TABLE 2.

Protein Identifications and False Discovery Rates Observed Using Dual Algorithm Searching

Expt No	Total Proteins Identified in SEQUEST Searches	Revised Total Proteins Identified Using Dual Algorithm Search	Overall FDRa Using Dual Algorithm Search	FDR of Single Peptides Retained in Dual Algorithm Approach
Y1	532	417	0.005	0.0
Y2	604	467	0.011	0.013
Y3	517	384	0.021	0.008
R1seed	221	141	0.71	0.0
R2root	258	174	0.00	0.0
R3leaf	247	153	0.65	0.0

^a Protein false discovery rates, determined as explained in Table 1.