For peptide mapping analysis and intact mass analysis, you can assign the following modifications to a protein sequence:

  1. Disulfide links, which form bonds between cysteine residues in a heavy chain and light chain or within the same chain.
  2. Static modifications, which are side-chain or terminal modifications that you can apply to a single site or all sites for a specified residue or terminal.
  3. Glycosylations, which refers to the attachment of sugar moieties at sites on the target sequence to form glycans.
  4. Variable modifications, which are possible side-chain or terminal modifications whose specific sites and number of occurrences might not be known.

For example, you can assign particular post-translations modifications (PTMs), such as phosphorylation or modifications arising from sample handling or digestion, such as over-alkylation, oxidation, or deamidation. You can specify modifications in any order, but the application always applies them in the above order.

For top down analysis, you select a sublist of variable modifications to generate a list of proteoforms for searching to identify fragment ions. You can edit the sublist of default modifications for quick loading before assigning them to the sequences. You can also create custom modifications before assigning them to the sequences.

Upon installation, the BioPharma Finder application provides a default list of variable modifications, including N-glycans, as side chain modifications. You can access this list from the Protein Sequence Editor and set a sublist for quick loading into a protein sequence. You can also select which modifications will be visible in the modification editing panes.

You can also create custom modifications before assigning them to the sequences.