In this paper, we use sensitivity, specificity, precision, and accuracy as performance measures for peptide classification [26]. We interpret the word “positive” as “differentially phosphorylated” and the term “negative” as “non-differentially phosphorylated”. In addition, we use the following notations: ∥∥ operator denotes the size of a set.
TP (True Positives): the set of all differentially phosphorylated peptides predicted as differentially phosphorylated.
FN (False Negatives): the set of all differentially phosphorylated peptides predicted as non-differentially phosphorylated.
TN (True Negatives): the set of all non-differentially phosphorylated peptides predicted as non-differentially phosphorylated.
FP (False Positives): the set of all non-differentially phosphorylated peptides predicted as differentially phosphorylated.