The following table describes the parameters on the Fragment Match Options page.

Fragment Match Options page parameters in the Options dialog box

Command or Option

Description

Loads the last saved default fragment match settings for the selected mass analyzer/activation type combination.

Saves the current fragment match settings as the default fragment match settings for the selected mass analyzer/activation type combination.

Loads the original factory fragment match settings for all mass analyzer/activation type combinations.

Charge Detail Level

Selects the target charge state to display from the following settings:

  • (Default) All: All fragment ions, regardless of charge
  • +1: Singly charged fragment ions
  • +2: Doubly charged fragment ions
  • +3: Triply charged fragment ions
  • +4 …: Additional charged fragment ions if available

Annotation Threshold

Specifies a peak intensity limit. Peaks below this limit are not annotated. This limit prevents the addition of too many labels to a spectrum, especially if the low-intensity peaks are possibly noise peaks.

  • (Default) % 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.

Default: 1.0

  • Absolute: An absolute intensity threshold.

Default: 1000

Show Legend

Determines whether a legend consisting of colored lines that denote the displayed ion series appears at the bottom of each spectrum image.

Show Reference Spectrum

Determines whether to display the reference spectrum from the reference spectrum library.

Ref. Spectrum Source

 

Use Search Settings

Annotates the spectra using the match tolerances and ion series settings that you chose for the search node.

Mass Analyzer

Specifies which mass analyzer was used to obtain the spectrum.

Match Tolerance

Specifies the mass tolerance. The application annotates the spectrum with ions that it assigns within this mass tolerance. You can use daltons or millimass units.

Activation Type

Specifies what type of activation produced the fragments.

Ion Series

Selects which types of ion series to annotate in the spectra.

Neutral Losses

Selects which types of neutral losses to annotate in the spectra.

Other

Annotates the spectra with immonium ions or precursor ions.

Abbreviations