Quantitative analysis by mass spectrometry (MS) is a major challenge in\ud proteomics as the correlation between analyte concentration and signal\ud intensity is often poor due to varying ionisation efficiencies in the\ud presence of molecular competitors. However, relative quantitation\ud methods that utilise differential stable isotope labelling and mass\ud spectrometric detection are available. Many drawbacks inherent to\ud chemical labelling methods (ICAT, iTRAQ) can be overcome by\ud metabolic labelling with amino acids containing stable isotopes (e.g. 13C\ud and/or 15N) in methods such as Stable Isotope Labelling with Amino\ud acids in Cell culture (SILAC). SILAC has also been used for labelling of\ud proteins in plant cell cultures (1) but is not suitable for whole plant\ud labelling. Plants are usually autotrophic (fixing carbon from atmospheric\ud CO2) and, thus, labelling with carbon isotopes becomes impractical. In\ud addition, SILAC is expensive.\ud Recently, Arabidopsis cell cultures were labelled with 15N in a medium\ud containing nitrate as sole nitrogen source. This was shown to be suitable\ud for quantifying proteins and nitrogen-containing metabolites from this cell\ud culture (2,3).\ud Labelling whole plants, however, offers the advantage of studying\ud quantitatively the response to stimulation or disease of a whole multicellular\ud organism or multi-organism systems at the molecular level.\ud Furthermore, plant metabolism enables the use of inexpensive labelling\ud media without introducing additional stress to the organism. And finally,\ud hydroponics is ideal to undertake metabolic labelling under extremely\ud well-controlled conditions.\ud We demonstrate the suitability of metabolic 15N hydroponic isotope\ud labelling of entire plants (HILEP) for relative quantitative proteomic\ud analysis by mass spectrometry. To evaluate this methodology,\ud Arabidopsis plants were grown hydroponically in 14N and 15N media and subjected to oxidative stress
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