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Identification of MS-Cleavable and Noncleavable Chemically Cross-Linked Peptides with MetaMorpheus
Journal of Proteome Research ( IF 4.4 ) Pub Date : 2018-06-11 , DOI: 10.1021/acs.jproteome.8b00141
Lei Lu , Robert J. Millikin , Stefan K. Solntsev , Zach Rolfs , Mark Scalf , Michael R. Shortreed , Lloyd M. Smith

Protein chemical cross-linking combined with mass spectrometry has become an important technique for the analysis of protein structure and protein–protein interactions. A variety of cross-linkers are well developed, but reliable, rapid, and user-friendly tools for large-scale analysis of cross-linked proteins are still in need. Here we report MetaMorpheusXL, a new search module within the MetaMorpheus software suite that identifies both MS-cleavable and noncleavable cross-linked peptides in MS data. MetaMorpheusXL identifies MS-cleavable cross-linked peptides with an ion-indexing algorithm, which enables an efficient large database search. The identification does not require the presence of signature fragment ions, an advantage compared with similar programs such as XlinkX. One complication associated with the need for signature ions from cleavable cross-linkers such as DSSO (disuccinimidyl sulfoxide) is the requirement for multiple fragmentation types and energy combinations, which is not necessary for MetaMorpheusXL. The ability to perform proteome-wide analysis is another advantage of MetaMorpheusXL compared with programs such as MeroX and DXMSMS. MetaMorpheusXL is also faster than other currently available MS-cleavable cross-link search software programs. It is imbedded in MetaMorpheus, an open-source and freely available software suite that provides a reliable, fast, user-friendly graphical user interface that is readily accessible to researchers.

中文翻译:

用MetaMorpheus鉴定MS可裂解和不可裂解的化学交联肽

蛋白质化学交联结合质谱法已成为分析蛋白质结构和蛋白质-蛋白质相互作用的一项重要技术。各种各样的交联剂已经得到很好的开发,但是仍然需要用于大规模分析交联蛋白的可靠,快速且用户友好的工具。在这里,我们报告MetaMorpheusXL,这是MetaMorpheus软件包中的一个新搜索模块,可识别MS数据中的MS可裂解和不可裂解的交联肽。MetaMorpheusXL通过离子索引算法识别MS可裂解的交联肽,从而可进行有效的大型数据库搜索。识别不需要签名碎片离子,与类似程序(例如XlinkX)相比,这是一个优势。与需要来自可裂解的交联剂(例如DSSO(二琥珀酰亚胺基亚砜))的特征离子相关的一种复杂情况是需要多种片段化类型和能量组合,而MetaMorpheusXL则不需要。与诸如MeroX和DXMSMS之类的程序相比,MetaMorpheusXL的另一个优势是能够进行蛋白质组分析。MetaMorpheusXL也比其他当前可用的MS可裂解的交叉链接搜索软件程序快。它嵌入MetaMorpheus,MetaMorpheus是一种开放源代码且可免费获得的软件套件,它提供了可靠,快速,用户友好的图形用户界面,研究人员可以轻松访问。对于MetaMorpheusXL而言,这不是必需的。与诸如MeroX和DXMSMS之类的程序相比,MetaMorpheusXL的另一个优势是能够进行蛋白质组分析。MetaMorpheusXL也比其他当前可用的MS可裂解的交叉链接搜索软件程序快。它嵌入MetaMorpheus,MetaMorpheus是一种开放源代码且可免费获得的软件套件,它提供了可靠,快速,用户友好的图形用户界面,研究人员可以轻松访问。对于MetaMorpheusXL而言,这不是必需的。与诸如MeroX和DXMSMS之类的程序相比,MetaMorpheusXL的另一项优势是能够进行蛋白质组分析。MetaMorpheusXL也比其他当前可用的MS可裂解的交叉链接搜索软件程序快。它嵌入MetaMorpheus,MetaMorpheus是一种开放源代码且可免费获得的软件套件,它提供了可靠,快速,用户友好的图形用户界面,研究人员可以轻松访问。
更新日期:2018-06-12
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