UNIT 13.20 Byonic: Advanced Peptide and Protein Identification Software

  1. Marshall Bern1,2,
  2. Yong J. Kil1,
  3. Christopher Becker1

Published Online: 1 DEC 2012

DOI: 10.1002/0471250953.bi1320s40

Current Protocols in Bioinformatics

Current Protocols in Bioinformatics

How to Cite

Bern, M., Kil, Y. J. and Becker, C. 2012. Byonic: Advanced Peptide and Protein Identification Software. Current Protocols in Bioinformatics. 40:13.20:13.20.1–13.20.14.

Author Information

  1. 1

    Protein Metrics Inc., San Carlos, California

  2. 2

    Palo Alto Research Center, Palo Alto, California

Publication History

  1. Published Online: 1 DEC 2012


Byonic is the name of a software package for peptide and protein identification by tandem mass spectrometry. This software, which has only recently become commercially available, facilitates a much wider range of search possibilities than previous search software such as SEQUEST and Mascot. Byonic allows the user to define an essentially unlimited number of variable modification types. Byonic also allows the user to set a separate limit on the number of occurrences of each modification type, so that a search may consider only one or two chance modifications such as oxidations and deamidations per peptide, yet allow three or four biological modifications such as phosphorylations, which tend to cluster together. Hence, Byonic can search for tens or even hundreds 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 Glycopeptide Search allows the user to identify glycopeptides without prior knowledge of glycan masses or glycosylation sites. Curr. Protoc. Bioinform. 40:13.20.1-13.20.14. © 2012 by John Wiley & Sons, Inc.


  • proteomics;
  • mass spectrometry;
  • post-translational modifications;
  • glycosylation;
  • glycopeptide;
  • phosphopeptide