Automated Assignment of MS/MS Cleavable Cross-Links in Protein 3D-Structure Analysis
Automated Assignment of MS/MS Cleavable Cross-Links in Protein 3D-Structure Analysis
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DOI：
10.1007/s13361-014-1001-1
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发表时间：
2015-01-01
影响因子：
3.2
通讯作者：
Sinz, Andrea
中科院分区：
文献类型：
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作者：
Goetze, Michael;Pettelkau, Jens;Sinz, Andrea
CID-MS/MS可切割交联剂对于交联产物的自动分析具有巨大的潜力，这对于进行结构蛋白质组学研究至关重要。所创建的特征片段离子模式可以很容易地用于交联产物的自动分配和识别。迄今为止，只有少数软件解决方案可以利用这些特性，但没有一个允许对可切割交联产品进行自动分析。MeroX软件填补了这一空白，并结合MS/MS可切割交联剂提供了蛋白质3d结构分析的强大工具。我们发现MeroX可以自动筛选特征片段离子，考虑到静态和可变肽修饰，并有效地对不同类型的交联进行评分。交叉链接的正确分配和错误发现率的计算不需要人工输入。MeroX的自解释图形用户界面为自动交叉链接搜索平台提供了方便的访问，该平台与常用的数据文件格式兼容，可以分析来自不同仪器的数据。MS/MS可切割交联剂与专用数据分析软件工具的组合为蛋白质的3d结构分析提供了自动化工作流程。MeroX可从www.StavroX.com获得。
CID-MS/MS cleavable cross-linkers hold an enormous potential for an automated analysis of cross-linked products, which is essential for conducting structural proteomics studies. The created characteristic fragment ion patterns can easily be used for an automated assignment and discrimination of cross-linked products. To date, there are only a few software solutions available that make use of these properties, but none allows for an automated analysis of cleavable cross-linked products. The MeroX software fills this gap and presents a powerful tool for protein 3D-structure analysis in combination with MS/MS cleavable cross-linkers. We show that MeroX allows an automatic screening of characteristic fragment ions, considering static and variable peptide modifications, and effectively scores different types of cross-links. No manual input is required for a correct assignment of cross-links and false discovery rates are calculated. The self-explanatory graphical user interface of MeroX provides easy access for an automated cross-link search platform that is compatible with commonly used data file formats, enabling analysis of data originating from different instruments. The combination of an MS/MS cleavable cross-linker with a dedicated software tool for data analysis provides an automated workflow for 3D-structure analysis of proteins. MeroX is available at www.StavroX.com.