title: Comparative evaluation of two isobaric labeling tags, DiART and iTRAQ.
abstract: Isobaric tags have broad applications in both basic and translational research, as demonstrated by the widely used isobaric tag for relative and absolute quantitation (iTRAQ). Recent results from large-scale quantitative proteomics projects, however, indicate that protein quantification by iTRAQ is often biased in complex biological samples. Here, we report the application of another isobaric tag, deuterium isobaric amine reactive tag (DiART), for quantifying the proteome of Thermoanaerobacter tengcongensis (T. tengcongensis), a thermophilic bacterium first discovered in China. We compared the performance of DiART with iTRAQ from several different aspects, including their fragmentation mechanisms, the number of identified proteins, and the accuracy of quantification. Our results revealed that, as compared with iTRAQ, DiART yielded significantly stronger reporter ions, which did not reduce the number of identifiable peptides, but improved the signal-to-noise ratio (S/N) for quantification. Remarkably, we found that, under identical chromatography and mass spectrometry (MS) conditions, DiART exhibited less reporter ions ratio compression than iTRAQ, probably due to more reporter ions with higher intensities produced by DiART labeling. Taken together, we demonstrate that DiART is a valuable alternative of iTRAQ with enhanced performance for quantitative proteomics.
authors.affiliation: Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.
authors.forename: Zhen
authors.initials: Z
authors.lastname: Chen
authors.forename: Quanhui
authors.initials: Q
authors.lastname: Wang
authors.forename: Liang
authors.initials: L
authors.lastname: Lin
authors.forename: Qi
authors.initials: Q
authors.lastname: Tang
authors.forename: James L
authors.initials: JL
authors.lastname: Edwards
authors.forename: Shuwei
authors.initials: S
authors.lastname: Li
authors.forename: Siqi
authors.initials: S
authors.lastname: Liu
mesh_terms: D000588:Amines / Q000737:chemistry; D001426:Bacterial Proteins / Q000032:analysis*; D003903:Deuterium / Q000737:chemistry; D007477:Ions / Q000737:chemistry; D010455:Peptides / Q000032:analysis; D020543:Proteome / Q000032:analysis / Q000302:isolation & purification; D040901:Proteomics / Q000379:methods*; D013194:Staining and Labeling / Q000379:methods; D053719:Tandem Mass Spectrometry / Q000379:methods*; D046968:Thermoanaerobacter / Q000737:chemistry*
chemical_list: D000588:Amines; D001426:Bacterial Proteins; D007477:Ions; D010455:Peptides; D020543:Proteome; D003903:Deuterium