Proteome Discoverer Daemon utility window parameters - Proteome Discoverer Software - Proteome Discoverer Daemon utility window parameters - Proteome Discoverer Software - Proteome Discoverer Software

Spectrum Files

Specifies the files to process.

By File

Executes the workflow once for each spectrum file.

MudPIT

Feeds all spectrum files into one workflow.

Treat as Replicates

Groups the samples by quantification channel and averages the abundance values for each channel across files.

Available only when you select the MudPIT option.

If you do not select the Treat as Replicates option, the application groups the samples by quantification channel and by file. It creates the sample groups and ratios only within files, not across files.

Load Files

Specifies the files to process and starts the processing.

Export Parameter File

Creates a parameter file that you can use to call the Daemon utility from the Xcalibur data system. The utility automatically translates the options that you set on the application interface and in the workflow used for the search into text commands in the parameter file.

Add

Opens the Open dialog box so that you can select the spectrum (RAW) file or files that you want to load.

Remove

Removes a file or files from the Load Files page.

Start

Executes the job.

Number of Rawfiles

Specifies the number of raw data files that appear in the Xcalibur Sequence Setup dialog box for processing. Not available for batch processing.

Export

Opens the Save a Parameter File dialog box so that you can specify the path and name of the parameter file. When you select Save in this dialog box, the utility writes the parameter file in XML format to the directory that you specified.

Workflows and Quan Method

Specifies the processing template, the consensus template, and the quantification method.

Processing

Specifies the processing workflow template that you want to import. The menu box lists only the templates that you selected in the current run since you started the utility. When you restart the application, the menu box does not list any templates. When you connect the application to another server, it verifies that the templates are still valid and can be run by the connected server.

Consensus

Specifies the consensus workflow template that you want to import. The menu box lists only the templates that you selected in the current run since you started the Daemon. When you restart the Daemon, the menu box does not list any templates. When you connect the Daemon to another server, it verifies that the templates are still valid and can be run by the connected server.

Quan Method

Specifies the quantification method to use.

Control Channel

Specifies the control channel to create ratios against when you use the Proteome Discoverer Daemon to process quantification samples.

Server Output Directory

Specifies the name and location of the output file or files.

Local Connection

For a local connection, specifies the name of the directory where you want the original output files placed on the server. For a remote host connection, specifies the path to the subdirectory on the processing computer.

Output Filename

Specifies the name of the output result file where you want to store the results of the search from MudPIT samples. Available only if you selected the MudPIT option in the Spectrum Files area.