Processing, analyzing, and interpreting mass spectrometry data involves several steps in the standard Proteome Discoverer application task flow. The following image is an overview of the task flow, including steps that precede using the application.

Proteome Discoverer task flow
Experiments produce raw data. The Proteome Discoverer application If you intend to use Sequest HT, download a FASTA database. Configure the quantification method, import the databases, make sure thatchemical modifications are active. See Configuring Proteome Discoverer. Create a study and an analysis. Identify the RAW data files that contain datain the sample. See Creating and working with studies. Modify the templates to include the appropriate target search database, PTMs,FDR strategy, and statistical methods. Run the analysis. The application executes the processing workflow and/orthe consensus workflow. (Optional) Review the quantification results and change any parameters. (Optional) Reprocess with different parameters to optimize the results. (Optional) Export the search results and data to other applications. Sort and filter the search report, generate graphs and views, and interpretthe search results. See Interpreting search results with the results file. NOTE You can filter data according to false discovery rates that you definethrough the use of specified decoy databases. Create a processing workflow and a consensus workflow by selecting from the default templates appropriate for the dataset. See Working with analyses and workflows.