title: Statistical design of quantitative mass spectrometry-based proteomic experiments.
abstract: We review the fundamental principles of statistical experimental design, and their application to quantitative mass spectrometry-based proteomics. We focus on class comparison using Analysis of Variance (ANOVA), and discuss how randomization, replication and blocking help avoid systematic biases due to the experimental procedure, and help optimize our ability to detect true quantitative changes between groups. We also discuss the issues of pooling multiple biological specimens for a single mass analysis, and calculation of the number of replicates in a future study. When applicable, we emphasize the parallels between designing quantitative proteomic experiments and experiments with gene expression microarrays, and give examples from that area of research. We illustrate the discussion using theoretical considerations, and using real-data examples of profiling of disease.
authors.affiliation: Department of Health Sciences Research, Mayo Clinic, Rochester, MN 55905, USA.
authors.forename: Ann L
authors.initials: AL
authors.lastname: Oberg
authors.forename: Olga
authors.initials: O
authors.lastname: Vitek
mesh_terms: D000704:Analysis of Variance; D000818:Animals; D006801:Humans; D013058:Mass Spectrometry / Q000379:methods*; D015233:Models, Statistical; D040901:Proteomics / Q000379:methods*; D011897:Random Allocation; D016032:Randomized Controlled Trials as Topic; D012107:Research Design; D018401:Sample Size