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This topic describes how to compare peptides, proteins, or ProteinProphet results across two or more runs.

Compare Runs Within a Single Folder

Navigate to the home page of an MS2 folder. For example, you could create and populate a folder to explore comparisons by completing the Discovery Proteomics Tutorial

  • In the MS2 Experiment Runs web part, click the checkboxes next to the runs you want to compare.
  • Click Compare and select a method of comparison. Options include:
    • ProteinProphet: your comparison will be based on the proteins assignments made by ProteinProphet. See Compare ProteinProphet.
    • Peptide: choose whether to include all peptides, those which exceed a given ProteinProphet probability, or those which meet the filter criteria in a saved grid. You can also opt to require a sequence map against a specific protein.
    • Search Engine Protein: indicate whether you want to display unique peptides, or all peptides. If you use a saved view, the comparison will respect both peptide and protein filters.
    • Spectra Count: choose how to group results and how to filter the peptide identifications.
  • After specifying necessary options, click Compare.

There is a summary of how the runs overlap at the top of the page for most types of comparison. It allows you to see the overlap of individual runs, or to combine the runs based on the run groups to which they are assigned and see how the groups overlap.

  • Click the to expand a section.
  • Depending on the type of comparison, the format of Comparison Details will differ.
  • Select (Grid Views) > Customize Grid to add columns to the comparison. Find the column you'd like to add (for example, protein quantitation data can be found under Protein Group > Quantitation in the tree on the left). Place a check mark next to the desired columns and click Save to create a saved grid.
  • Select (Grid Views) > Customize Grid and click on the Filter tab to apply filters. On the left side, place a check mark next to the column on which you'd like to filter, and then specify your filter criteria. Click Save to save the filters with your grid.


The comparison grid will show a protein or a peptide if it meets the filter criteria in any one of the runs. Therefore, it's possible that the values shown for the protein or peptide in every run shown may not meet the criteria.

For more information on setting and saving grids, see the View an MS2 Run help page. If you compare without picking a grid, the comparison results will be displayed without filters.

Compare Runs Across Folders

In the MS2 Runs web part, click (Grid Views) > Folder Filter > Current folder and subfolders.

The MS2 Experiment Runs list now contains runs in the current folder and subfolders, so you can select the runs of your choice for comparison, just as described above for a single folder.

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