title: Peptide-Centric Approaches Provide an Alternative Perspective To Re-Examine Quantitative Proteomic Data.
abstract: Quantitative proteomics can provide rich information on changes in biological functions and processes. However, its accuracy is affected by the inherent information degeneration found in bottom-up proteomics. Therefore, the precise protein inference from identified peptides can be mistaken since an ad hoc rule is used for generating a list of protein groups that depends on both the sample type and the sampling depth. Herein, we propose an alternative approach for examining quantitative proteomic data which is peptide-centric instead of protein-centric. We discuss the feasibility of the peptide-centric approach which was tested on several quantitative proteomic data sets. We show that peptide-centric quantification has several advantages over protein level analysis: (1) it is more sensitive for sample segregation, (2) it avoids the issues associated with protein inference, and (3) it can retrieve significant peptides lost in protein-centric quantification for further downstream analysis.
authors.affiliation: Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa , 451 Smyth Road, Ottawa, Ontario Canada , K1H8M5.
authors.forename: Zhibin
authors.initials: Z
authors.lastname: Ning
authors.affiliation: Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa , 451 Smyth Road, Ottawa, Ontario Canada , K1H8M5.
authors.forename: Xu
authors.initials: X
authors.lastname: Zhang
authors.affiliation: Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa , 451 Smyth Road, Ottawa, Ontario Canada , K1H8M5.
authors.forename: Janice
authors.initials: J
authors.lastname: Mayne
authors.affiliation: Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa , 451 Smyth Road, Ottawa, Ontario Canada , K1H8M5.
authors.forename: Daniel
authors.initials: D
authors.lastname: Figeys
mesh_terms: D000595:Amino Acid Sequence; D008969:Molecular Sequence Data; D010455:Peptides / Q000032:analysis* / Q000737:chemistry; D025341:Principal Component Analysis; D011506:Proteins / Q000737:chemistry; D040901:Proteomics / Q000379:methods*; D021241:Spectrometry, Mass, Electrospray Ionization
chemical_list: D010455:Peptides; D011506:Proteins