Byonic annotates key elements of the spectrum, including the most commonly observed ion series for the type of fragmentation (a, b, y, c, z, b++, y++, etc.), common neutral losses from the precursor (e.g., M–98 for loss of phosphoric acid), immonium ions for certain amino acids, and oxonium ions for glycans as described here - MS2 Spectrum Annotations.
Byonic is also capable of annotating internal fragments, but this feature must be enabled by the user. Also note, internal fragments do not influence the scoring metrics for the peptide.
As an example, in the spectrum of TSCVQQPPCFPLKIPPNDPR, an abundant yet unannotated signal can be seen at m/z 1376.
Enabling internal fragment annotations identify the i(7-18) fragment as the 7th - 18th amino acids derived from the precursor ion shown here -TSCVQQPPCFPLKIPPNDPR.