Most of them require identifiers to complete the specification. Spaces between monosaccharides are optional, and unused monosaccharides can be left out or included with zero (0) occurrences. Byonic’s internal tables contain the most likely N- and O-linked glycan compositions, but allow only one glycan per peptide.
Selection macros must contain at least one forward slash in order to distinguish them from other words in the selection language. The user can then specify any number of modification rules via a pull-down menu containing all the modifications listed in , as shown in Figure 3. For convenience, frequently used modifications are listed twice, at the top and again in the complete list. When you type a command that has more than one argument, color color-name, selection-expression in this case, a comma must separate the arguments. The three pull-down menus in each row select modification type, target residues, and fine control.
The various numbers in the peptide list columns are explained in more detail below. Disabling objects eliminates them from the viewer, but disabling named-selections just turns off the pink dots that highlight them in the viewer. Byonic actually outputs the absolute value of the logarithm base 10 of the p-value. Score – Byonic score, the “raw” indicator of PSM correctness. The keyword also enables the user to customize the N-glycosylation search to specific glycan masses, rather than rely on Byonic’s predefined tables.