Figure 3

Protein view and lines of evidence. The spot details page provides information about peptide and protein identification from, for example, one spot on a 2D gel. First, the name and additional information is presented (here B1-1 see top box). Those proteins which pass the significance criteria set for protein identification from peptide identifications are presented in the second box. Multiple thresholds can be used to analyze the data more elaborately. Here only the first of two possible thresholds yields confident protein identifications. One protein with two distinct access numbers (for the same sequence; 156523 and 60278) was successfully identified by two supporting peptides with one and two MS/MS spectra, respectively. Both protein identifiers and spectrum ids are hyperlinks that lead to more detailed information. The drop-down box displays the plug-ins which are available to analyze the underlying sequence using different tools. The final box shows potentially interesting results, which have not lead to confident protein identifications when applying the thresholds. Neither result is expanded, although details are accessible by clicking the plus sign in front of either section. The first section hosts peptides that map onto amino acid sequences in the database whereas the second shows all those peptides that could not be matched.