1. On the Windows desktop, double-click the Proteome Discoverer application.
  2. On the Start Page, select Administration > Maintain FASTA files.
  3. In the FASTA Files View, if you have not downloaded FASTA files to the application before, select Check For Updates.
  4. The Job Queue opens and runs a process that downloads the annotation database from Annotation Server. Wait for this step to complete before proceeding.
  5. To return to the FASTA Files view, select FASTA Files under Content Management.
  6. Select Download.
  7. In the Download from Annotation Server dialog box, do the following.
  8. For Taxonomy ID, enter 4932.
  9. Select the Include all subcategories checkbox.
  10. For Database, select sp_incl_isoforms.
  11. The sp refers to Swiss-Prot.
  12. Select Import.
  13. The Run Queue downloads the yeast protein database. Depending on your network speed, this process might take a few minutes to complete.
  14. Continue with Configure the quantification method.