Current Bioinformatics Seminar
Time: 11AM Tuesdays.
Venue: Davis Auditorium and Online
7 July 2026
Assessment of false discovery rate control in tandem mass spectrometry analysis using entrapment
Uri KeichUniversity of Sydney
A critical challenge in mass spectrometry proteomics is accurately assessing error control, especially given that software tools employ distinct methods for reporting errors. Many tools are closed-source and poorly documented, emphasizing the need for independent validation. In our recent work we analyzed the three prevalent entrapment-based estimation methods for validating false discovery rate (FDR) control using entrapment experiments. We found that one is invalid, one provides only a lower bound on errors, and one is valid but often under-powered. As an alternative we developed a new estimation method that is valid but more powerful at certifying tools that genuinely control the FDR. An estimation method is only one half of an entrapment experiment, the other being the entrapment sequences. We will discuss how different entrapment constructions change the results and how we interpret them. Moreover, this raises the intriguing question of what FDR in this context really means. Joint work with Bo Wen, Jack Freestone, Michael Riffle, Michael J. MacCoss, William S. Noble