2011 Articles

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

Kryglyak, Leonid; Singh, Mona; Perlman, David H.; Tavazoie, Saeed; Caudy, Amy A.; Ruse, Christian; Amini, Sasan; Bloom, Joshua S.; Khan, Zia

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