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Open Access Methodology article

ROCS: a Reproducibility Index and Confidence Score for Interaction Proteomics Studies

Jean-Eudes Dazard*, Sudipto Saha and Rob M Ewing*

Author Affiliations

Division of Bioinformatics, Center for Proteomics and Bioinformatics, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH, 44106, USA

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BMC Bioinformatics 2012, 13:128  doi:10.1186/1471-2105-13-128

Published: 8 June 2012

Additional files

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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Additional file 2:

Figure S1. Scatter plots of protein spectral counts vs. protein MASCOT scores (left-hand-side) and protein MASCOT scores vs. protein marginal inclusion probabilities (right-hand-side) in all AP-MS control and bait experiments. Figure S2: Scatter plot of peptide PROPHET probabilities (Prob) onto the peptide MASCOT scores (Score) in all AP-MS control and bait experiments. Figure S3: Empirical Probability Density Function (PDF - left) and Cumulative Density Function (CDF - right) plots of peptide scores (top) and peptide probabilities (bottom) in all AP-MS control and bait experiments. Figure S4: Optimizing the determination of the peptide MASCOT score threshold in all AP-MS bait experiments. Figure S5: Number of Indicator Prey Proteins and Reproducible Experimental Replicates and the joint inclusion probability for the protein-based analysis in all AP-MS bait experiments. Figure S6: FDR sensitivity as a function of Confidence Score cutoff and marginal inclusion probability threshold in all AP-MS bait experiments. Figure S7: FDR and GO semantic similarity analyses in all AP-MS bait experiments. Figure S8: Density distribution plots of bait-prey Confidence Scores at procedural stages “N”, “R” and “S” in all AP-MS bait experiments. Figure S9: Quantile-Quantile plots of bait vs. control marginal inclusion probabilities in all AP-MS bait experiments. Figure S10: Correlation and regression relationships between protein MASCOT scores and protein marginal inclusion probabilities at different procedural stages from the initial “Naïve” stage (“N”), to the “Reproducible” stage (“R”), and to the final “Specific” stage (“S”) in all AP-MS bait experiments. Figure S11: Stability of the Coefficient of Variation (CV) of the mean marginal inclusion probability as a function of procedural stages from the initial “Naïve” stage (“N”), to the “Reproducible” stage (“R”), and to the final “Specific” stage (“S”) in all AP-MS bait experiments. Figure S12: Confidence Intervals (95% CIs) of the median bait-prey semantic similarity for SAINT-only and SAINT in conjunction with ROCS at the different ROCS procedural stages “N” (SAINT-only), “R”, and “S” (ROCSSAINT) in all AP-MS bait experiments. Figure S13: FDR computed from SAINT posterior probability output (PSAINT) as a function of procedural stages: from the initial “Naïve” stage (“N” – SAINT-only), to the “Reproducible” stage (“R”), and to the final “Specific” stage (“S” – ROCS-SAINT) in all AP-MS bait experiments [20,28,32,35-37].

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Additional file 3: Table S1:

ROCS lists of Indicator Prey Proteins (IPI) and Reproducible Experimental Replicates (RER) in all AP-MS control and bait experiments (each on a single Excel tab-sheet in a single file).

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Additional file 4: Table S2:

Biological validation of ROCS protein-protein interaction (PPI) scoring results for the Specific Prey Proteins between SAINT (Posterior Probability PSAINT), ComPASS (D − score) and our method ROCS (C − score) in all AP-MS bait experiments (each on a separate Excel tab-sheet in a single file).

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Additional file 5: Table S3:

Comparison of protein-protein interaction (PPI) scoring for the Specific Prey Proteins between SAINT (Posterior Probability PSAINT), ComPASS (D − score) and our method ROCS (C − score) in all AP-MS bait experiments (each on a separate Excel tab-sheet in a single file).

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Additional file 6: Table S4:

Comparison of SAINT protein-protein interaction (PPI) scoring for the Specific Prey Proteins at the different ROCS procedural stages “N” (SAINT-only), “R”, and “S” (ROCS-SAINT) in all AP-MS bait experiments (each on a separate Excel tab-sheet in a single file).

Format: XLS Size: 142KB Download file

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