title: A comparison of the consistency of proteome quantitation using two-dimensional electrophoresis and shotgun isobaric tagging in Escherichia coli cells.
abstract: An important consideration in the measurement of quantitative changes in protein expression is the consistency of the observations for a given technique as well as the reproducibility of the experiment. A quantitative assessment of the technical and biological variability is crucial to avoid erroneous inferences and conclusions. Two methods for measuring quantitative changes in protein expression are two-dimensional electrophoresis (2-DE) and shotgun proteomics of isobaric-tagged samples using iTRAQ reagents. An assessment of changes in Escherichia coli protein expression in response to rhsA induction demonstrates that half of the quantified protein expression ratios have a coefficent of variation (CV) less than 0.31 using 2-DE and less than 0.24 using isobaric tags; whereas 95% of the quantified protein expression ratios have a CV less than 0.81 using 2-DE and less than 0.53 using isobaric tags. The selective removal of outlier data points from the shotgun method using Grubb's and Rosner's statistical outlier tests improves the consistency of the quantitation data obtained.
authors.affiliation: School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY 14853-5201, USA.
authors.forename: Leila H
authors.initials: LH
authors.lastname: Choe
authors.forename: Kunal
authors.initials: K
authors.lastname: Aggarwal
authors.forename: Zsofia
authors.initials: Z
authors.lastname: Franck
authors.forename: Kelvin H
authors.initials: KH
authors.lastname: Lee
mesh_terms: D002853:Chromatography, Liquid; D015180:Electrophoresis, Gel, Two-Dimensional / Q000379:methods*; D004926:Escherichia coli / Q000378:metabolism; D029968:Escherichia coli Proteins / Q000032:analysis*; D005456:Fluorescent Dyes; D015870:Gene Expression; D013058:Mass Spectrometry; D020543:Proteome / Q000032:analysis*; D040901:Proteomics / Q000379:methods*; D015203:Reproducibility of Results
chemical_list: D029968:Escherichia coli Proteins; D005456:Fluorescent Dyes; D020543:Proteome