Prerequisites
- Before using the Sequest HT search engine, set the parameters that configure the Sequest HT node and the Sequest protein-scoring calculation.
Procedure
- From the application menu bar, select Administration > Configuration.
- Under Processing Settings, expand the Sequest folder.
- Select Sequest HT Node.
- The Sequest HT node configuration parameters appear. For information about these parameters, see the Sequest configuration parameters topic in the Proteome Discoverer Help.
- In the Automatic box, specify whether you want the Proteome Discoverer application to automatically estimate the workload level.
- The default option is True, which means that the application automatically estimates the workload level.
- (Optional) If you set the Automatic parameter to False, do the following:
- In the Number of Spectra Processed at Once box, enter the maximum number of spectra that the Sequest HT search engine can process at once.
- In the Number of Parallel Tasks box, enter the number of search tasks that Sequest HT can perform at the same time.
If you set this parameter to 0, this search engine performs as many parallel tasks as the number of available CPUs can handle. - Do one of the following:
- If you are using the Sequest HT search engine to search low-resolution data, set the XCorr confidence thresholds under the XCorr Confidence Thresholds (low-resolution data) parameter.
- If you are using the Sequest HT search engine to search high-resolution data, set the XCorr confidence thresholds under the XCorr Confidence Thresholds (high-resolution data) parameter.
- The application considers these threshold values only when the workflow includes the Fixed Value PSM Validator node. The Target Decoy PSM Validator node and the Percolator node assign false discovery rates differently.
- To apply any changes to the settings of the node configuration parameters, select Apply.
- In the message box, select OK.
NOTE
Select
to return to the default values.