The following table describes the parameters that you can use to configure the MSPepSearch node.
Parameter | Definition |
|---|---|
Default Confidence Thresholds | |
High Confidence Threshold | Specifies that peptide matches with this score or higher be considered of high confidence. Range: 0–no maximum; default: 450 |
Medium Confidence Threshold | Specifies that peptide matches with this score or higher be considered of medium confidence. NOTE: When the MSPepSearch node is used in conjunction with the Percolator node, the confidence assigned to the peptide spectral match is based on the Percolator q-value rather than the MSPepSearch score. Range: 0–no maximum; default: 400 |
Parallel Processing | |
Max. # Parallel Jobs | Specifies the maximum number of MSPepSearch processes to run in parallel. The application runs the maximum number of processes until it completes all of them. If left at 0, the application automatically adjusts the number of processes according to the number of processing cores. Do not enter a number greater than the number of processing cores. Range: 0; default: 0; maximum: unchecked |
Max. # Input Spectra | Specifies the maximum number of input spectra written for each Mascot generic format (MGF) file. For example, if the total number of input spectra is 12000 with the Max # Input Spectra set to 10,000 and the Max # of Parallel Jobs is set to 8, the MSPepSearch node first runs 8 concurrent jobs for 10,000 spectra each. After a batch finishes, the next batch of 10,000 runs. In total, twelve MSPepSearch processes are run to complete the search of the input dataset. Range: 10,000–no maximum; default: 10,000 |