You can enter a protein sequence manually or import a FASTA file directly into the Theoretical Protein/Peptide Manager.
Procedure
- On the BioPharma Finder Home page, in the Experiment Types pane, select the Sequence Manager link.
- The Sequence Manager opens.
- At the top of the window, select the Theoretical Protein/Peptide Manager tab.
- The Theoretical Protein/Peptide Manager opens.
Figure Theoretical Protein/Peptide Manager page - To manually create a protein sequence, type or paste the sequence in the Enter Peptide or Protein Sequence box, using the following guidelines:
- Begin each chain in the protein sequence on a separate line.
- Above each chain, type a greater-than sign (>) followed by the chain name to distinguish each chain.
- Use the designated single-letter amino acid codes.
TIP
You can copy and paste the sequence chain from a FASTA file using Notepad or another text editing tool.
- To import a protein sequence from a FASTA file, select Import Protein Fasta on the command bar, locate and select the FASTA file (.fasta) you want to import, and then select Open.
NOTE
FASTA files must not exceed 1 MB for import.
- The editable Enter Peptide or Protein Sequence area 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.
- If the entered chain contains invalid amino acids or an invalid format, an error message appears.
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.
- (Optional) Select the Perform Digestion checkbox above the Enter Peptide or Protein Sequence area if you want the application to perform a theoretical digestion of the sequence using user-specified digestion parameters.