False Discovery Rate (FDR) explained. What does it really mean?
Scaffold requires proteins to contain at least one 50% peptide before we count it as good. This seems to help substantially with both memory usage and the ProteinProphet fitting (not shown). In this case, a single 50% peptide ID could correspond to a low-percentage protein probability (as shown by the Protein Probability Calculation chart). Incidentally, this fixed “internal” filter is the reason why we limit lowering the protein probability to the 20% level. Usually we don’t see this much of an effect from the 50% threshold because most data sets contain some level of smear between the correct and incorrect distribution. The dramatic separation between good IDs and bad in general is representative of a high quality dataset.
