FdrCategory Comment (#2402)

MetaMorpheus/EngineLayer/ProteinScoringAndFdr/FdrCategory.cs

@@ -6,6 +6,25 @@
 
 namespace EngineLayer
 {
+    /// <summary>
+    /// This enum is used to categorize the FDR of a peptide based on its cleavage specificity.
+    /// FullySpecific: The peptide is cleaved only at protease-specified cleavage sites.
+    /// SemiSpecific: The peptide is cleaved on one terminus at protease-specified cleavage sites and at non-specific site on the other terminus.
+    /// NonSpecific: The peptide is cleaved at non-specific sites on both termini.
+    /// 
+    /// In the Speedy Non-Specific Search use case, all three categories are used with modern search. For each spectrum, the lowest q-value peptide is chosen
+    /// rather than the highest scoring peptide.
+    /// 
+    /// In a classic NonSpecific search, I believe that only the NonSpecific category is used. Further, I believe that it includes peptides that are cleaved
+    /// at one or more protease-specified cleavage sites, but also at non-specific sites.
+    /// 
+    /// The Single-N or Single-C protease is a special case. The modern search table is populated only with peptide fragments including the specified terminus.
+    /// Fragments from the other terminus are not included.
+    /// 
+    /// This is not the same as Semi-Trypsin, which is a classic search where the protein is digested into peptides and then the database is further updated
+    /// the full set of peptides that could be generated by terminal degradation.
+    /// 
+    /// </summary>
     public enum FdrCategory
     {
         //Cleavage Specificity