The Fragment Match Spectrum view displays the annotated spectrum of the identified peptide. It is the same graph as that shown in the Peptide Spectrum Match Identification Details view. However, in the Fragment Match Spectrum view, you can scroll from one peptide to another on the PSMs page and quickly display the annotated spectrum for each peptide. You can also display the Fragment Match Spectrum view for a spectrum on the MS/MS Spectrum Info page.

NOTE

The Spectra to Store parameter of the MSF Files node specifies which spectra are stored. You can see spectra only if the result file includes the peptide spectrum. You must reprocess the consensus workflow when you need a spectrum that is not available in the current result file.

The matched fragments of the spectrum are colored according to their fragment type, such as red for b ions and blue for y ions.

The types of fragment ions observed in an MS/MS spectrum depend on several factors, such as the primary sequence, the energy source, and the charge state.

In addition to the proton carrying the charge, c ions and y ions abstract an additional proton from the precursor peptide.

Structures of six singly charged sequence ions
Structures of six singly charged sequence ions

Procedure

  1. Open a result file and select the PSMs tab.
  2. Select a peptide row.
  3. Select View > Fragment Match Spectrum, or select Fragment Match Spectrum View .
  4. The Fragment Match Spectrum view opens.
  5. Fragment Match Spectrum view
  6. Confirm that matched ions, which are color-coded, are assigned to major fragments.
  7. You can use the Fragment Match Options dialog box to change the settings that the application uses to annotate the spectrum with fragment assignments.
  8. To display the Fragment Match Options dialog box, right-click the fragment match spectrum and select Fragment Match Options.