WHICH INFORMATION IS PROVIDED FOR EACH PHOSPHOSITE?

A typical output looks like this:
For each phosphosite, general information such as the position of the phosphosite within protein sequence, the amino acid type (serine, threonine or tyrosine) and the surrounding sequence within the protein sequence is provided.

Furthermore, if a site matches with one out of 22 kinase motifs that we included in Phosida, the matching motifs/kinases are listed (...click here for more information about the motifs).

In addition, the best localization p-value for the chosen phosphosite is displayed. The p-value presents the probability that the site is phosphorylated within one of the detected phosphorylated peptides. The p-values are derived from the PTM scoring of MSQuant (...click here for more information about the derivation of p-values).

Then all peptides that have been phosphorylated according to Mascot and MSQuant are listed. Each peptide is uniquely distinguished by its sequence, experiment and the number of phosphorylated sites in the peptide. For each entry the p-value of the chosen site, that provides the probability that the peptide is phosphorylated at that position, is listed.