When you use the Mascot node as the search engine in a quantification workflow, you can set the dynamic and static modifications as parameters. Samples with isotopic labels and several PTMs might require that you specify several dynamic modifications usable within a single search. (You can specify up to nine modifications.)

With the Mascot node, you can use the modification groups specified as part of a quantification method on the Mascot server. You can use the node’s From Quan Method parameter in the Parameters pane to select the quantification modifications to search for, rather than manually specifying each modification with the Dynamic and Static Modifications parameter.

NOTE

Using a Mascot quantification method to retrieve the modification groups to use does not affect how the Proteome Discoverer application performs the quantification. The application itself exclusively performs the quantification. You must specify in the application’s quantification methods any labels used for the quantification.

Special Processing Workflow Nodes and Node Settings

Ensure that the Mascot Node is selected on the Administration page, see Configure Mascot search engine parameters. Do not use the modifications that you specify as part of the modification groups in the selected quantification method as additional dynamic or static modifications.

To use the modifications associated with the Mascot quan method in the search, do the following:

Procedure

  1. Add the Mascot Node to the processing workflow.
  2. Select the From Quan Method parameter in the Parameters pane under Modification Groups.
  3. Select from the list.
From Quan Method list example

Special Consensus Workflow Nodes and Node Settings

No special nodes or settings required.

Further Information

(Optional) If you want to group these modifications, do the following:

Procedure

  1. Go to the editor in the Mascot server window, and select Configuration Editor > Quantitation.
  2. After you group the modifications, define them as fixed, variable, or exclusive.
  3. You can also define them directly for the method in reporter ion quantification or for each component in precursor ion quantification.

Refer to the Mascot documentation for information on grouping modifications and defining the groups.

For information on the Mascot node, see the Mascot node in the Proteome Discoverer Help.