Systematic Assessment of Entrapment Approaches in DIA Proteomics FDR Validation

Target decoy-based analysis is the universal approach for identification in bottom-up discovery proteomics. A modern data analysis software typically uses different scores and complex data analysis paradigms. It is important to ensure that the false positive rate is controlled as specified.

Such a validation is typically done with an entrapment analysis. The core concept of an entrapment analysis is that the software is blind to the difference between the real targets and entrapment targets facilitating the estimation of the entrapment FDR rate (eFDR) of the software based on the rate of identification of entrapment proteins. While being intuitive, overlooking the complexity of generating an entrapment space can lead to wrong interpretation of the results, that can either be too conservative or too optimistic FDR evaluation.