Define amino acids for de novo sequencing - BioPharma Finder Software - Peptide Mapping Analysis User Guide - View Peptide Mapping Analysis results - Define amino acids for de novo sequencing - Identify components using de novo sequencing - Process and Review page - BioPharma Finder Software - BioPharma Finder Software

Prerequisites

1. You are performing de novo sequencing for a component in your Peptide Mapping Analysis experiment results. You have loaded experiment results, selected the unidentified component of interest, and are editing the de novo sequencing parameters in the De Novo Sequencing dialog box.

Procedure

1. In the De Novo Sequencing dialog box, select Select Amino Acids at the bottom of the window.
3. The Select Amino Acids dialog box opens, displaying a list of the default modified amino acids (left) and a list of the 20 natural amino acids (right).
4. See the list of modified amino acids in Predict MS/MS spectra using the kinetic model and the natural amino acids in Amino acid letter codes.
5. The de novo search uses all of the amino acids in the list on the right.
2. To add an amino acid to the list on the right, select a name in the list on the left and select Add.
3. The selected amino acid appears in the list on the right for inclusion in the de novo sequencing.
3. To exclude an amino acid from the sequencing, select a name in the list on the right and select Remove.
4. The selected amino acid disappears from the list on the right and is no longer included in the de novo sequencing.
5. When you select an item from these lists, the Code box displays the one-letter amino acid code that the application uses for the residue for de novo sequencing
6. The Residue Monoisotopic Mass box displays the monoisotopic mass of that item (if available).
7. If these fields are blank, enter the code and mass values in the corresponding fields.
4. Select OK to apply your changes.