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bioRxiv

A community audit of error control in crosslinking mass spectrometry

Fischer, L, Amaral, B. C, Birklbauer, M. J, Bruce, J. E, Carvalho, P. C, Chalkley, R. J, Clasen, M. A, Dorfer, V, Gozzo, F. C, Heck, A. J. R, Hoopmann, M. R, Iacobucci, C, Keller, A, Kolbowski, L, Lenz, S, Lima, D. B, Liu, F, Mechtler, K, Moritz, R. L, Mueller, F, Ruta, J, Schriemer, D. C, Shteynberg, D. D, Trnka, M. J, Viner, R, Rappsilber, J

Preprint source: bioRxiv: Bioinformatics

Abstract

In a community effort, we audited error control in twelve crosslinking mass spectrometry pipelines using two ground-truth designs that expose a lower bound on false identifications. Some pipelines passed, whereas for others these verifiably false identifications alone exceeded the requested false discovery rate up to 29-fold at the protein-protein interaction level. The audit also tracked improvement between software versions, supporting its use for regression testing.

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