For performance evaluation, the output of a de novo sequencing algorithm is typically represented in one of two forms: a ranked list of predicted peptides or a ranked list of amino acids. Each entry in this list can then be marked as "correct" or "incorrect," based on a comparison to a ground truth annotation. At the peptide level, this annotation is straightforward: the predicted peptide sequence must match the ground truth peptide exactly, perhaps allowing for isomeric (Leu ↔ Ile) or isobaric (deamidated Asn ↔ Asp) substitutions. At the amino acid level, the annotation is somewhat more complex because we must also consider the masses of the preceding and following amino acids. In practice, the most common procedure is to follow the procedure from the DeepNovo paper , requiring that a predicted amino acid have either a prefix or suffix that differs by no more than 0.5 Da in mass from the corresponding amino acid sequence in the ground truth peptide.