The effectiveness of filtering glycopeptide peak list files for Y ions.,Molecular Omics

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The effectiveness of filtering glycopeptide peak list files for Y ions.
Molecular Omics ( IF 3.0 ) Pub Date : 2020-02-17 , DOI: 10.1039/c9mo00178f
Robert J Chalkley ₁ , Katalin F Medzihradszky , Zsuzsanna Darula , Adam Pap , Peter R Baker

Affiliation

Intact glycopeptide analysis is becoming more common with developments in mass spectrometry instrumentation and fragmentation approaches. In particular, collision-based fragmentation approaches such as higher energy collisional dissociation (HCD) and radical-driven fragmentation approaches such as electron transfer dissociation (ETD) provide complementary information, but bioinformatic strategies to utilize this combined information are currently lacking. In this work we adapted a software tool, MS-Filter, to search HCD peak list files for predicted Y ions based on matched EThcD results to propose additional glycopeptide assignments. The strategy proved to be extremely powerful for O-glycopeptide data, and also of benefit for N-linked data, where it allowed rescue of low confidence results from database searching.

中文翻译：

过滤Y离子糖肽峰列表文件的有效性。

随着质谱仪器和片段化方法的发展，完整的糖肽分析变得越来越普遍。特别是，基于碰撞的碎片化方法（例如高能碰撞解离（HCD））和自由基驱动的碎片化方法（例如电子转移解离（ETD））提供了补充信息，但是目前缺乏利用这种组合信息的生物信息学策略。在这项工作中，我们采用了一种软件工具MS-Filter，以根据匹配的EThcD结果在HCD峰列表文件中搜索预测的Y离子，从而提出其他糖肽分配方案。事实证明，该策略对O-糖肽数据极为有效，对N链接数据也有好处，因为它可以挽救数据库搜索带来的低置信度结果。

更新日期：2020-02-06

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