Combined Statistical Analyses of Peptide Intensities and Peptide Occurrences Improves Identification of Significant Peptides from MS-Based Proteomics Data

• Published in: Journal of proteome research Vol. 9; no. 11; pp. 5748 - 5756
• Main Authors: Webb-Robertson, Bobbie-Jo M, McCue, Lee Ann, Waters, Katrina M, Matzke, Melissa M, Jacobs, Jon M, Metz, Thomas O, Varnum, Susan M, Pounds, Joel G
• Format: Journal Article
• Language: English
• Published: United States American Chemical Society 05.11.2010
• Subjects: Analysis of Variance; BASIC BIOLOGICAL SCIENCES; CALCULATION METHODS; CONCENTRATION RATIO; DATA ANALYSIS; Data Interpretation, Statistical; Environmental Molecular Sciences Laboratory; INORGANIC, ORGANIC, PHYSICAL AND ANALYTICAL CHEMISTRY; LIQUID COLUMN CHROMATOGRAPHY; Mass Spectrometry; MASS SPECTROSCOPY; PEPTIDES; Peptides - analysis; PROTEINS; Proteomics - methods; SENSITIVITY; Sensitivity and Specificity; STATISTICS; quantitative statistical analysis; Missing data; qualitative statistical analysis; imputation; peak intensity comparison

Liquid chromatography−mass spectrometry-based (LC−MS) proteomics uses peak intensities of proteolytic peptides to infer the differential abundance of peptides/proteins. However, substantial run-to-run variability in intensities and observations (presence/absence) of peptides makes data analysis quit...