Import a FASTA file containing a protein sequence - BioPharma Finder Software - Intact Mass Analysis User Guide - Create protein sequences - Import a FASTA file containing a protein sequence - BioPharma Finder Software - BioPharma Finder Software

Procedure

1. On the BioPharma Finder Home page, in the Experiment Types pane, select the Sequence Manager link.
2. The Sequence Manager opens.
2. On the right side of the Sequence Manager, select the New Protein button.
3. The Protein Sequence Editor opens.
3. In the Protein Sequence Editor, select Import Fasta File on the command bar.
4. The Open dialog box opens.
4. Locate and select the FASTA file (.fasta) you want to import and select Open.

5. NOTE

   FASTA files must not exceed 1 MB for import.

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

8. TIP

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

9. Additionally, the read-only information fields (Monoisotopic Mass, Average Mass, and Formula) in the Protein Sequence Information > Target Protein pane update to reflect the properties of the entire protein.
10. In the Protein Sequence Information > Chain pane, you can view the Monoisotopic Mass and Average Mass properties for an individual chain by selecting the chain number from the dropdown menu.
5. On the left side of the Protein Sequence Editor, in the Protein Sequence Information pane > Target Protein area, enter the following information:
1. Name: Type the name of the protein sequence.
2. Description: (Optional) Type a description for the protein sequence.
3. Category: Select the category for the protein sequence from the dropdown menu.
6. Save the protein sequence.
7. The application adds the saved sequence to the Sequence Manager table.

8. 

9. 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.

10. 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.