A community audit of error control in crosslinking mass spectrometry

Lutz Fischer; B.C. do Amaral; Micha Johannes Birklbauer; James E. Bruce; Paulo C. Carvalho; Robert J. Chalkley; Milan Avila Clasen; Viktoria Dorfer; Fabio Cesar Gozzo; Albert J.R. Heck; Michael R. Hoopmann; Claudio Iacobucci; Andrew Keller; Lars Kolbowski; Swantje Lenz; Diogo Borges Lima; Fan Liu; Karl Mechtler; Robert L. Moritz; Fränze Müller; Julia Ruta; David C. Schriemer; David D. Shteynberg; Michael J. Trnka; Rosa Viner; Juri Rappsilber

doi:10.1101/2025.04.27.649519

BioinformaticsbioRxivApr 27, 2025

Preprint

A community audit of error control in crosslinking mass spectrometry

Lutz Fischer iD, B.C. do Amaral iD, Micha Johannes Birklbauer iD, James E. Bruce iD, Paulo C. Carvalho iD, Robert J. Chalkley iD, Milan Avila Clasen iD, Viktoria Dorfer iD, Fabio Cesar Gozzo iD, Albert J.R. Heck, Michael R. Hoopmann iD, Claudio Iacobucci iD, Andrew Keller iD, Lars Kolbowski iD, Swantje Lenz iD, Diogo Borges Lima iD, Fan Liu iD, Karl Mechtler iD, Robert L. Moritz iD, Fränze Müller iD, Julia Ruta iD, David C. Schriemer iD, David D. Shteynberg iD, Michael J. Trnka iD, Rosa Viner iD, Juri Rappsilber iD

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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