You can retrieve annotations of all identified proteins from the Annotation Server by using the Protein Annotation node in the consensus workflow. This node retrieves annotation information from the server to include in the result file.
For general protein annotation information, see Protein annotation.
Special Processing Workflow Nodes and Node Settings
No special nodes or settings required.
Special Consensus Workflow Nodes and Node Settings
Add the Protein Annotation node to the consensus workflow, or start with a workflow that includes it, such as: CWF_Comprehensive_Enhanced Annotation
Connect the Protein Annotation node to the ProteinScorer node if the application does not automatically connect it.
You can select user-defined aspects in the Protein Annotation node in a consensus workflow. When you click on each numbered aspect, a dropdown list appears from which you can choose any predefined and user-defined aspect. The Protein Annotation node has up to six annotation aspects available for the Annotation Aspects parameter that you can apply to the annotation.
The list contains all aspects marked “Active” in the Administration view.
The application uses the new annotation aspects in its consensus workflow and displays the results of the annotation in the result file.
Further Information
For information about protein annotation databases, see Work with Annotation Aspects.
The annotation is restricted to FASTA database formats of UniProt (Swiss-Prot, TrEMBL), NCBI (RefSeq), and Annotation Server downloads.
- Gene Ontology (GO) annotations, which are displayed in the GO Accessions column of the results report file. These also include GO Slim annotations, which are displayed in the Molecular Function, Cellular Component, and Biological Process columns of the result file.
- In addition, you can define your own categories of GO Slim annotations. In the Proteome Discoverer application, the categories containing user-defined GO Slim terms are called annotation aspects. For information on defining new annotation aspects, see Work with Annotation Aspects.
- Protein family (Pfam) annotations, which are displayed in the Pfam IDs column of the result file.
- Wiki Pathways annotations, which is displayed in the following column:
- For Wiki Pathways annotations, the node displays the WikiPathways, WikiPathway Accessions, and Gene Symbol columns of the result file.
- Gene identifications from the Entrez Gene database, which are displayed in the Entrez Gene ID column of the result file.
- Gene identifications from the reference genomes of the genetically sequenced organisms in the Ensembl genome database, which are displayed in the Ensemble Gene ID and Chromosome columns of the Proteins page of the result file.
UniProt PTM modifications documented in the UniProt database, which are displayed on the Protein Identification Details view in the Proteins page of the result file.