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Issue 12, 2006
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Comparison of spectral counting and metabolic stable isotope labeling for use with quantitative microbial proteomics

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Abstract

Spectral counting, a promising method for quantifying relative changes in protein abundance in mass spectrometry-based proteomic analysis, was compared to metabolic stable isotope labeling using 15N/14N “heavy/light” peptide pairs. The data were drawn primarily from a Methanococcus maripaludis experiment comparing a wild-type strain with a mutant deficient in a key enzyme relevant to energy metabolism. The dataset contained both proteome and transcriptome measurements. The normalization technique used previously for the isotopic measurements was inappropriate for spectral counting, but a simple adjustment for sampling frequency was sufficient for normalization. This adjustment was satisfactory both for M. maripaludis, an organism that showed relatively little expression change between the wild-type and mutant strains, and Porphyromonas gingivalis, an intracellular pathogen that has demonstrated widespread changes between intracellular and extracellular conditions. Spectral counting showed lower overall sensitivity defined in terms of detecting a two-fold change in protein expression, and in order to achieve the same level of quantitative proteome coverage as the stable isotope method, it would have required approximately doubling the number of mass spectra collected.

Graphical abstract: Comparison of spectral counting and metabolic stable isotope labeling for use with quantitative microbial proteomics

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Publication details

The article was received on 31 Jul 2006, accepted on 29 Sep 2006 and first published on 11 Oct 2006


Article type: Paper
DOI: 10.1039/B610957H
Citation: Analyst, 2006,131, 1335-1341
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    Comparison of spectral counting and metabolic stable isotope labeling for use with quantitative microbial proteomics

    E. L. Hendrickson, Q. Xia, T. Wang, J. A. Leigh and M. Hackett, Analyst, 2006, 131, 1335
    DOI: 10.1039/B610957H

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