title: Statistical inference from multiple iTRAQ experiments without using common reference standards.
abstract: Isobaric tags for relative and absolute quantitation (iTRAQ) is a prominent mass spectrometry technology for protein identification and quantification that is capable of analyzing multiple samples in a single experiment. Frequently, iTRAQ experiments are carried out using an aliquot from a pool of all samples, or "masterpool", in one of the channels as a reference sample standard to estimate protein relative abundances in the biological samples and to combine abundance estimates from multiple experiments. In this manuscript, we show that using a masterpool is counterproductive. We obtain more precise estimates of protein relative abundance by using the available biological data instead of the masterpool and do not need to occupy a channel that could otherwise be used for another biological sample. In addition, we introduce a simple statistical method to associate proteomic data from multiple iTRAQ experiments with a numeric response and show that this approach is more powerful than the conventionally employed masterpool-based approach. We illustrate our methods using data from four replicate iTRAQ experiments on aliquots of the same pool of plasma samples and from a 406-sample project designed to identify plasma proteins that covary with nutrient concentrations in chronically undernourished children from South Asia.
authors.affiliation: Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA.
authors.forename: Shelley M
authors.initials: SM
authors.lastname: Herbrich
authors.forename: Robert N
authors.initials: RN
authors.lastname: Cole
authors.forename: Keith P
authors.initials: KP
authors.lastname: West
authors.forename: Kerry
authors.initials: K
authors.lastname: Schulze
authors.forename: James D
authors.initials: JD
authors.lastname: Yager
authors.forename: John D
authors.initials: JD
authors.lastname: Groopman
authors.forename: Parul
authors.initials: P
authors.lastname: Christian
authors.forename: Lee
authors.initials: L
authors.lastname: Wu
authors.forename: Robert N
authors.initials: RN
authors.lastname: O'Meally
authors.forename: Damon H
authors.initials: DH
authors.lastname: May
authors.forename: Martin W
authors.initials: MW
authors.lastname: McIntosh
authors.forename: Ingo
authors.initials: I
authors.lastname: Ruczinski
mesh_terms: D001798:Blood Proteins / Q000737:chemistry*; D002138:Calibration; D002648:Child; D015362:Child Nutrition Disorders / Q000097:blood*; D002853:Chromatography, Liquid; D006801:Humans; D009390:Nepal; D010446:Peptide Fragments / Q000032:analysis*; D040901:Proteomics; D012015:Reference Standards; D053719:Tandem Mass Spectrometry / Q000379:methods / Q000592:standards* / Q000706:statistics & numerical data*; D014357:Trypsin / Q000737:chemistry
chemical_list: D001798:Blood Proteins; D010446:Peptide Fragments; D014357:Trypsin