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.