Methods for combining peptide intensities to estimate relative protein abundance.
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.
Carrillo
Brian
B
Department of Biomedical Engineering, McGill University, Montreal, Canada.
Yanofsky
Corey
C
Laboissiere
Sylvie
S
Nadon
Robert
R
Kearney
Robert E
RE
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
D011506:Proteins