oxide (2 H2 O) per day for 14 d. ABD was measured by label-free quantitation and FSR was calculated from time-dependent changes in peptide mass isotopomer abundances. One-hundred and one proteins had at least 1 unique peptide and were used in the assessment of protein ABD. Fifty-four of these proteins met more stringent criteria and were used in the assessment of FSR data. The median (M), lower- (Q1 ) and upper-quartile (Q3 ) values for protein FSR (%/d) were M = 1.63, Q1 = 1.07, Q3 = 3.24. The technical CV of ABD data had a median value of 3.6% (Q1 1.7% - Q3 6.7%), whereas the median CV of FSR data was 10.1% (Q1 3.5% - Q3 16.5%). These values compare favorably against other assessments of technical repeatability of proteomics data, which often set a CV of 20% as the upper bound of acceptability. This article is protected by copyright. All rights reserved