The Spectrum Files RC configuration parameter specifies the fragment ions to use for different activation types used to identify the peptides during the search. Supported ion series types are a, b, c, x, y, and z. (These values rarely need to be changed.) During a search, if you use an activation type that no ion series types are defined for, the application uses the b and y ion series.

In the following table, the ions that you chose in the file appear next to the Ion Series Settings parameter.

Spectrum Files RC node configuration parameters

Parameter

Definition

Ion Series Settings

Specifies the fragment ions to use to identify the peptides for a specific activation type.

  • CID: by: Creates b and y ion fragments.
  • HCD: by: Creates b and y ion fragments.
  • ECD: cyz: Creates c, y, and z ion fragments.
  • ETD: cyz: Creates c, y, and z ion fragments.
  • EThcD: bcyz: Creates b, c, y, and z ion fragments.
  • UVPD: abxyz: Creates a, b, x, y, and z ion fragments.