Byonic: Advanced Peptide and Protein Identification Software

Marshall Bern1, Yong J. Kil2, Christopher Becker2

1 Palo Alto Research Center, Palo Alto, California, 2 Protein Metrics Inc., San Carlos, California
Publication Name:  Current Protocols in Bioinformatics
Unit Number:  Unit 13.20
DOI:  10.1002/0471250953.bi1320s40
Online Posting Date:  December, 2012
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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.

Keywords: proteomics; mass spectrometry; post‐translational modifications; glycosylation; glycopeptide; phosphopeptide

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Table of Contents

  • Introduction
  • Basic Protocol 1: Setting Up a Byonic Search
  • Basic Protocol 2: Viewing the Search Results in Excel
  • Basic Protocol 3: Viewing the Search Results in the Interactive Viewer
  • Support Protocol 1: Installing Byonic
  • Guidelines for Understanding Results
  • Commentary
  • Literature Cited
  • Figures
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Literature Cited

Literature Cited
   Bern, M., Cai, Y., and Goldberg, D. 2007. Lookup peaks: A hybrid of de novo sequencing and database search for protein identification by tandem mass spectrometry. Anal. Chem. 79:1393‐1400.
   Bern, M., Finney, G., Hoopmann, M.R., Merrihew, G., Toth, M.J., and MacCoss, M.J. 2009. Deconvolution of mixture spectra from ion‐trap data‐independent‐acquisition tandem mass spectrometry. Anal. Chem. 82:833‐841.
   Bern, M., Saladino, J., and Sharp, J.S. 2010. Conversion of methionine into homocysteic acid in heavily oxidized proteomics samples. Rapid Commun. Mass Spectrom. 24:768‐772.
   Bhatia, S., Kil, Y.J., Ueberheide, B., Chait, B.T., Tayo, L., Cruz, L., Lu, B., Yates, J.R., and Bern, M. 2012. Constrained de novo sequencing of cone snail toxins. J. Proteome Res. 11:4191‐4200.
   Charvatova, O., Foley, B.L., Bern, M.W., Sharp, J.S., Orlando, R., and Woods, R.J. 2008. Quantifying protein interface footprinting by hydroxyl radical oxidation and molecular dynamics simulation: Application to galectin‐1. J. Am. Soc. Mass Spectrom. 19:1692‐1705.
   Craig, R. and Beavis, R.C. 2004. TANDEM: Matching proteins with tandem mass spectra. Bioinformatics 20:1466‐1467.
   Eng, J., McCormack, A.L., and Yates, J.R. 1994. An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database. J. Am. Soc. Mass Spectrom. 5:976‐989.
   Kil, Y.J., Becker, C., Sandoval, W., Goldberg, D., and Bern, M. 2011. Preview: A program for surveying shotgun proteomics tandem mass spectrometry data. Anal. Chem. 83:5259‐5267.
   Perkins, D.N., Pappin, D.J., Creasy, D.M., and Cottrell, J.S. 1999. Probability‐based protein identification by searching sequence databases using mass spectrometry data. Electrophoresis 20:3551‐3567.
   Zhu, Y., Guo, T., Park, J.E., Li, X., Meng, W., Datta, A., Bern, M., Lim, S.K., and Sze, S.K. 2009. Elucidating in vivo structural dynamics in integral membrane protein by hydroxyl radical footprinting. Mol. Cell Proteomics 8:1999‐2010.
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