title: iTRAQ protein quantification: a quality-controlled workflow.
abstract: Reporter ion-based methods are among the major techniques to quantify peptides and proteins. Two main labels, tandem mass tag (TMT) and iTRAQ, are widely used by the proteomics community. They are, however, often applied as out-of-the-box methods, without thorough quality control. Thus, due to undiscovered limitations of the technique, irrelevant results might be trusted. To address this issue, we here propose a step-by-step quality control of the iTRAQ workflow. From sample preparation to final ratio calculation we provide metrics and techniques assessing the actual effectiveness of iTRAQ quantification as well as a novel method for more reliable protein ratio estimation.
authors.affiliation: Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V., Dortmund, Germany.
authors.forename: Julia M
authors.initials: JM
authors.lastname: Burkhart
authors.forename: Marc
authors.initials: M
authors.lastname: Vaudel
authors.forename: René P
authors.initials: RP
authors.lastname: Zahedi
authors.forename: Lennart
authors.initials: L
authors.lastname: Martens
authors.forename: Albert
authors.initials: A
authors.lastname: Sickmann
mesh_terms: D007202:Indicators and Reagents; D007477:Ions; D007554:Isotopes; D024101:Mitochondrial Proteins / Q000032:analysis; D010455:Peptides / Q000032:analysis; D011506:Proteins / Q000032:analysis*; D040901:Proteomics / Q000379:methods / Q000592:standards* / Q000706:statistics & numerical data; D011786:Quality Control; D029701:Saccharomyces cerevisiae Proteins / Q000032:analysis; D053719:Tandem Mass Spectrometry / Q000592:standards / Q000706:statistics & numerical data; D057188:Workflow
chemical_list: D007202:Indicators and Reagents; D007477:Ions; D007554:Isotopes; D024101:Mitochondrial Proteins; D010455:Peptides; D011506:Proteins; D029701:Saccharomyces cerevisiae Proteins