To search spectrum libraries, you use the MSPepSearch node.
The spectrum library search reports the three scores shown in the following table. Dot score and reversed dot score are secondary scores, and their values are not shown by default.
Score | Description |
|---|---|
MSPepSearch | Is the main score of MSPepSearch. |
Dot score | Is the score from a cross-correlation computed between two spectra. |
Reverse dot score | Is the reversed spectral dot product. |
Before creating the workflow, you must configure the Proteome Discoverer application to use spectrum libraries. See Working with spectrum library searches.
Special Processing Workflow Nodes and Node Settings
Follow the instructions in Create a workflow, but use:
- The MSPepSearch node for the search engine node
- Any PSM validation node
The basic processing workflow for searching spectrum libraries with the MSPepSearch node.
Special Consensus Workflow Nodes and Node Settings
No special nodes or settings required.
Further Information
For a description of the parameters available in the MSPepSearch node, see the MSPepSearch node in the Proteome Discoverer Help.