Statistically inferring protein-protein associations with affinity isolation LC-MS/MS assays.

Sharp JL, Anderson KK, Hurst GB, Daly DS, Pelletier DA, Cannon WR, Auberry DL, Schmoyer DD, McDonald WH, White AM, Hooker BS, Victry KD, Buchanan MV, Kery V, Wiley HS
J Proteome Res. 2007 6 (9): 3788-95

PMID: 17691832 · DOI:10.1021/pr0701106

Affinity isolation of protein complexes followed by protein identification by LC-MS/MS is an increasingly popular approach for mapping protein interactions. However, systematic and random assay errors from multiple sources must be considered to confidently infer authentic protein-protein interactions. To address this issue, we developed a general, robust statistical method for inferring authentic interactions from protein prey-by-bait frequency tables using a binomial-based likelihood ratio test (LRT) coupled with Bayes' Odds estimation. We then applied our LRT-Bayes' algorithm experimentally using data from protein complexes isolated from Rhodopseudomonas palustris. Our algorithm, in conjunction with the experimental protocol, inferred with high confidence authentic interacting proteins from abundant, stable complexes, but few or no authentic interactions for lower-abundance complexes. The algorithm can discriminate against a background of prey proteins that are detected in association with a large number of baits as an artifact of the measurement. We conclude that the experimental protocol including the LRT-Bayes' algorithm produces results with high confidence but moderate sensitivity. We also found that Monte Carlo simulation is a feasible tool for checking modeling assumptions, estimating parameters, and evaluating the significance of results in protein association studies.

MeSH Terms (14)

Algorithms Bacterial Proteins Bayes Theorem Biological Assay Chromatography, Liquid Mass Spectrometry Models, Statistical Monte Carlo Method Odds Ratio Protein Interaction Mapping Proteins Proteomics Rhodopseudomonas Sensitivity and Specificity

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