PhosphoHunter: An Efficient Software Tool for Phosphopeptide Identification

Table 3

Performance of PhosphoHunter in terms of phosphorylated spectra detection (1500 MS/MS spectra analyzed, 750 phosphorylated peptides + 750 nonphosphorylated peptides) with the statistical validation.

Intensity threshold

TP

FP

FN

TN

Sens

Spec

Acc

FDR

Prec

TP: true positive, spectra of phosphorylated peptides passing the neutral loss check and for which at least a hit was found; FP: false positive, spectra of nonphosphorylated peptides passing the neutral loss check and for which at least a hit was found; 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).