The Protein Details page displays information about the selected protein and all of the peptides from the run that matched that protein.

Grouping: Standard

In most cases, you will use the Standard option in the Grouping box in the View section of the page.

After you have chosen this option and clicked the Go button next to it, you can customize the grid using one of the built-in custom grids available on the Grid Views menu in the Peptide web part. Or you may use Customize Grid to create your own version.

If you wish to see information on the proteins selected as matches by the search engine, choose Grid Views > SearchEngineProtein. In the resulting grid view, the putative protein appears under the Database Sequence Name column.

If you wish to see the protein-level scores calculated by the ProteinProphet tool, choose Grid Views > ProteinProphet. Each row of the resulting grid view shows a protein. Expand the "+" next to any row to show the peptides that were matched to the particular protein.

Grouping: Protein Groups

The Protein Groups option in the Grouping box under the Views web part is more narrowly useful than the Standard option. Use it if you want to drill into the members of the particular protein groups.

If you have selected this option in the Grouping box and clicked the Go button next to it, results appear in a grid view in the Protein Groups web part below. Each row of this grid view shows a protein group. Expand the "+" next to a row to show the proteins that are members of that group. Use the Expanded box in the View section and click Go to expand all proteins.

Protein Details

The Protein Details page displays the following information about the protein:

  • The protein sequence's name, or names in the case of indistinguishable proteins
  • The sequence mass, which is the sum of the masses of the amino acids in the protein sequence
  • The amino acid (AA) coverage, which is the number of amino acids in the peptide matches divided by the number of amino acids in the protein and multiplied by 100
  • The mass coverage, which is the sum of the masses of the amino acids in the peptide matches divided by the sequence mass of the protein and multiplied by 100
The Protein Details page also displays the full amino acid sequence of the putative protein in black. The matched peptide sequences are highlighted, as shown in the following image.

Peptides

The Peptides section of the page displays information about the peptide matches from the run, according to any currently applied sorting or filtering parameters.

Tip: If you’re interested in reviewing the location of certain peptides in the sequence or wish to focus on a certain portion of the sequence, try sorting and filtering on the SequencePosition column in the PeptideProphet results view.

Annotations

The Annotations section of the page displays annotations for the protein sequence, including (if available):

  • The sequence name
  • The description of the sequence
  • Name of the gene or genes that encodes the sequence
  • Organisms in which the sequence occurs
  • Links to various external databases and resources
The annotations web part is collapsed by default, but can be expanded by clicking the [+] in the web part title.

Discussion

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