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In quantitative mass spectrometry-based proteomics, the metabolic incorporation of a single source of  15 N-labeled nitrogen has many advantages over using stable isotope-labeled amino acids. However, the lack of a robust computational framework for analyzing the resulting spectra has impeded wide use of this approach. We have addressed this challenge by introducing a new computational methodology for analyzing  15 N spectra in which quantification is integrated with identification. Application of this method to an  Escherichia coli  growth transition reveals significant improvement in quantification accuracy over previous methods.

Accurate proteome-wide protein quantification from high-resolution 15N mass spectra