Is Byonic a search engine like Mascot, SEQUEST, etc.?
Yes, Byonic can do anything Mascot, SEQUEST, etc. can do, and more besides.
Why is Byonic better?
Byonic extends the state-of-the-art in two ways: its scorer is more accurate and allows a much wider range of search possibilities. The “scorer” is the algorithm that matches peptides to mass spectra by comparing the predicted fragmentation of the peptide with the observed peaks in the spectra, in consideration of the precursor mass accuracy and precision. Byonic incorporates a substantial amount of chemical knowledge into its fragmentation prediction, such as reduced CID fragmentation on the C-terminal side of proline and strong neutral losses from certain modifications. This expert system knowledge means that Byonic is more sensitive (more true positives) and specific (fewer false positives) than other search engines for exactly the same search as objectively measured using a decoy database strategy. Moreover, Byonic enables a wider variety of searches than the other search engines. With Modification Fine Control™, Byonic can search for 10s or even 100s of modification types simultaneously without a prohibitively large combinatorial explosion. Byonic’s Wildcard Search™ allows the user to search for unanticipated or even unknown modifications alongside known modifications. Finally, Byonic’s glycosylation search allows the user to identify glycopeptides without prior knowledge of glycan masses or glycosylation sites.
How much better is Byonic?
The performance advantage depends upon the data, the search, and the skill of the user. On exactly the same search, Byonic’s advantage ranges from about 20% to 300% more spectra identified at the same False Discovery Rate (FDR), with the advantage increasing with the difficulty of the search. Easy searches are ones with small search spaces (such as due to a small protein database or a small number of modification types) and difficult searches are ones with large search spaces (such as due to nonspecific digestion, a large number of modification types, and low precursor mass accuracy).
What’s the difference between Byonic and Preview?
Preview offers an initial peek preview of your data to help you set the parameters for a much more sensitive Byonic search. Preview advises the user on mass accuracy, digestion specificity, and the prevalence of ~ 60 common modifications. Preview optionally recalibrates the m/z measurements to improve sensitivity/specificity for subsequent searches (using any search engine).