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The MS2 run detail page shows data from a single run of tandem mass spectrometry data. Explore details of how the search was performed, metadata, and detailed information about proteins and peptides.

Run Overview Section

The run overview provides metadata about the run and how the search was performed. This information is derived from the pepXML file associated with the run. Or for COMET searches, this metadata comes from a comet.def (definitions) file within the tar.gz file.

Information shown includes:

  • Search Enzyme: The enzyme applied to the protein sequences by the search tool when searching for possible peptide matches (not necessarily the enzyme used to digest the sample).
  • Search Engine: The search tool used to make peptide and protein matches.
  • Mass Spec Type: The type of MS instrument used to analyze the sample.
  • Quantitation: The source of quantitation algorithms used.
  • File Name: The name of the file where the search results are stored.
  • Path: The location of the file named above.
  • FASTA File: The name and location of the copy of the protein sequence database searched.
Links here let you:
  • Rename the run
  • Show Modifications to proteins
  • Show tandem.xml: the search protocol definition file used by the search engine
  • Show Peptide Prophet Details
  • Show Protein Prophet Details

View Section

The View panel lets you select among different ways of grouping and filtering your results shown in the Peptides and Proteins section. There are special filters available in the View section that offer specialized features not available in typical grid filtering. Not all options are available in all Groupings of data. Views you create here can be saved for reuse.


  • Select an option for grouping the Peptides and Proteins grid:
    • Standard lists all the peptides from the run. If you choose columns from ProteinProphet or the search engine assigned protein, the peptides will be grouped under those columns. Use (Grid Views) > Customize Grid to change the columns shown.
    • Protein Groups Shows proteins, grouped under the ProteinProphet assigned groups.
  • If you select the Expanded checkbox the data will all be expanded by default to show components.
  • Click Go.
To add or remove columns for any grouping, select (Grid Views) > Customize Grid.

Hyper Charge Filter

The Hyper charge filter section allows you select the minimum Hyper value for peptides in charge states 1+, 2+ and/or 3+, then click Go.

Minimum Tryptic Ends

The Minimum tryptic ends specifies how many ends of the peptide are required to match a tryptic pattern: 0 means all peptides will be displayed; 1 means the peptide must have at least one tryptic end; and 2 means both ends must be tryptic.

Highest Score Filter

In this section, check the box to filter out all except the highest Hyper score for a peptide, then click Go.

RawScore Filter (Comet only)

  • RawScore filter offered for the COMET search engine specifies different raw score thresholds for each charge state. For example, if you enter 200, 300, and 400 in these three text boxes, you are specifying 1+ peptides with raw scores greater than 200, 2+ peptides with raw scores greater than 300, and 3+ peptides with raw scores greater than 400.

Saved Views

You can save a specific combination of grouping, filtering parameters, column layout, and sorting as a named view. Click Save View to do so. Later selecting that saved view from the menu will apply those same parameters to other runs or groups of runs. This makes it easier to keep your analysis consistent across different datasets.

Manage Views

To delete an existing view, select a default, or indicate whether you want to use the current view the next time you look at another MS2 run, click Manage Views.

Peptides and Proteins Section

The Peptides/Proteins section displays the peptides and/or proteins from the run according to the sorting, filtering, and grouping options you select in the View section.

You can customize the display and layout of the Peptides/Proteins section, as with other data grids:

  • Choose a custom grid view from the (Grid Views) menu. For the Standard grouping, these options are provided:
    • SearchEngineProtein: See information on the proteins selected as matches by the search engine. The putative protein appears under the Database Sequence Name column.
    • ProteinProphet: Includes the protein-level scores calculated by the ProteinProphet tool.
  • Choose which columns of information are displayed, and in what order, by selecting (Grid Views) > Customize Grid. Learn more in the topics: Peptide Columns and Protein Columns.
  • Sort the grid, including sorting by multiple columns at once.
  • Filter the grid using the column header menu option Filter.

Getting More Detail

Some of the fields in the rows of peptide and protein data are links to more detailed information.

  • Click the to expand rows in the Protein Groups grouping and see Protein Details.
  • Click the Scan number or the Peptide name to go to the Peptide Spectrum page, which displays the MS2 spectrum of the fragmented peptide.
  • Click the Protein name to go to the Protein Details page, which displays information on that protein and the peptides from the run that matched it.
  • Click the dbHits number to go to the Protein Hits page, which displays information on all the proteins from the database that the peptide matched.


You can export data from the MS2 Peptides/Proteins page to several other file types for further analysis and collaboration. Before you export, make sure the grid you have applied includes the data you want to export.

Learn more about exporting MS2 data in this topic: Export MS2 Runs

Viewing a GO Piechart

If Gene Ontology annotations have been loaded, you can display a GO Piechart for any run. Learn more in this topic: View Gene Ontology Information

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