Procedure

  1. On the BioPharma Finder Home page, in the Experiment Types pane, select the Sequence Manager link.
  2. The Sequence Manager opens.
  3. On the right side of the Sequence Manager, select the New Protein button.
  4. The Protein Sequence Editor opens.
  5. On the left side of the Protein Sequence Editor, in the Protein Sequence Information pane > Target Protein area, enter the following information:
  6. Name: Type the name of the protein sequence.
  7. Description: (Optional) Type a description for the protein sequence.
  8. Category: Select the category for the protein sequence from the dropdown menu.
  9. On the right side of the Protein Sequence Editor, expand the Manual Input Protein Sequence pane and then add one chain in the protein sequence at a time as follows:
  10. Type the name of the chain in the Chain Name box.
  11. Type or paste the new chain sequence into the editable box.
  12. Select the Apply button.
  13. Manual Input Protein Sequence pane
    Figure Manual Input Protein Sequence pane

  14. TIP

    Chain names can contain up to 250 alphanumeric characters.

  15. TIP

    You can copy and paste the sequence chain from a FASTA file using Notepad or another text editing tool.

  16. NOTE

    A FASTA file might contain comment lines that begin with a greater-than sign (>), similar to the chain name line.

    When you copy a chain sequence, do not include these additional comment lines. The application interprets comment lines as sequence building blocks.

  17. Protein sequence chains with comment lines copied from a FASTA file
    Figure Protein sequence chains with comment lines copied from a FASTA file

  18. NOTE

    For Top Down Analysis, a protein sequence can only have one chain.

  19. If the entered chain contains invalid amino acids or an invalid format, an error message appears.
  20. The Protein Sequence Map on the left side of the page updates and displays the added chain.
  21. The name of the chain appears above the chain sequence, indicated by a greater-than sign (>) to distinguish each chain.

  22. TIP

    In the Protein Sequence Map, cysteine (C) residues are traced in yellow for easy visibility.

  23. Additionally, the read-only information fields (Monoisotopic Mass, Average Mass, and Formula) in the Protein Sequence Information pane > Target Protein area update to reflect the properties of the entire protein.
  24. In the Protein Sequence Information pane > Chain area, you can view the Monoisotopic Mass and Average Mass properties for an individual chain by selecting the chain number from the dropdown menu.
  25. Repeat the previous step to add additional chains as needed.
  26. Save the protein sequence.
  27. The application adds the saved sequence to the Sequence Manager table.

IMPORTANT

For Intact Mass Analysis, 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.

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.

NOTE

For Intact Mass Analysis, for experiments involving cleaved protein subunits (light chain, heavy chain, Fc subunits, etc.), each subunit should be treated as an individual sequence, rather than a chain within the entire protein.

You must create an individual sequence for each subunit in the protein. Then, when you create an Intact Mass Analysis experiment, you can include all of the individual subunit sequences in the analysis.