Max-Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam, Germany.
Mol Cell Proteomics. 2012 Sep;11(9):619-28. doi: 10.1074/mcp.M112.017178. Epub 2012 May 5.
This study reports the comprehensive comparison of (15)N 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 (15)N 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.
本研究报告了（15）N 代谢标记和无标记蛋白质组学策略在定量方面的综合比较，特别关注植物蛋白质组学。我们对广泛的混合比例和蛋白质加载的蛋白质组覆盖范围、动态范围和定量精度进行了调查，旨在帮助研究人员在实验设计过程中进行决策。无标记策略的主要特点之一是适用于所有起始材料，这是代谢标记的一个限制。然而，特别是在混合比例高达 10 倍的情况下，（15）N 代谢标记被证明更精确。与本研究结果所依据的通常做法相反，我们建议在代谢标记中使用不等混合比例可以进一步提高定量的蛋白质组覆盖范围。另一方面，无标记策略与低蛋白质加载相结合，可以扩展定量的动态范围，并且在非常高的比例下更精确，这对于某些类型的实验可能很重要。
