You can download a FASTA file to a location other than the default URL that is shown in the Annotation Server configuration, see Edit the workflow Annotation server settings.

Procedure

  1. Do one of the following:
  2. From the application menu bar, select Administration > Maintain FASTA Files.
  3. Select Maintain FASTA Files .
  4. The Administration page opens with the FASTA Files view.
  5. Select Check for Updates.
  6. The Proteome Discoverer application updates the available databases in the job queue.
  7. To return to the FASTA Files view, select FASTA Files under Content Management in the Configuration view.
  8. The Download button on the FASTA Files view becomes available.
  9. Select Download.
  10. In the Taxonomy ID box, do the following:
  11. Enter the taxonomy identification number of the appropriate organism-specific sequence database in the Annotation Server.
  12. The taxonomy identification number is a unique number identifying a biological species, a particular subspecies, or a bacterial strain. You can find the organism’s taxonomy identification number on the UniProt™ website (http://www.uniprot.org/taxonomy) or at the NCBI (National Center for Biotechnology Information) website (https://www.ncbi.nlm.nih.gov/).
    - In the box to the right of the Taxonomy menu on the UniProt website, enter the name of the organism, for example, Baker yeast.
    - Select Search .
    - (Optional) Under the Taxon heading, select the name of the subspecies, for example, Saccharomyces cerevisiae.
  13. The taxonomy identifier number appears under the Taxon Identifier.
  15. (Optional) To include data for a subspecies or subcategory of the selected species in the downloaded database, select the Include All Subcategories checkbox in the Download from the Annotation Server dialog box.
  16. From the Database dropdown list in the Download from the Annotation Server dialog box, select the name of the original source database to download the proteins from.
  17. The default database is SwissProt.
  18. Completed Download from the Annotation Server dialog box
    Completed Download from the Annotation Server dialog box
  19. Select Import.
  20. The application displays the download as a job running in the job queue.
  21. When the job queue displays “Completed” in the Execution State column, select FASTA Files under Content Management in the Configuration view to return to the FASTA Files view.
  22. The downloaded database might take several minutes to appear and opens in the FASTA Files view.
  23. If you do not see the downloaded database after a few minutes, select Refresh.
    The following figure shows the Saccharomyces cerevisiae (4932) species database that was downloaded from the SwissProt database.
  25. If you select the SwissProt database, all proteins of the specified organism that are present in the SwissProt database are downloaded. The FASTA file is automatically given the scientific name of the organism and the database source, with the taxonomy identification in parentheses, for example, Saccharomyces cerevisiae (SwissProt TaxID =4932). The Last Modified column indicates the date that the database was last updated on the server.
  27. If no databases appear in the list, follow the procedure in Update a FASTA file from the Annotation Server.