title: Comparing the Diagnostic Classification Accuracy of iTRAQ, Peak-Area, Spectral-Counting, and emPAI Methods for Relative Quantification in Expression Proteomics.
abstract: Diagnostic classification accuracy is critical in expression proteomics to ensure that as many true differences as possible are identified with acceptable false-positive rates. We present a comparison of the diagnostic accuracy of iTRAQ with three label-free methods, peak area, spectral counting, and emPAI, for relative quantification using a spiked proteome standard. We provide the first validation of emPAI for intersample relative quantification and find clear differences among the four quantification approaches that could be considered when designing an experiment. Spectral counting was observed to perform surprisingly well in all regards. Peak area performed best for smaller fold differences and was shown to be capable of discerning a 1.1-fold difference with acceptable specificity and sensitivity. The performance of iTRAQ was dramatically worse than the label-free methods with low abundance proteins. Using the iTRAQ data set for validation, we also demonstrate a novel iTRAQ analysis regime that avoids the use of ratios in significance testing and outperforms a common commercial alternative.
authors.affiliation: Bioscience Technology Facility, Department of Biology, University of York , York YO10 5DD, United Kingdom.
authors.forename: Adam A
authors.initials: AA
authors.lastname: Dowle
authors.affiliation: Departments of Mathematics and Chemistry, University of York , York YO10 5DD, United Kingdom.
authors.forename: Julie
authors.initials: J
authors.lastname: Wilson
authors.affiliation: Bioscience Technology Facility, Department of Biology, University of York , York YO10 5DD, United Kingdom.
authors.forename: Jerry R
authors.initials: JR
authors.lastname: Thomas
mesh_terms: D002965:Classification / Q000379:methods; D019937:Diagnostic Techniques and Procedures; D006801:Humans; D013058:Mass Spectrometry; D040901:Proteomics / Q000379:methods* / Q000592:standards; D012372:ROC Curve; D012015:Reference Standards; D013194:Staining and Labeling
keywords: emPAI; expression proteomics; iTRAQ; label-free; peak area; relative quantification; spectral counting