Journal
ANALYTICAL CHEMISTRY
Volume 75, Issue 24, Pages 6912-6921Publisher
AMER CHEMICAL SOC
DOI: 10.1021/ac034790h
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Funding
- NCRR NIH HHS [RR11823-08] Funding Source: Medline
- NIAID NIH HHS [F32AI54333] Funding Source: Medline
- NIDDK NIH HHS [F32DK59731] Funding Source: Medline
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Quantitative shotgun proteomic analyses are facilitated using chemical tags such as ICAT and metabolic labeling strategies with stable isotopes. The rapid high-throughput production of quantitative shotgun proteomic data necessitates the development of software to automatically convert mass spectrometry-derived data of peptides into relative protein abundances. We describe a computer program called RelEx, which uses a least-squares regression for the calculation of the peptide ion current ratios from the mass spectrometry-derived ion chromatograms. RelEx is tolerant of poor signal-to-noise data and can automatically discard nonusable chromatograms and outlier ratios. We apply a simple correction for systematic errors that improves the accuracy of the quantitative measurement by 32 +/- 4%. Our automated approach was validated using labeled mixtures composed of known molar ratios and demonstrated in a real sample by measuring the effect of osmotic stress on protein expression in Saccharomyces cerevisiae.
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