You can set configuration parameters for the Sequest HT node and the Sequest HT protein-scoring calculation.
The following table lists the parameters that you can use to configure the Sequest HT node.
Parameter | Definition |
|---|---|
Work Load Level | |
Automatic | Determines whether to automatically estimate the workload level. The parameter options are as follows:
|
Number of Spectra Processed at Once | Specifies the maximum number of spectra that the Sequest HT search engine processes at once. The larger the number, the more memory is required. The application uses this parameter only if the Automatic parameter is set to False. Range: 1,000–no maximum; default: 3,000 |
Number of Parallel Tasks | Specifies the number of parallel searches that the Sequest HT search engine can perform. The default setting of 0 indicates that this search engine performs as many tasks as the available CPUs allow. The application uses this parameter only if the Automatic parameter is set to False. Range: 0–no maximum; default: 0 |
XCorr Confidence Thresholds (low-resolution data) | |
z=1: High Confidence XCorr | Displays PSMs that match this score with a green confidence marker. Default: 1.5 |
z=1: Medium Confidence XCorr | Displays PSMs that do not match the High Confidence XCorr score but match this score with a yellow confidence marker. Displays PSMs that do not match this score with a red marker. Default: 0.7 |
z=2: High Confidence XCorr | Displays PSMs that match this score with a green confidence marker. Default: 2 |
z=2: Medium Confidence XCorr | Displays PSMs that do not match the High Confidence XCorr score but match this score with a yellow confidence marker. Displays PSMs that do not match this score with a red marker. Default: 0.9 |
z=3: High Confidence XCorr | Displays PSMs that match this score with a green confidence marker. Default: 2.5 |
z=3: Medium Confidence XCorr | Displays PSMs that do not match the High Confidence XCorr score but match this score with a yellow confidence marker. Displays PSMs that do not match this score with a red marker. Default: 1.2 |
z>=4: High Confidence XCorr | Displays PSMs that match this score with a green confidence marker. Default: 3 |
z>=4: Medium Confidence XCorr | Displays PSMs that do not match the High Confidence XCorr score but match this score with a yellow confidence marker. Displays PSMs that do not match this score with a red marker. Default: 1.5 |
XCorr Confidence Thresholds (high-resolution data) | |
z=1: High Confidence XCorr | Displays PSMs that match this score with a green confidence marker. Default: 1.2 |
z=1: Medium Confidence XCorr | Displays PSMs that do not match the High Confidence XCorr score but match this score with a yellow confidence marker. Displays PSMs that do not match this score with a red marker. Default: 0.7 |
z=2: High Confidence XCorr | Displays PSMs that match this score with a green confidence marker. Default: 1.9 |
z=2: Medium Confidence XCorr | Displays PSMs that do not match the High Confidence XCorr score but match this score with a yellow confidence marker. Displays PSMs that do not match this score with a red marker. Default: 0.8 |
z=3: High Confidence XCorr | Displays PSMs that match this score with a green confidence marker. Default: 2.3 |
z=3: Medium Confidence XCorr | Displays PSMs that do not match the High Confidence XCorr score but match this score with a yellow confidence marker. Displays PSMs that do not match this score with a red marker. Default: 1 |
z>=4: High Confidence XCorr | Displays PSMs that match this score with a green confidence marker. Default: 2.6 |
z>=4: Medium Confidence XCorr | Displays PSMs that do not match the High Confidence XCorr score but match this score with a yellow confidence marker. Displays PSMs that do not match this score with a red marker. Default: 1.2 |