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. 2012 Dec:Chapter 13:13.20.1-13.20.14.
doi: 10.1002/0471250953.bi1320s40.

Byonic: advanced peptide and protein identification software

Marshall Bern  1   2 , Yong J Kil  1 , Christopher Becker  1
Affiliations

Byonic: advanced peptide and protein identification software

Marshall Bern et al. Curr Protoc Bioinformatics. 2012 Dec.

Abstract

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.

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Figures

Figure 1
Figure 1
The input GUI with the Digestion and Machine Parameters tab open.
Figure 2
Figure 2
GUI view with the Modifications tab open.
Figure 3
Figure 3
GUI view with the Advanced tab open.
Figure 4
Figure 4
Byonic output (Summary worksheet) as viewed in Excel.
Figure 5
Figure 5
Byonic output as viewed in Byonic’s interactive Viewer.
See this image and copyright information in PMC

References

    1. Bern M, Cai Y, Goldberg D. Lookup peaks: a hybrid of de novo sequencing and database search for protein identification by tandem mass spectreometry. Anal Chem. 2007;79:1393–1400. - PubMed
    1. Bern M, Finney G, Hoopmann MR, Merrihew G, Toth MJ, MacCoss MJ. Deconvolution of mixture spectra from ion-trap data-independent-acquisition tandem mass spectrometry. Anal Chem. 2009;82:833–841. - PMC - PubMed
    1. Bern M, Saladino J, Sharp JS. Conversion of methionine into homocysteic acid in heavily oxidized proteomics samples. Rapid Commun Mass Spectrom. 2010;24:768–772. - PMC - PubMed
    1. Bhatia S, Kil YJ, Ueberheide B, Chait BT, Tayo L, Cruz L, Lu B, Yates JR, Bern M. Constrained de novo sequencing of cone snail toxins. J Proteome Res. 2012 to appear. - PMC - PubMed
    1. Charvatova O, Foley BL, Bern MW, Sharp JS, Orlando R, Woods RJ. Quantifying protein interface footprinting by hydroxyl radical oxidation and molecular dynamics simulation: application to galectin-1. J Am Soc Mass Spectrom. 2008;19:1692–1705. - PMC - PubMed

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