Improved Analysis of Cross-Linking Mass Spectrometry Data with Kojak 2.0, Advanced by Integration into the Trans-Proteomic Pipeline
Improved Analysis of Cross-Linking Mass Spectrometry Data with Kojak 2.0, Advanced by Integration into the Trans-Proteomic Pipeline
复制标题
通过集成到跨蛋白质组管道中，利用 Kojak 2.0 改进了交联质谱数据的分析
DOI：
10.1021/acs.jproteome.2c00670
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发表时间：
2023
影响因子：
4.4
通讯作者：
Davis, Trisha N.
中科院分区：
文献类型：
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作者：
Hoopmann, Michael R.;Shteynberg, David D.;Zelter, Alex;Riffle, Michael;Lyon, Andrew S.;Agard, David A.;Luan, Qing;Nolen, Brad J.;MacCoss, Michael J.;Davis, Trisha N.
化学交联蛋白质的碎片化离子光谱分析是蛋白质组学研究中用于确定蛋白质相互作用、空间取向和结构的既定技术。在这里，我们提出了Kojak版本2.0，主要更新的原始Kojak算法，这是开发来识别交联肽的碎片离子光谱使用数据库搜索方法。本文介绍的Kojak 2.0的最新功能包括一个大大改进的算法，更新了评分指标，支持可裂解的交联剂，以及识别15 N标记的同源多聚体之间的交联。Kojak 2.0现在已集成到Trans-Proteomic Pipeline中，可以访问该套件中的数十种其他工具。特别是，用于验证交联的PeptideProphet和iProphet工具提高了在用户定义的阈值下正确识别交联的灵敏度和准确性。这些新功能提高了算法的通用性，使其能够在更广泛的实验设计和分析管道中使用。Kojak 2.0仍然是开源和多平台的。
Fragmentation ion spectral analysis of chemically cross-linked proteins is an established technology in the proteomics research repertoire for determining protein interactions, spatial orientation, and structure. Here we present Kojak version 2.0, a major update to the original Kojak algorithm, which was developed to identify cross-linked peptides from fragment ion spectra using a database search approach. A substantially improved algorithm with updated scoring metrics, support for cleavable cross-linkers, and identification of cross-links between15N-labeled homomultimers are among the newest features of Kojak 2.0 presented here. Kojak 2.0 is now integrated into the Trans-Proteomic Pipeline, enabling access to dozens of additional tools within that suite. In particular, the PeptideProphet and iProphet tools for validation of cross-links improve the sensitivity and accuracy of correct cross-link identifications at user-defined thresholds. These new features improve the versatility of the algorithm, enabling its use in a wider range of experimental designs and analysis pipelines. Kojak 2.0 remains open-source and multiplatform.