A SILAC Study of Biological Variability in the Mouse: the Murine Cardiac Proteome

摘要

SILAC mice at the F2 generation showed an incorporation in the heart of ca. 95percent with a spread of +/- 3percent. Neither the overall incorporation nor the spread improved with subsequent generations. Because their diets are not identical, there are protein abundance differences between the labeled and unlabeled sedentary control animals. The result of the first two listed items is that the SILAC Mouse is best used as a global internal standard. Due to the time and resource intensive nature of comprehensive proteomic projects the analysis of large numbers of biological replicates is not a viable approach. As a compromise, biological replicates can be pooled into a single sample. While averaging separate biological replicates reduces the overall experimental variability, pooling only reduces the pure population variability. However, we find that in these experiments pure population variability is the single largest component of overall variability, contributing nearly 50percent. The variability in technical replicates is quite small (0.016 log2 units). Metabolic incorporation of stable isotopes reduces the sample prep variability to a value essentially equivalent to technical replicates.