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Wiley, Proteomics, 20(11), p. 4105-4108, 2011

DOI: 10.1002/pmic.201100297

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Can the false-discovery rate be misleading?

Journal article published in 2011 by Rodrigo Barboza, Daniel Cociorva, Tao Xu, Valmir C. Barbosa ORCID, Jonas Perales, Richard H. Valente, Felipe M. G. França ORCID, John R. Yates, Paulo C. Carvalho
This paper is made freely available by the publisher.
This paper is made freely available by the publisher.

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Abstract

The decoy-database approach is currently the gold standard for assessing the confidence of identifications in shotgun proteomic experiments. Here, we demonstrate that what might appear to be a good result under the decoy-database approach for a given false-discovery rate could be, in fact, the product of overfitting. This problem has been overlooked until now and could lead to obtaining boosted identification numbers whose reliability does not correspond to the expected false-discovery rate. To overcome this, we are introducing a modified version of the method, termed a semi-labeled decoy approach, which enables the statistical determination of an overfitted result.