In this step, you explore the results of the ProteinProphet analysis.

Group Peptides by Protein

  • Open an MS2 run for viewing.
  • In the View section, under Grouping, select Standard and click Go
  • In the Peptides and Proteins section, click (Grid Views) > ProteinProphet.

You will see scored results for proteins found in the sample. Note that the first two dozen proteins shown have values of .99 - 1.0 in the Prob (protein probability) column. These are likely the proteins that made up the mixture in the original sample.

To view the peptides that were found in the sample and determined to comprise an identified protein, click the "+" next to the protein group to expand it.

Note that there may often be more than one protein per group, but the sample data contains only one protein per group. The following image shows the expanded protein group.

To see how the individual peptides found map to the protein sequence, click the protein name link as circled above.

The peptides found are highlighted in the sequence.

Hover over and click the highlighted area of the sequence for details.

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