Many different approaches for stable isotopic labeling to compare proteins from test and control samples using mass spectrometry have been described (Tao and Aebersold, 2003). These include in vitro labeling techniques employing commercially available reagents such as ICAT, iTRAQ and other chemical modification strategies, and in vivo labeling utilizing an organism/cell line's nutrient fixation processes for label incorporation. In vivo or metabolic labeling typically uses isotopically labeled amino acids (as in SILAC) or ubiquitously incorporated nutrients such as ammonia or nitrate for 15N or acetate or glucose for ~(13)C. We are primarily interested in ubiquitous incorporation strategies for relative quantification of proteins in plants. Here we explore two different strategies for relative quantification utilizing 15N-metabolic labeling of the model plant Arabidopsis thaliana using growth in light vs. dark as a simple test scenario.
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