Phosphopep glossary and usage guide
Buttons used in PhosphoPep
KEGG pathways for this protein
cytoscape network with this protein
for protein interaction networks in String
up protein information in Peptide Atlas
protein sequence at Scansite
Importantly, as the current knowledge about cellular pathways is far from complete, only a portion of the phosphoproteins can be placed into defined pathways. This partial knowledge also applies for the orthologous protein information as well as to the prediction of a kinase for a given phosphorylation sites.
Scores and numbers used in PhosphoPep
When interpreting tandem mass spectrometry data, it is crucial to determine if an identification is correct. The PeptideProphet computes a probability if a given fragment ion spectrum was correctly identified by a given database search algorithm and assigns a score accordingly.
The range of the score is from 0 (worst) to 1(best). Depending on the dataset or database the probabilities vary slightly at a given threshhold/score.
As we analyze peptides in our tandem mass spectrometry experiments we have to digest the proteins using a protease. This is normally done using trypsin. Trypsin cleaves after arginine and lysine but exhibits also some unspecific cleavage. 2 tryptic ends means that both ends were correctly cut by trypsin.
Molecular mass of the phosphopeptide.
The delta correlation score (dCn) is a score computed by the Sequest algorithm which we use to interpret tandem mass spectra. Oversimplified, the dCn is a measure of the distance between the best database search hit and the the second best. In the case of phosphopeptides the dCn also correlates to the correctness of the phosphorylation site assignment within the phosphopeptide sequence.
The number of times this phosphopeptide was identified in our experiments.
Maps to # gene models/maps to # of transcripts.
Download user guide
For additional information, please download this primer on how to assess the quality of a phosphopeptide identified using tandem mass spectrometry.