Additional file 1: Supplemental Methods.

Data set and Database Search. Determination of Protein Spectral Counts, Protein MASCOT Scores, and Protein Marginal Inclusion Probabilities. Raw Input Dataset Structure. Initial Pre-filtering. Derivation of Marginal and Joint Inclusion Probabilities of Indicator Prey Proteins. Identification of Reproducible Experimental Replicates and Reproducible Prey Proteins. Confidence Score and Identification of Specific Prey Proteins. Automatic Estimation of an Optimal Confidence Score Cutoff Derivation of Coefficient of Variations Formulas. Testing Stability on Multi-scale Sets of Experimental Replicates.

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Dazard et al. BMC Bioinformatics 2012 13:128   doi:10.1186/1471-2105-13-128