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Title: Inferring Protein Associations Using Protein Pulldown Assays

Abstract

Background: One method to infer protein-protein associations is through a “bait-prey pulldown” assay using a protein affinity agent and an LC-MS (liquid chromatography-mass spectrometry)-based protein identification method. False positive and negative protein identifications are not uncommon, however, leading to incorrect inferences. Methods: A pulldown experiment generates a protein association matrix wherein each column represents a sample from one bait protein, each row represents one prey protein and each cell contains a presence/absence association indicator. Our method evaluates the presence/absence pattern across a prey protein (row) with a Likelihood Ratio Test (LRT), computing its p-value with simulated LRT test statistic distributions after a check with simulated binomial random variates disqualified the large sample 2 test. A pulldown experiment often involves hundreds of tests so we apply the false discovery rate method to control the false positive rate. Based on the p-value, each prey protein is assigned a category (specific association, non-specific association, or not associated) and appraised with respect to the pulldown experiment’s goal and design. The method is illustrated using a pulldown experiment investigating the protein complexes of Shewanella oneidensis MR-1. Results: The Monte Carlo simulated LRT p-values objectively reveal specific and ubiquitous prey, as well as potential systematic errors.more » The example analysis shows the results to be biologically sensible and more realistic than the ad hoc screening methods previously utilized. Conclusions: The method presented appears to be informative for screening for protein-protein associations.« less

Authors:
; ; ; ; ;
Publication Date:
Research Org.:
Pacific Northwest National Laboratory (PNNL), Richland, WA (US), Environmental Molecular Sciences Laboratory (EMSL)
Sponsoring Org.:
USDOE
OSTI Identifier:
899480
Report Number(s):
PNNL-SA-49349
6504; KP1501021; TRN: US200708%%308
DOE Contract Number:  
AC05-76RL01830
Resource Type:
Conference
Resource Relation:
Conference: 2006 Joint Statistical Meetings: Statistics for an Uncertain World: Meeting Global Challenges, August 6-10, Seattle, WA, 5 pages
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; AFFINITY; DESIGN; PROTEINS; STATISTICS; proteins; Monte Carolo; pulldown experiment; Environmental Molecular Sciences Laboratory

Citation Formats

Sharp, Julia L., Anderson, Kevin K., Daly, Don S., Auberry, Deanna L., Borkowski, John J., and Cannon, William R.. Inferring Protein Associations Using Protein Pulldown Assays. United States: N. p., 2007. Web.
Sharp, Julia L., Anderson, Kevin K., Daly, Don S., Auberry, Deanna L., Borkowski, John J., & Cannon, William R.. Inferring Protein Associations Using Protein Pulldown Assays. United States.
Sharp, Julia L., Anderson, Kevin K., Daly, Don S., Auberry, Deanna L., Borkowski, John J., and Cannon, William R.. Thu . "Inferring Protein Associations Using Protein Pulldown Assays". United States. doi:.
@article{osti_899480,
title = {Inferring Protein Associations Using Protein Pulldown Assays},
author = {Sharp, Julia L. and Anderson, Kevin K. and Daly, Don S. and Auberry, Deanna L. and Borkowski, John J. and Cannon, William R.},
abstractNote = {Background: One method to infer protein-protein associations is through a “bait-prey pulldown” assay using a protein affinity agent and an LC-MS (liquid chromatography-mass spectrometry)-based protein identification method. False positive and negative protein identifications are not uncommon, however, leading to incorrect inferences. Methods: A pulldown experiment generates a protein association matrix wherein each column represents a sample from one bait protein, each row represents one prey protein and each cell contains a presence/absence association indicator. Our method evaluates the presence/absence pattern across a prey protein (row) with a Likelihood Ratio Test (LRT), computing its p-value with simulated LRT test statistic distributions after a check with simulated binomial random variates disqualified the large sample 2 test. A pulldown experiment often involves hundreds of tests so we apply the false discovery rate method to control the false positive rate. Based on the p-value, each prey protein is assigned a category (specific association, non-specific association, or not associated) and appraised with respect to the pulldown experiment’s goal and design. The method is illustrated using a pulldown experiment investigating the protein complexes of Shewanella oneidensis MR-1. Results: The Monte Carlo simulated LRT p-values objectively reveal specific and ubiquitous prey, as well as potential systematic errors. The example analysis shows the results to be biologically sensible and more realistic than the ad hoc screening methods previously utilized. Conclusions: The method presented appears to be informative for screening for protein-protein associations.},
doi = {},
journal = {},
number = ,
volume = ,
place = {United States},
year = {Thu Feb 01 00:00:00 EST 2007},
month = {Thu Feb 01 00:00:00 EST 2007}
}

Conference:
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