accurate proteome-wide protein quantification from high-resolution 15n mass spectra从高分辨率精确proteome-wide蛋白量化15 n质谱.pdfVIP

Khan et al. Genome Biology 2011, 12:R122 /2012/12/12/R122 METHOD Open Access Accurate proteome-wide protein quantification from high-resolution 15N mass spectra 1,2,3 2,4,5† 2,4 6 2,7 2,8,9 Zia Khan , Sasan Amini , Joshua S Bloom , Cristian Ruse , Amy A Caudy , Leonid Kruglyak , Mona Singh1,2, David H Perlman2,4,10 and Saeed Tavazoie2,4,11* Abstract 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. Background the samples are subjected to the same extraction, sample Experimental methods for proteome-wide quantification handling, digestion, chromatography, and ionization using liquid chromatography coupled mass spectrometry conditions. This eliminates much of the technical varia- (LC-MS) rest heavily on computational methods that tion between individual samples. Consequently, the final analyze mass spectra for peptide and protein quantifica- relative abundance measurements, in the form of ratios tion [1]. Computational analysis typically relies on two of the