Figure 5From: A sampling framework for incorporating quantitative mass spectrometry data in protein interaction analysisPerformance comparison of PPI inference methods. Performance of our sampling approach applied to PPI inference methods that operate on binary bait-prey interaction data (Hart et al. [16], PE [9], and SAI [21]), and compared to state-of-the-art methods that make use of spectral counts (HGSCore [6] and SAINT [13]). For each method that operates on binary data, two curves are plotted: (i) a dashed curve that shows the performance of the method when applied to a direct binarization of the spectral count data (i.e., converting all nonzero spectral counts to 1s)—a common approach—and (ii) a solid curve showing performance upon applying our sampling approach with p = 0.3. We evaluate performance according to the number of PPI inferences (out of the highest-confidence 25,000 or 2,500) validated on gold standard tests, as explained in the main text. The plot shows performance relative to a baseline method of simply ranking PPIs in decreasing order of observed spectral counts. All methods were run using default parameter settings.Back to article page