title: A correlation algorithm for the automated quantitative analysis of shotgun proteomics data.
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.
authors.affiliation: Department of Cell Biology, The Scripps Research Institute, La Jolla, California 92037, USA.
authors.forename: Michael J
authors.initials: MJ
authors.lastname: MacCoss
authors.forename: Christine C
authors.initials: CC
authors.lastname: Wu
authors.forename: Hongbin
authors.initials: H
authors.lastname: Liu
authors.forename: Rovshan
authors.initials: R
authors.lastname: Sadygov
authors.forename: John R
authors.initials: JR
authors.lastname: Yates
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D001331:Automation; D019992:Databases as Topic; D013058:Mass Spectrometry / Q000379:methods; D008969:Molecular Sequence Data; D010455:Peptides / Q000032:analysis / Q000737:chemistry; D011506:Proteins / Q000032:analysis / Q000737:chemistry; D040901:Proteomics / Q000379:methods*; D012441:Saccharomyces cerevisiae / Q000737:chemistry
chemical_list: D010455:Peptides; D011506:Proteins