You can globally modify the default colors and fonts that the application uses to annotate fragment peaks in spectra. The ion tables in the Peptide Spectrum Match Identification Details dialog box also use these colors. When you save these settings, they become the global default settings for a particular mass analyzer/activation type combination.

You can restore the factory default settings, which use the most common ion series, match tolerance, neutral losses, and PTMs for the selected mass analyzer/activation type combination.

Procedure

  1. Choose Tools > Options to display the Fragment Match Options page of the Options dialog box.
  3. In the Charge Detail Level area, select the target charge state to display. Choose from the following settings:
  4. (Default) All: All fragment ions, regardless of charge
  5. +1: Singly charged fragment ions
  6. +2: Doubly charged fragment ions
  7. +3: Triply charged fragment ions
  8. +4 …: Additional charged fragment ions if available
  9. In the Annotation Threshold area, specify a peak intensity limit.
  10. Peaks below this limit are not annotated. This limit prevents adding too many labels to a spectrum, especially if the low-intensity peaks are possibly noise peaks.
  11. (Default) 1.0% of Base Peak: An intensity threshold as a percentage of the base peak in the spectrum. The base peak is the largest peak in a spectrum.
  12. Absolute: An absolute intensity threshold.
  13. To display a legend at the bottom of each spectrum image that shows colored lines to denote the displayed ion series, select the Show Legend checkbox.
  14. To display the reference spectrum from the reference spectrum library, select the Show Reference Spectrum checkbox.
  15. To choose the spectrum source, select the Ref. Spectrum Source dropdown menu.
  16. To annotate the spectra using the match tolerances and ion series that you chose for the search node, select the Use Search Settings checkbox.
    –or–
  17. Clear the Use Search Settings checkbox to activate these options and set the following:
  18. In the Match Tolerances area, indicate the mass analyzer and the mass tolerance.
    - In the Mass Analyzer box, select the mass analyzer that was used to obtain the spectrum.
    - In the Match Tolerance box, specify the mass tolerance, in daltons or millimass units.
  19. The application annotates the spectrum with ions that it assigns within this mass tolerance.
  20. In the Activation Type area, select the type of activation that produced the fragments.
  21. In the Ion Series area, select which types of ion series to annotate in the spectra.
  22. In the Neutral Losses area, select which types of neutral losses to annotate in the spectra.
  23. In the PTMs area, select the spectra ions that have lost H3PO4 to annotate.
  24. This loss is represented as –P in the ion list.
  25. In the Other area, select whether to annotate the spectra with immonium ions or precursor ions.