Relative Retention Time Estimation Improves N-Glycopeptide Identifications by LC-MS/MS.,Journal of Proteome Research

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Relative Retention Time Estimation Improves N-Glycopeptide Identifications by LC-MS/MS.
Journal of Proteome Research ( IF 3.8 ) Pub Date : 2020-03-30 , DOI: 10.1021/acs.jproteome.0c00051
Joshua Klein ₁ , Joseph Zaia _{1,

2}

Affiliation

Glycopeptides identified by tandem mass spectrometry rely on the identification of the peptide backbone sequence and the attached glycan(s) by the incomplete fragmentation of both moieties. This may lead to ambiguous identifications where multiple structures could explain the same spectrum equally well due to missing information in the mass spectrum or incorrect precursor mass determination. To date, approaches to solving these problems have been limited, and few inroads have been made to address these issues. We present a technique to address some of these challenges and demonstrate it on previously published data sets. We use a linear modeling approach to learn the influence of the glycan composition on the retention time of a glycopeptide and use these models to validate glycopeptides within the same experiment, detecting over 400 incorrect cases during the MS/MS search and correcting 75 cases that could not be identified based on mass alone. We make this technique available as a command line executable program, written in Python and C, freely available at https://github.com/mobiusklein/glycresoft in source form, with precompiled binaries for Windows.

中文翻译：

相对保留时间估计可通过LC-MS / MS改进N-糖肽的鉴定。

通过串联质谱法鉴定的糖肽依赖于通过两个部分的不完全断裂来鉴定肽主链序列和连接的聚糖。这可能导致模棱两可的识别，其中由于质谱中缺少信息或前驱物质量测定不正确，多个结构可以很好地解释同一光谱。迄今为止，解决这些问题的方法是有限的，并且很少有解决这些问题的方法。我们提出一种技术来解决其中一些挑战，并在以前发布的数据集上进行演示。我们使用线性建模方法来了解聚糖成分对糖肽保留时间的影响，并使用这些模型来验证同一实验中的糖肽，在MS / MS搜索过程中检测到400多个错误病例，并纠正仅凭质量无法识别的75个病例。我们以Python和C编写的命令行可执行程序的形式提供了该技术，并以预编译二进制文件的形式免费提供了https://github.com/mobiusklein/glycresoft的源代码形式。

更新日期：2020-03-30

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