A Correlation Algorithm for the Automated Quantitative Analysis of Shotgun Proteomics Data

Michael J. MacCoss, Christine C. Wu, Hongbin Liu, Rovshan Sadygov, John R. Yates

Research output: Contribution to journalArticle

232 Citations (Scopus)

Abstract

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.

Original languageEnglish (US)
Pages (from-to)6912-6921
Number of pages10
JournalAnalytical Chemistry
Volume75
Issue number24
DOIs
StatePublished - Dec 15 2003
Externally publishedYes

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Mass spectrometry
Ions
Peptides
Systematic errors
Chemical analysis
Isotopes
Yeast
Labeling
Computer program listings
Proteins
Throughput
Proteomics
Osmotic Pressure

ASJC Scopus subject areas

  • Analytical Chemistry

Cite this

A Correlation Algorithm for the Automated Quantitative Analysis of Shotgun Proteomics Data. / MacCoss, Michael J.; Wu, Christine C.; Liu, Hongbin; Sadygov, Rovshan; Yates, John R.

In: Analytical Chemistry, Vol. 75, No. 24, 15.12.2003, p. 6912-6921.

Research output: Contribution to journalArticle

MacCoss, Michael J. ; Wu, Christine C. ; Liu, Hongbin ; Sadygov, Rovshan ; Yates, John R. / A Correlation Algorithm for the Automated Quantitative Analysis of Shotgun Proteomics Data. In: Analytical Chemistry. 2003 ; Vol. 75, No. 24. pp. 6912-6921.
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