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Phosphopep glossary and usage guide

Buttons used in PhosphoPep

    View KEGG pathways for this protein
    Start cytoscape network with this protein
    View orthologs/homolog information
    Search for protein interaction networks in String
    Look up protein information in Peptide Atlas
    Search 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

PeptideProphet          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.

Tryptic Termini            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.

Peptide Mass              Molecular mass of the phosphopeptide.

DeltaCN                      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.

# Obs                          The number of times this phosphopeptide was identified in our experiments.

# Mappings                  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.

ISB Phosphopep