For any peptides workdlows like PTM, Disulfides, SVA or HDX worfklows, you can set Digestion searches under the Byonic node.
Figure 1 : Byonic settings from PTM workflow (Processing nodes tab)
The digestion section allows the user to set the residues recognized by the digestion enzyme as shown. For example, in figure 2 below, the enzyme is trypsin, so the user entered RK for arginine and lysine and chose C-terminal for the cleavage side.
Figure 2 : Byonic MSMS digestion search option
• Cleavage site(s) identifies specific cleavage sites. When the Cleavage site(s) box is blank, specific cleavage sites are limited to protein termini.
• Cleavage side designates the C-, N- or both termini for the cleavage side. For example, RK; DE for Cleavage site(s) along with C-terminal; N-terminal for Cleavage side would be appropriate for digestion by a combination of trypsin and Asp-N.
Digestion specificity balances search specificity and performance. For example, the “Fully specific (fastest)” search selected in the figure below, requires that both the N- and C-terminal cleavages be C-terminal to R or K. Nonspecific cleavage at either or both endpoints is supported.
A nonspecific search will search all peptides but favors specified digestions. In Figure 2, Cleavage Site(s) is set to RK which searches all peptides but favors tryptic peptides. For a true no-enzyme search, leave the Cleavage Site(s) box blank.
• Missed cleavages limits the maximum number of missed cleavages. In Figure 2, a setting of two missed cleavages limits internal R’s and K’s not followed by P to 2. The default value for Missed cleavages is -1, which allows any number of internal R’s and K’s.
NOTE: "Digestion" column in the Samples tab does not affect MSMS search in any way. This column is only used to populate columns beginning with "Digest ..." in Byologic. These columns can then be used to do filtering. The dropdown does not change how Byonic searches the data or how Byologic combines results.
Then after processing the data you should have from the project pane the possibility to check the digestion column (digestion type),
and from the Peptides tables (Byologic) you will see populate those columns:
- Digest Name,
- Digest Start Peptide
- Digest End peptide
- Digest N-term ragged
- Digest C-term ragged
- Digest misscleveage
NOTE: So those fields should be able to be display as well within the report by drag & dropping.