Byonic and the Byos Peptide workflows (PTM, SVA, SS, HCP, etc.) can support a limited number of non-standard amino acid residues by redefining one-letter amino acid abbreviations using fixed modifications. Byos (Byonic Node) accepts B, Z, U, O, J, and X in FASTA protein databases. The non-standard amino acid masses are:
| Abbreviation | Mass | Comments |
| B | 114.042927 | Same as N |
| Z | 128.058578 | Same as Q |
| U | 150.95363 | Selenocysteine |
| O | 237.147730 | Pyrrolysine |
| J | 100.0 | |
| X | 110.05 | Close to averagine |
Typically, users will create a Byos workflow with a fixed modification setting on B, Z, U, O, J, or X to set the desired non-standard amino acid residue mass. The same abbreviation letter is used to include the non-standard amino acid residue in the FASTA database protein sequence(s).
Example:
By placing a fixed modification of +13.04768 on J, the user can make J in a FASTA database have mass 113.04768, correct for hydroxyproline. This can be entered in the Modifications custom text box as Hydroxyproline / +13.04768 @ J | fixed
J is then used to represent hydroxyproline in the FASTA database protein sequence(s).
NOTE: Byos uses amino acid sequence to predict relative peak intensity of MS/MS fragmentation spectra. A fixed modification on J will not give the same score as a +15.9949 variable modification on P.