Figure 2

Protein view: graphical comparison of experiments. The figure shows an example of the graphical display used to present all the phosphosites stored for a given protein entry. The protein is represented by a horizontal bar, with the positions of known domains and phosphosites indicated by colored boxes and vertical lines, respectively. The top panel depicts a complete summary of all modifications, in which phosphosites are color coded according to whether they were fully resolved by the experiment, because sometimes the position of a phosphosite cannot be unambiguously determined by mass spectrometry. Thus, confidently determined positions are shown in red, uncertain positions in orange, and positions that have been retrieved from literature or other sources and are still awaiting manual curation to confirm their status in gray. The peptide maps for each experiment are then shown underneath, in which related experiments are grouped together to allow easy comparison. The color coding is the same as above with the exception that gray is now used to highlight residues that have been seen phosphorylated but not in that particular experiment. Further information about individual peptides can be retrieved via links from the lines representing them. These peptide pages include details about the sequence of the peptide, experimental data (such as protease and software used for their identification), whether the peptide is unique for a gene/protein, its position in the full-length protein, and whether there exist sequence variations with respect to the Ensembl sequence.