Statistically inferring protein-protein associations with affinity isolation LC-MS/MS assays.
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.
Sharp
Julia L
JL
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
Anderson
Kevin K
KK
Hurst
Gregory B
GB
Daly
Don S
DS
Pelletier
Dale A
DA
Cannon
William R
WR
Auberry
Deanna L
DL
Schmoyer
Denise D
DD
McDonald
W Hayes
WH
White
Amanda M
AM
Hooker
Brian S
BS
Victry
Kristin D
KD
Buchanan
Michelle V
MV
Kery
Vladimir
V
Wiley
H Steven
HS
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
D001426:Bacterial Proteins; D011506:Proteins