Download FASTA files to Proteome Discoverer - Proteome Discoverer Software - Download FASTA files to Proteome Discoverer - Proteome Discoverer Software - Proteome Discoverer Software

You must add a FASTA file to the Proteome Discoverer application before you can perform a search with the Sequest HT node. (This procedure also applies to some third-party nodes.) You can download FASTA files from two sources:

• You can download a controlled protein database directly from the Proteome Discoverer application Annotation Server and add it to a FASTA file. These controlled databases offer you access to standard protein information.
• The Annotation Server database provides extensive information about proteins, peptides, and genes. In addition, the Annotation Server gives you the ability to select proteins of a specified taxonomy to download and use as a FASTA file.
• You can add a FASTA file that you download from other sources onto your hard drive and then register it.

If you are using the Mascot search engine, ask your administrator to download FASTA files to the Mascot server. The FASTA file must be on the server that is running Mascot before you can perform a search with the Mascot search engine.