Precision, Proteome Coverage, and Dynamic Range of Arabidopsis Proteome Profiling Using 15N Metabolic Labeling and Label-free Approaches

This study reports the comprehensive comparison of N-15 metabolic labeling and label free proteomic strategies for quantitation, with particular focus on plant proteomics. Our investigation of proteome coverage, dynamic range and quantitative precision for a wide range of mixing ratios and protein loadings aim to aid the investigators in the decision making process during experimental design. One of the main characteristics of the label free strategy is the applicability to all starting material, which is a limitation to the metabolic labeling. However, particularly at mixing ratios up to 10-fold the N-15 metabolic labeling proved to be more precise. Contrary to usual practice based on the results from this study, we suggest that nonequal mixing ratios in metabolic labeling could further increase the proteome coverage for quantitation. On the other hand, the label free strategy, in combination with low protein loading allows the extension of the dynamic range for quantitation and it is more precise at very high ratios, which could be important for certain types of experiments. Molecular & Cellular Proteomics 11: 10.1074/mcp.M112.017178, 619-628, 2012.