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Learning from Decoys to Improve the Sensitivity and Specificity of Proteomics Database Search Results

Figure 1

The concept of FlexiFDR method.

The linear regression line of decoy hits is represented by the line equation to show the effect of increasing mass on decoy hits (PSMs) in QTOF dataset. Two lines are shown for two different charge states (+2 and +3). When a simple FDR is calculated on MassWiz scores (shown by dotted line), many correct hits (green and blue dots) are lost in lower mass regions with high density. The FlexiFDR method uses a line for every charge state (colored solid lines), parallel to the decoy line of that charge, as a dynamic threshold based on decoy results to estimate FDR. The scores are transformed using this equation of line. This method helps in enhancing the true hits and decreasing the false hits at <1%FDR and reduces the time spent for manual validation.

Figure 1

doi: https://doi.org/10.1371/journal.pone.0050651.g001