Abstract
BackgroundTandem affinity purification coupled with mass-spectrometry (TAP/MS) analysis is a popular method for the identification of novel endogenous protein-protein interactions (PPIs) in large-scale. Computational analysis of TAP/MS data is a critical step, particularly for high-throughput datasets, yet it remains challenging due to the noisy nature of TAP/MS data.ResultsWe investigated several major TAP/MS data analysis methods for identifying PPIs, and developed an advanced method, which incorporates an improved statistical method to filter out false positives from the negative controls. Our method is named PPIRank that stands for PPI ranking in TAP/MS data. We compared PPIRank with several other existing methods in analyzing two pathway-specific TAP/MS PPI datasets from Drosophila.ConclusionExperimental results show that PPIRank is more capable than other approaches in terms of identifying known interactions collected in the BioGRID PPI database. Specifically, PPIRank is able to capture more true interactions and simultaneously less false positives in both Insulin and Hippo pathways of Drosophila Melanogaster.
Highlights
Tandem affinity purification coupled with mass-spectrometry (TAP/MS) analysis is a popular method for the identification of novel endogenous protein-protein interactions (PPIs) in large-scale
PPIRank outperformed existing methods in capturing true interactions with higher specificity [19]. To characterize this method in more detail, we performed a comprehensive analysis of two pathway-specific tandem affinity purification (TAP)/MS PPI datasets from Drosophila Melanogaster: the Insulin and the Hippo pathway
We performed a number of tests to evaluate PPIRank results: first, we examined whether PPIRank can identify more known interactions than other approaches. 27156 known interactions in Drosophila were collected from BioGRID PPI database
Summary
Tandem affinity purification coupled with mass-spectrometry (TAP/MS) analysis is a popular method for the identification of novel endogenous protein-protein interactions (PPIs) in large-scale. Co-IP is usually used to identify interactions between specific proteins It is carried out by immunoprecipitation with an antibody against a organisms [7,8,9,10,11]. Another advantage of TAP/MS technique is that it can be combined with other quantitative proteomics approaches to characterize the dynamics of protein-complex assembly [12,13]
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