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A comparison of the consistency of proteome quantitation using two‐dimensional electrophoresis and shotgun isobaric tagging in Escherichia coli cells
Author(s) -
Choe Leila H.,
Aggarwal Kunal,
Franck Zsofia,
Lee Kelvin H.
Publication year - 2005
Publication title -
electrophoresis
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.666
H-Index - 158
eISSN - 1522-2683
pISSN - 0173-0835
DOI - 10.1002/elps.200410336
Subject(s) - shotgun , shotgun proteomics , isobaric process , quantitative proteomics , isobaric labeling , consistency (knowledge bases) , proteome , chromatography , protein expression , reproducibility , chemistry , proteomics , coefficient of variation , biology , computational biology , biochemistry , computer science , gene , physics , artificial intelligence , thermodynamics
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.