Due to the abundance of phosphorylation sites in proteins, database search engines like Byonic face the challenge of handling an exponentially growing number of candidates during searches.
To address this issue, Byonic offers an advanced command to restrict the number of potential candidates assigned to an MS/MS spectrum. This command is also utilized for O-glycosylation, which encounters similar challenges to phosphorylation (see article).
Refer to the following section titled "Applying the 'isobar_score_filter' Advanced Command" in the referenced article to learn how this command, 'isobar_score_filter', effectively reduces the pool of potential candidates.