How is the FDR calculated in the peptide-spectrum matching step in the BioPharmaView™ software?

For research use only. Not for use in diagnostic procedures.

Answer

The false discovery rate (FDR) is calculated as a function of MS/MS scoring in BioPharmaView™ and BFV Flex software. Matches outside of the m/z tolerance are considered false positives by the software. The number of false positives are divided by the total number of matches within that score threshold. The excerpt below was taken from the BPV Flex User Guide (2.1) and provides further details regarding the FDR plot.


Use the Matching m/z Tolerance (±ppm) slider to change the value shown in the text box. Matches within that tolerance are shown as green circles in the plot. Matches that are outside of the tolerance, and not considered matches in the processed results, are shown as blue circles in the plot. By adjusting the slider, and optionally zooming in the y-axis, the user can choose a m/z tolerance that is appropriate for the data. Adjust the Matching m/z Tolerance to see the impact on the false discovery rate (FDR) plot. Using a higher tolerance allows more false positive identifications. The FDR plot can be used as a guide to determine the minimum score required for identification. Typically a MS/MS score corresponding to 1% FDR is used. The score could be entered on the Explore and Optimize pane and the data reprocessed if that FDR is required. Additionally, the Matching m/z
Tolerance could be entered in the Explore and Optimize pane and the data reprocessed if that tolerance is required.

Use the slider in the Min. Score Required for Identification section to change the value shown in the text box shown below.



Peptides with scores above this identification threshold are shown as solid circles in the plot and these are the results that will be marked as auto-validated.