Institute for Systems Biology, Seattle, Washington, 98109, USA.
J Am Soc Mass Spectrom. 2016 Nov;27(11):1728-1734. doi: 10.1007/s13361-016-1435-8. Epub 2016 Jul 28.
Protein-protein interactions are an important element in the understanding of protein function, and chemical cross-linking shotgun mass spectrometry is rapidly becoming a routine approach to identify these specific interfaces and topographical interactions. Protein cross-link data analysis is aided by dozens of algorithm choices, but hindered by a lack of a common format for representing results. Consequently, interoperability between algorithms and pipelines utilizing chemical cross-linking remains a challenge. pepXML is an open, widely-used format for representing spectral search algorithm results that has facilitated information exchange and pipeline development for typical shotgun mass spectrometry analyses. We describe an extension of this format to incorporate cross-linking spectral search results. We demonstrate application of the extension by representing results of multiple cross-linking search algorithms. In addition, we demonstrate adapting existing pepXML-supporting software pipelines to analyze protein cross-linking results formatted in pepXML. Graphical Abstract ᅟ.
蛋白质-蛋白质相互作用是理解蛋白质功能的一个重要因素，而化学交联shotgun 质谱分析正在迅速成为一种常规方法，用于鉴定这些特定的界面和拓扑相互作用。蛋白质交联数据分析得益于数十种算法选择，但由于缺乏表示结果的通用格式而受到阻碍。因此，利用化学交联的算法和管道之间的互操作性仍然是一个挑战。pepXML 是一种用于表示光谱搜索算法结果的开放的、广泛使用的格式，它促进了典型 shotgun 质谱分析的信息交换和管道开发。我们描述了这种格式的扩展，以纳入交联光谱搜索结果。我们通过表示多个交联搜索算法的结果来演示这种扩展的应用。此外，我们还展示了如何调整现有的支持 pepXML 的软件管道来分析 pepXML 格式的蛋白质交联结果。
