1. Open the Sequence Manager by selecting Sequence Manager on the BioPharma Finder home page.
  2. Select New Protein to the right of the sequence table.
  3. The Protein Sequence Editor opens with the Manual Input Protein Sequence pane expanded.
  4. image/svg+xml Command bar
    Protein Sequence Editor
  5. NOTE

    If the resolution or text size of you computer screen is not set properly, you might not be able to see some of the features on the Protein Sequence Editor.

    To correct this problem, use the recommended screen resolution of 1920×1080 pixels and consider changing the text size.

  6. To import a FASTA file, select Import FASTA File in the command bar and then browse to the folder containing the FASTA file.
  7. The dialog box displays all of the FASTA files in the selected folder.
  8. The FASTA file must have the ".fasta" extension for the application to be able to find the file.
  9. Select a FASTA file to import, and then select Open.
  10. You can import FASTA files of 1 MB or less.
  11. If a FASTA file contains invalid amino acids or an invalid format, an error message appears. If an error message appears during the import operation, open the FASTA file in a text editor such as Notepad and verify the format of each chain.
  12. The application displays the protein sequence information from the FASTA file in the Protein Sequence Map pane of the Protein Sequence Editor, with cysteine residues highlighted in yellow for easy visibility.
  13. In addition, the Protein Sequence Information pane displays both the monoisotopic and average masses of the sequence in the Target Protein area and the monoisotopic and average masses of the first chain in the Chain area. To view the masses of a different chain, select the chain number from the Chain list.
  14. Imported sequence in the Protein Sequence Map pane
    Imported sequence in the Protein Sequence Map pane
  15. NOTE

    For intact mass analysis experiments only: If your unreduced intact protein is a homodimer, you must include two copies of each chain in the Protein Sequence Map and indicate any disulfide bonds linking the chains.

    For example, if your sample is a monoclonal antibody, include two copies of both the light chain and the heavy chain. Then, in the Protein Sequence Map pane, manually add disulfide bonds between the applicable cysteine residues, using the procedure in Manage disulfide links. The target protein monoisotopic and average masses update as you link the chains.

    Manually adding disulfide bonds in a protein sequence is required only for intact mass analysis experiments. This feature is disabled for peptide mapping analysis experiments.

  16. NOTE

    Furthermore, for intact mass analysis of peptides (or protein subunits), you must create an individual sequence for each subunit for the application to match the masses correctly.

    For example, if your sample is a monoclonal antibody that you have cleaved into its light chain, Fc, and Fd subunits, you must create individual sequences for each of the three subunits. When you create the intact mass analysis experiment, you can select all three individual sequence files and add them to the experiment.

  17. In the Target Protein area, type the name of the sequence and select its category from the Category drop-down list.
  18. See Select the experiment category for a sequence.
  19. Save the new sequence.
  20. See Save a protein or peptide sequence.
  21. The application adds the saved sequence to the table on the Sequence Manager page.