How to interpret Confidence scores? Especially when some datasets have the highest protein confidence at <100% (i.e. ~65% in one case)? #558
Description
I've been using Peptide Shaker for a while with SearchGUI results, and I'm still not sure I understand how the "confidence" score is determined. I'm currently running some datasets using the X!Tandem, MSGF+, and OMSSA algorithms in SearchGUI, and some of the resulting Peptide Shaker outputs have unusual confidence values. For example, one dataset has the highest proteins (i.e. the bait and known binding proteins in an IP-MS dataset) at only 66%, even though they are listed as "validated". How would I interpret such a result?
Also, there is a related thing I don't understand with the Confidence scores. I know the Peptide Shaker window lists something about "1% FDR" when analyzing SearchGUI results. Is this related to the confidence values, or are they two separate cutoffs? i.e. is the confidence score some sort of p-value, q-value, etc. related to the aforementioned false discovery rate?