Figure 2.

A Screenshot of IDPicker GUI report. Three samples from cancer subjects and three samples from control subjects were arranged in a tree hierarchy to reflect their biological meaning. Each sample has three replicate LC-MS/MS experiments that were grouped together. The final protein identification report arranges the protein, peptide, and spectral identifications in the above-described hierarchy. The numbers of identifications at each node are reported by summarizing the identifications of its child nodes. For example, the above report starts with the “root” level of hierarchy, designated by the “/” label, that summarizes all identifications present in the analysis. Following the root node, the numbers of identifications for next lower level hierarchies (cancer and control groups) are summarized, followed by each sample and individual technical replicate. The report also contains a navigation frame (shown on the left side) that allows the user to browse the protein identifications using different indices. Users can also manually validate the spectral matches using a built-in spectrum viewer. For example, the bottom window highlights the fragment ion matches of a tandem mass spectrum that was mapped to the peptide “IAQWQSFQLEGGLK”.