Automated Glycan Sequencing from Tandem Mass Spectra of N-Linked Glycopeptides.
Automated Glycan Sequencing from Tandem Mass Spectra of N-Linked Glycopeptides.
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DOI：
10.1021/acs.analchem.5b04858
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发表时间：
2016-06-07
影响因子：
7.4
通讯作者：
Tang H
中科院分区：
文献类型：
--
作者：
Yu CY;Mayampurath A;Zhu R;Zacharias L;Song E;Wang L;Mechref Y;Tang H
质谱已成为人类血液样品蛋白质组生物标志物分析的常规实验工具，部分原因是信息学工具的大量可用性。作为哺乳动物中最常见的蛋白质翻译后修饰（PTMs）之一，蛋白质糖基化在多种人类疾病中发生改变，因此可能是疾病进展的候选标志物。虽然质谱仪器的性能已经有所提高，但使用现有软件发现糖基化相关标记物目前并不简单。蛋白质糖基化的完整表征需要鉴定样品中的完整糖肽，包括鉴定修饰位点以及连接聚糖的结构。在本文中，我们提出了GlycoSeq，一个开源的软件工具，实现了一个启发式迭代聚糖测序算法，再加上先验知识的碰撞诱导解离串联质谱的糖肽内的聚糖结构的自动阐明。GlycoSeq采用由聚糖合成途径定义的糖苷键规则来消除不可能的聚糖结构并构建合理的聚糖树。我们在从乳腺癌患者获得的N-连接糖肽细胞系的两组串联质谱上测试了该工具。在N-连接聚糖合成途径中采用酶促特异性后，GlycoSeq的测序结果与手动策划的聚糖结构高度一致。因此，GlycoSeq可用于MS/MS分析中糖肽中聚糖结构的表征。GlycoSeq作为开源软件在https://github.com/chpaul/GlycoSeq/上发布。
Mass spectrometry has become a routine experimental tool for proteomic biomarker analysis of human blood samples, partly due to the large availability of informatics tools. As one of the most common protein post-translational modifications (PTMs) in mammals, protein glycosylation has been observed to alter in multiple human diseases, and thus may potentially be candidate markers of disease progression. While mass spectrometry instrumentation has seen advancements in capabilities, discovering glycosylation-related markers using existing software is currently not straightforward. Complete characterization of protein glycosylation requires the identification of intact glycopeptides in samples, including identification of the modification site as well as the structure of the attached glycans. In this paper, we present GlycoSeq, an open-source software tool that implements a heuristic iterated glycan sequencing algorithm coupled with prior knowledge for automated elucidation of the glycan structure within a glycopeptide from its collision-induced dissociation tandem mass spectrum. GlycoSeq employs rules of glycosidic linkage as defined by glycan synthetic pathways to eliminate improbable glycan structures and build reasonable glycan trees. We tested the tool on two sets of tandem mass spectra of N-linked glycopeptides cell lines acquired from breast cancer patients. After employing enzymatic specificity within the N-linked glycan synthetic pathway, the sequencing results of GlycoSeq were highly consistent with the manually curated glycan structures. Hence, GlycoSeq is ready to be used for the characterization of glycan structures in glycopeptides from MS/MS analysis. GlycoSeq is released as open source software at https://github.com/chpaul/GlycoSeq/.