title: Methods for combining peptide intensities to estimate relative protein abundance.
abstract: BACKGROUND
  Labeling techniques are being used increasingly to estimate relative protein abundances in quantitative proteomic studies. These techniques require the accurate measurement of correspondingly labeled peptide peak intensities to produce high-quality estimates of differential expression ratios. In mass spectrometers with counting detectors, the measurement noise varies with intensity and consequently accuracy increases with the number of ions detected. Consequently, the relative variability of peptide intensity measurements varies with intensity. This effect must be accounted for when combining information from multiple peptides to estimate relative protein abundance.
  
  
  RESULTS
  We examined a variety of algorithms that estimate protein differential expression ratios from multiple peptide intensity measurements. Algorithms that account for the variation of measurement error with intensity were found to provide the most accurate estimates of differential abundance. A simple Sum-of-Intensities algorithm provided the best estimates of true protein ratios of all algorithms tested.
authors.affiliation: Department of Biomedical Engineering, McGill University, Montreal, Canada.
authors.forename: Brian
authors.initials: B
authors.lastname: Carrillo
authors.forename: Corey
authors.initials: C
authors.lastname: Yanofsky
authors.forename: Sylvie
authors.initials: S
authors.lastname: Laboissiere
authors.forename: Robert
authors.initials: R
authors.lastname: Nadon
authors.forename: Robert E
authors.initials: RE
authors.lastname: Kearney
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D007553:Isotope Labeling / Q000379:methods*; D008969:Molecular Sequence Data; D010449:Peptide Mapping / Q000379:methods*; D011506:Proteins / Q000032:analysis* / Q000737:chemistry*; D012680:Sensitivity and Specificity
chemical_list: D011506:Proteins