title: iTRAQ-Based and Label-Free Proteomics Approaches for Studies of Human Adenovirus Infections.
abstract: Both isobaric tags for relative and absolute quantitation (iTRAQ) and label-free methods are widely used for quantitative proteomics. Here, we provide a detailed evaluation of these proteomics approaches based on large datasets from biological samples. iTRAQ-label-based and label-free quantitations were compared using protein lysate samples from noninfected human lung epithelial A549 cells and from cells infected for 24 h with human adenovirus type 3 or type 5. Either iTRAQ-label-based or label-free methods were used, and the resulting samples were analyzed by liquid chromatography (LC) and tandem mass spectrometry (MS/MS). To reduce a possible bias from quantitation software, we applied several software packages for each procedure. ProteinPilot and Scaffold Q+ software were used for iTRAQ-labeled samples, while Progenesis LC-MS and ProgenesisF-T2PQ/T3PQ were employed for label-free analyses. R (2) correlation coefficients correlated well between two software packages applied to the same datasets with values between 0.48 and 0.78 for iTRAQ-label-based quantitations and 0.5 and 0.86 for label-free quantitations. Analyses of label-free samples showed higher levels of protein up- or downregulation in comparison to iTRAQ-labeled samples. The concentration differences were further evaluated by Western blotting for four downregulated proteins. These data suggested that the label-free method was more accurate than the iTRAQ method.
authors.affiliation: Institute of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland ; Life Science Zurich Graduate School, Molecular Life Science Program, Switzerland.
authors.forename: Hung V
authors.initials: HV
authors.lastname: Trinh
authors.forename: Jonas
authors.initials: J
authors.lastname: Grossmann
authors.forename: Peter
authors.initials: P
authors.lastname: Gehrig
authors.forename: Bernd
authors.initials: B
authors.lastname: Roschitzki
authors.forename: Ralph
authors.initials: R
authors.lastname: Schlapbach
authors.forename: Urs F
authors.initials: UF
authors.lastname: Greber
authors.forename: Silvio
authors.initials: S
authors.lastname: Hemmi
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