What is the false discovery rate (FDR) and how is it calculated?
In newer releases of Scaffold (Scaffold 3), the FDR is actually calculated and displayed in the Scaffold application. Check the bottom left of the screen, in a little box. These data are displayed in all of Scaffold’s views. Scaffold calculates False Discovery Rate (FDR) in two different ways depending on whether the data has been searched against a decoy database. The method Scaffold has used for calculating FDR can be determined from the color of text in the box in the lower left corner of the Scaffold window. If the search was not performed against a decoy database, Scaffold uses a probabilistic method and displays the text in green. If a decoy database has been used, Scaffold uses an empirical method and displays the text in black. Probabilistic Method: This is the approach used by the Trans-Proteomic Pipeline and the Protein Prophet algorithm. In this method, Scaffold calculates its protein FDR by using the assigned protein probabilities. Consider the following situation: Four pro
