Compare runs within a single folder
You can compare peptides, proteins, or ProteinProphet results across two or more runs.
- Navigate to the MS2 Dashboard. Alternatively, add the MS2 Experiment Runs web part to a folder's Portal page.
- In the MS2 Experiment Runs web part, click the checkboxes next to the runs you want to compare.
- Click the Compare button.
- Choose a method of comparison.
- If you are using the ProteinProphet comparison, your comparison will be based on the proteins assignments made by ProteinProphet. See the Compare ProteinProphet documentation for details.
- If you are using the Peptide comparison, choose which peptides to include. If you choose a filter based on a custom view, the comparison will use only the peptides included in the view.
- If you are using the Search Engine Protein comparison, indicate whether you want to display unique peptides, or all peptides. If you use a saved view created when examining a single run, the comparison will respect both peptide and protein filters.
- If you are using the Peptide (Legacy) comparison, choose which columns to include in the comparison results. If you use a saved view created when examining a single run, the comparison will only use the peptide filters.
- If you are using the ProteinProphet (Legacy) comparison, specify which columns to display in the comparison grid. If you use a saved view created when examining a single run, the comparison will only use the protein group filters.
- If you are using the Spectra Count comparison, choose how to group results and how to filter the peptide identifications.
- On the left side you can see the protein or peptide that was present in at least one of the runs. There is one or more columns for each of the runs being compared showing the requested value in that particular run.
- If you are using the ProteinProphet comparison:
- Select Views -> Customize View to apply filters to your comparison. Click on the Filter tab 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. For example, to filter on the ProteinProphet probability, click on the Filter tab, expand the Protein Group node in the tree and select Prob. Choose Is Greater Than Or Equal To from the drop-down, and type in the desired probability threshold.
- Select Views -> Customize View 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 view.
- There is a summary of how the runs overlap at the top of the page. 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.
Notes:
- The comparison grid will show a protein or a peptide if it meets the filter criteria in any one of the runs. Therefore, the values shown for the protein or peptide in one of the runs may not meet the criteria.
- For more information on setting and saving views, see "The View Section" of the View an MS2 Run help page. If you compare without picking a view, the comparison results will be displayed without filters.
Compare runs across folders
- On the MS2 Dashboard in the MS2 Experiment Runs web part, click 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.