When a ProteinPilot Software search is complete, a ProteinPilot report is generated that contains all the false discovery rate (FDR) analysis information. More information on using the large and small ProteinPilot reports can be found here.
When doing method optimization, you often want to review data across a set of experiments/search results to investigate whether the protein/peptide ID numbers have increased or decreased. The FDR Comparison Template (FDR Comparison_V5.0p.xlsx) is a convenient tool that allows the input of the FDR results from ProteinPilot reports to create an output of easy visual results. This Excel tool is installed with the software and can be found here: C:\Program Files\AB SCIEX\ProteinPilot\WorkflowDirectory (Instructions for use are included in the first tab of the Excel tool.)
- Briefly, the user will:
- Input the FDR results into the Input tab from the ProteinPilot Reports generated from each database search
- Enter metadata describing the parameters used/varied in each experiment into the Metadata tab
- User sets either a single reference to which results will be compared or can select specific reference searches for each result to be compared
- Trend plots are generated that allow the user to visualize the results
- Flexible Viewer tab allows many different visuals to be constructed from the results and the metadata