Table I. Comparison of different peak list filtering approaches. Three different peak list filtering approaches are compared for their ability to identify phosphopeptides and pinpoint modification sites.

	20 + 20	4 per 100	5 per 100
Spectra	2334	2378	2282
Phosphosites	2437	2488	2397
Correct	1924	1910	1883
Incorrect	130	136	161
Ambiguous	220	255	211
One Site	164	187	142
FLR (%)	6.3	6.6	7.9
Ambiguous (%)	9.0	10.2	8.8