Table 4.

Comparison of Inspect and SEQUEST^a

	Inspect	SEQUEST
Total Spectra	1089	962
2+ Spectra	700	645
3+ Spectra	389	317
2+ Peptides	619	589
3+ Peptides	333	287
Run Time	0.5 h	36h

^aThe test data set of 6410 MS/MS spectra from S. cerevisiae was run permitting up to two phosphorylations per peptide. All results were filtered to 1% false positives and then compared between programs. Shown are only the spectra with a phosphorylated peptide annotation. The rows for peptides are counts of nonredundant phosphopeptide species.