title: Statistically inferring protein-protein associations with affinity isolation LC-MS/MS assays.
abstract: 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.
authors: Clemson University, 237 Barre Hall, Clemson, South Carolina 29634-0313, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99352, USA. julia.1.sharp@gmail.com
authors: Julia L
authors: JL
authors: Sharp
authors: Kevin K
authors: KK
authors: Anderson
authors: Gregory B
authors: GB
authors: Hurst
authors: Don S
authors: DS
authors: Daly
authors: Dale A
authors: DA
authors: Pelletier
authors: William R
authors: WR
authors: Cannon
authors: Deanna L
authors: DL
authors: Auberry
authors: Denise D
authors: DD
authors: Schmoyer
authors: W Hayes
authors: WH
authors: McDonald
authors: Amanda M
authors: AM
authors: White
authors: Brian S
authors: BS
authors: Hooker
authors: Kristin D
authors: KD
authors: Victry
authors: Michelle V
authors: MV
authors: Buchanan
authors: Vladimir
authors: V
authors: Kery
authors: H Steven
authors: HS
authors: Wiley
mesh_terms: D000465:Algorithms; D001426:Bacterial Proteins / Q000737:chemistry; D001499:Bayes Theorem; D001681:Biological Assay; D002853:Chromatography, Liquid / Q000379:methods; D013058:Mass Spectrometry / Q000379:methods; D015233:Models, Statistical; D009010:Monte Carlo Method; D016017:Odds Ratio; D025941:Protein Interaction Mapping; D011506:Proteins / Q000737:chemistry*; D040901:Proteomics / Q000379:methods*; D012241:Rhodopseudomonas / Q000378:metabolism; D012680:Sensitivity and Specificity
chemical_list: D001426:Bacterial Proteins; D011506:Proteins