An analysis in Proteome Discoverer is divided in to two workflows: the Processing Step and Consensus Step. Each step has a dedicated set of nodes, which are unique to either the Processing Step workflow or the Consensus Step workflow. A workflow is composed of a series of nodes, and each node performs an individual step of the data analysis. Depending on the workflow’s purpose, it usually consist of 5 to 10 nodes. Most nodes have their own parameters to set. The basic functions of the workflows are:
- In the Processing Step workflow, the software searches the database and assigns PrSMs. If the analysis is quantitative, the processing workflow also performs feature detection.
- The Consensus Step workflow filters the preliminary results (for example, by the FDR node) and groups them into proteoforms, isoforms, and proteins. The results display these groups. If there is quantitative analysis in the processing workflow, then the consensus workflow performs the required feature mapping and statistical analysis.
You can run multiple processing workflows separately and then combine them in the consensus workflow for unified reporting. Due to this behavior, the Processing Step(s) appear nested within the Consensus Step.
To simplify creating a workflow, the software includes a set of fit-for-purpose templates. Build your workflow from the provided templates, which have been tested and optimized for confident proteome analysis. Many of the node parameters already have their appropriate settings in the template.
Proteome Discoverer has three types of templates: processing workflow templates, consensus workflow templates, and analysis templates, which contain both the processing and consensus workflows. The templates are named for their intended use. For example, the Comprehensive Discovery template includes nodes that cover the largest search space.