Each workflow consists of a string of nodes that depend on your quantification method (if any) and the question that your data answers. There are two main types of workflows:
Workflow type | Definition |
|---|---|
Processing workflow | Processes data from one or more RAW data files, from which it generates the primary search results (for example, the results of a sequence database search by an engine such as Sequest HT) or extracting the raw quantification values (for example, the extracted reporter peak intensities where samples use isobaric tags). The processing workflow accepts spectrum container files such as RAW and MZML files as input and produces MSF files as output. |
Consensus workflow | Collects and assembles the data from one or more processing workflow results. The consensus workflow accepts MSF file or files as input and produces a result file as output. The application can create different result files from the same MSF file and can combine different MSF files into one result file called a multiconsensus report. |
Usually, an analysis contains one processing workflow and one consensus workflow, but some advanced analyses for reprocessing can have more than one processing workflow.
Most users create workflows from workflow templates, which are XML files that have a .pdProcessingWF or a .pdConsensusWF suffix. There are various templates to support the different quantification methods, mass spectrometers, and biological experiments that you might use. The templates’ default node configurations are usually appropriate, but you can change the nodes and change their parameters if needed.
For information on creating workflows, see the following topics: