Byonic: Advanced Peptide and Protein Identification Software

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Abstract
Table of Contents
Figures
Literature Cited

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. 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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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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Materials

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Figures

Figure 13.20.1 The input GUI with the Digestion and Machine Parameters tab open.

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Figure 13.20.2 GUI view with the Modifications tab open.

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Figure 13.20.3 GUI view with the Advanced tab open.

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Figure 13.20.4 Byonic output (Summary worksheet) as viewed in Excel.

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Figure 13.20.5 Byonic output as viewed in Byonic's interactive Viewer.

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Videos

Literature Cited

Literature Cited
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