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

In quantitative mass spectrometry-based proteomics, the metabolic incorporation of a single source of N-15-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 N-15 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.