title: Integral quantification accuracy estimation for reporter ion-based quantitative proteomics (iQuARI).
abstract: With the increasing popularity of comparative studies of complex proteomes, reporter ion-based quantification methods such as iTRAQ and TMT have become commonplace in biological studies. Their appeal derives from simple multiplexing and quantification of several samples at reasonable cost. This advantage yet comes with a known shortcoming: precursors of different species can interfere, thus reducing the quantification accuracy. Recently, two methods were brought to the community alleviating the amount of interference via novel experimental design. Before considering setting up a new workflow, tuning the system, optimizing identification and quantification rates, etc. one legitimately asks: is it really worth the effort, time and money? The question is actually not easy to answer since the interference is heavily sample and system dependent. Moreover, there was to date no method allowing the inline estimation of error rates for reporter quantification. We therefore introduce a method called iQuARI to compute false discovery rates for reporter ion based quantification experiments as easily as Target/Decoy FDR for identification. With it, the scientist can accurately estimate the amount of interference in his sample on his system and eventually consider removing shadows subsequently, a task for which reporter ion quantification might not be the solution of choice.
authors.affiliation: Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V., Dortmund, Germany.
authors.forename: Marc
authors.initials: M
authors.lastname: Vaudel
authors.forename: Julia M
authors.initials: JM
authors.lastname: Burkhart
authors.forename: Sonja
authors.initials: S
authors.lastname: Radau
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: D019843:Archaeal Proteins / Q000737:chemistry* / Q000302:isolation & purification; D001792:Blood Platelets / Q000378:metabolism*; D002851:Chromatography, High Pressure Liquid; D005189:False Positive Reactions; D006367:HeLa Cells; D006801:Humans; D010449:Peptide Mapping / Q000379:methods / Q000592:standards; D020543:Proteome / Q000737:chemistry* / Q000302:isolation & purification; D040901:Proteomics; D020027:Pyrococcus furiosus / Q000737:chemistry*; D012015:Reference Standards; D053719:Tandem Mass Spectrometry / Q000592:standards
chemical_list: D019843:Archaeal Proteins; D020543:Proteome