Configure MSPepSearch - Proteome Discoverer Software - Configure MSPepSearch - Proteome Discoverer Software - Proteome Discoverer Software

Procedure

1. From the application menu bar, select Administration > Configuration.
2. Under Processing Settings, select MSPepSearch.
3. The MSPepSearch settings page opens.

4. 

3. Configure the Default Confidence Thresholds settings as follows:
1. For High Confidence Threshold, enter a number.
2. For Medium Confidence Threshold, enter a number.
3. When you use the MSPepSearch node with the Percolator node, the confidence assigned to the peptide spectral match is based on the Percolator q-value rather than the MSPepSearch score.
4. Configure the Parallel Processing settings as follows.
1. (Optional) For Max. # Parallel Jobs, enter a number.
2. The default value, 0, causes the application to use half of the available processors for the search. The maximum number of allowable processes is equal to the total number of processors on the computer.
1. For Max # Input Spectra, enter the maximum number of spectra to send to MSPepSearch for each process.
2. The default, 10,000, is usually appropriate.