Bern Marshall, Kil Yong J, Becker Christopher
Protein Metrics Inc, San Carlos, California.
Palo Alto Research Center, Palo Alto, California.
Curr Protoc Bioinformatics. 2012 Dec;Chapter 13:13.20.1-13.20.14. doi: 10.1002/0471250953.bi1320s40.
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.
Byonic是一款用于通过串联质谱鉴定肽和蛋白质的软件包名称。这款软件直到最近才开始商业化，与之前的搜索软件如SEQUEST和Mascot相比，它提供了范围更广的搜索可能性。Byonic允许用户定义基本上数量不受限的可变修饰类型。Byonic还允许用户对每种修饰类型的出现次数设置单独的限制，这样在搜索时，对于每个肽段，可能仅考虑一两种偶然修饰，如氧化和脱酰胺，同时允许三四种生物修饰，如磷酸化，因为这些修饰往往聚集在一起。因此，Byonic能够同时搜索数十种甚至数百种修饰类型，而不会出现过大的组合爆炸问题。Byonic的通配符搜索允许用户在搜索已知修饰的同时搜索意外的甚至未知的修饰。最后，Byonic的糖肽搜索允许用户在无需预先了解聚糖质量或糖基化位点的情况下鉴定糖肽。
