Precision, proteome coverage, and dynamic range of Arabidopsis proteome profiling using (15)N metabolic labeling and label-free approaches.

Molecular & Cellular Proteomics : MCP
Borjana ArsovaWaltraud Schulze

Abstract

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.

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Citations

Sep 22, 2015·Journal of Proteome Research·Rodrigo S ReisPeter M Waterhouse
May 6, 2016·Frontiers in Plant Science·Heidi Pertl-ObermeyerWaltraud X Schulze
May 16, 2014·Electrophoresis·William O SladeLeslie M Hicks
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Jan 1, 2015·Nature Plants·Rodrigo S ReisPeter M Waterhouse
Sep 18, 2012·Journal of Proteome Research·Henrik Zauber, Waltraud X Schulze
Jul 3, 2016·Molecular & Cellular Proteomics : MCP·Heidi Pertl-ObermeyerWaltraud X Schulze
Oct 13, 2017·Frontiers in Plant Science·Gene Hart-SmithMarc R Wilkins
Jun 20, 2020·Nature Communications·Sonia TarazonaAna Conesa

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