The Peptide Spectrum Match Identification Details view shows the analyzed spectra of the selected peptide sequence on the PSMs page. You can use this view to gauge how good the match is between a spectrum and a peptide found in the searched database. This view displays a color-coded amino acid sequence, where the colors represent the application's confidence level of the match.

For the fragment ions that the application uses, see Displaying fragment ions.

Procedure

  1. In an open result report, double-click a peptide row in the PSMs table.
  2. The Peptide Spectrum Match Identification Details view opens.
  3. Peptide Spectrum Match Identification Details view
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    No.DescriptionNo.Description

    1

    The Peptide Summary pane displays information about the peptide spectra and the conditions of the search.

    3

    The Options pane on the left is where you choose the data that appears in the Fragment Matches and Fragment Spectrum panes. For information on setting the options on this panel, see Set global default fragment match options.

    2

    The Fragment Matches pane consists of fragment ion tables that display the ion fragments that you selected in the Fragments area of the Options pane.

    4

    The Fragment Spectrum pane displays an extracted plot of the data that you selected in the Options pane.

For descriptions of the features in the Peptide Spectrum Match Details Identification view, see Peptide Spectrum Match Identification Details view parameters in the Proteome Discoverer Help.

You can use the Options dialog box (opened by the Tools > Options command) to change the colors of the ion series and their backgrounds. You can also use this dialog box to change fonts. Refer to the Set global default fragment match options in the Proteome Discoverer Help.

NOTE

Avoid using the Cambria Math font in the Peptides Identification Details view, especially in the larger sizes, because it can obscure the data.