You can specify a contaminant FASTA file and up to three additional FASTA files containing the proteins that you want to mark (that is, identify). You can also specify the listed name of the additional columns in the results report. The Contaminant column that has an X symbol marking the proteins, which appear in the specified contaminants FASTA file.
For example, a core facility receives a sample from a microbiological laboratory and a request to search the data against the proteins of all known bacteria. If the preceding experiment involved a proteome of E. coli, it is likely that the HPLC column retains some E. coli peptides and that proteins are detected on the basis of these peptides. It is helpful if you can specify the E. coli FASTA file as an additional contaminant database and have the proteins highlighted in an additional column.
In this example, the results report contains a Contaminant column on the Proteins, Peptide Groups, and PSMs pages that displays an X symbol next to the proteins marked as contaminants in the searched FASTA file.
Special Processing Workflow Nodes and Node Settings
No special nodes or settings required.
Special Consensus Workflow Nodes and Node Settings
To mark proteins, start with one of the enhanced annotation consensus workflows and add the Protein Marker node. For example, you can use:
CWF_Comprehensive_Enhanced Annotation.pdConsensusWF
Optionally, you can add the Protein Marker node and the nodes listed in the figure below to a consensus workflow. Connect the Protein Marker node to the Peptide and Protein Filter node.
The following figure shows the additional column on the Proteins page.
Further Information
For more information on the Protein Marker Node, see the Protein Annotation node in the Proteome Discoverer Help.