Research Article

PhosphoHunter: An Efficient Software Tool for Phosphopeptide Identification

Table 1

Number of MS/MS spectra selected through the analysis of the neutral loss peaks.

Intensity thresholdSelected MS/MS spectra
PhosphorylatedNonphosphorylatedTotal%


Intensity threshold values (from 0 to 100) and number of MS/MS spectra which pass the neutral loss check, subdivided by phosphorylated and nonphosphorylated peptides. Percent of phosphorylated peptides over the total number of selected spectra.