You can specify modifications in any order, but the application always applies them in the following order:

  1. Disulfide links:
  2. You can assign disulfide links only to protein sequences assigned the Intact Protein or Unknown category. The application disables the disulfide linking capability for all other categories.
  3. Static modifications:
  4. There are three types of static modifications: Side chain, C-terminal, and N-terminal modifications.
  5. Glycosylations:
  6. The application applies all possible glycosylations of the user-specified type to one or more of the available glycosylation sites on the target sequence.
  7. The "Glycans" appendix lists all of the N-linked glycans included in the default modifications list, the N-linked glycans included in the N-glycan-specific search (sorted by host cell-line type), and the O-linked glycans (peptide mapping analysis only).
  8. NOTE

    The application supports O-linked glycans for peptide mapping analysis only.

  9. NOTE

    The algorithm that detects possible glycosylation sites was designed for use on intact proteins. If it is applied to digested peptides, it might fail to identify motifs that have been truncated by a cleavage.

    To address this issue when using a peptide as a target sequence, append an amino acid to the sequence to complete the motif, and then define and apply a custom modification that subtracts the mass of that amino acid.

  10. Variable modifications:
  11. There are three types of variable modifications: Side chain, C-terminal, and N-terminal modifications.
  12. The application applies all possible combinations between zero and a user-specified maximum number of variable modifications to the target sequence.

When you select glycosylations and variable modifications, the application first searches for matches that include static or disulfide bonds, and then tries to match masses with various glycosylations and variable modification combinations. The combinations of variable modifications are limited to the specified maximum number of modifications. Setting the maximum number of modifications to a high value can greatly increase the number of combinations and the search time. The maximum number of modifications does not include glycosylations.

If the measured mass of a components lies within a user-supplied tolerance of the mass in the associated target sequence, the application displays the matched target sequence in an identification column in the component list results.