PhosphoHunter: An Efficient Software Tool for Phosphopeptide Identification

Table 5

Performance of Mascot and Inspect in terms of phosphorylated spectra detection (1500 MS/MS spectra analyzed, 750 phosphorylated peptides + 750 nonphosphorylated peptides).

Tool	TP	FP	FN	TN	Sens	Spec	Acc	FDR	Prec
Mascot
Inspect

TP: true positive, spectra of phosphorylated peptides in which the first hit (or the majority) of the hit list is phosphorylated; FP: false positive, spectra of nonphosphorylated peptides in which the first hit (or the majority) of the hit list is phosphorylated; FN: false negative; TN: true negative; Sens: sensitivity or recall, TP/(TP + FN); Spec: specificity, TN/(TN + FP); Acc: accuracy, (TP + TN)/all spectra; FDR: false discovery rate, FP/(TP + FP); Prec: precision, TP/(TP + FP); -measure, 2 precision recall/(precision + recall).