Uses and misuses of the fudge factor in quantitative discovery proteomics

Selecting proteins with significant differential abundance is the cornerstone of many relative quantitative proteomics experiments. To do so, a trade-off between p-value thresholding and fold-change thresholding can be performed because of a specific parameter, named fudge factor, and classically noted s0 . We have observed that this fudge factor is routinely turned away from its original (and statistically valid) use, leading to important distortion in the distribution of p-values, jeopardizing the protein differential analysis, as well as the subsequent biological conclusion. In this article, we provide a comprehensive viewpoint on this issue, as well as some guidelines to circumvent it.