De novo glycan structure search with the CID MS/MS spectra of native N-glycopeptides
De novo glycan structure search with the CID MS/MS spectra of native N-glycopeptides
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DOI：
10.1093/glycob/cwp034
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发表时间：
2009-07-01
期刊：
影响因子：
4.3
通讯作者：
Renkonen, Risto
中科院分区：
文献类型：
--
作者：
Peltoniemi, Hannu;Joenvaara, Sakari;Renkonen, Risto
我们的研究目的是自动分析N-糖肽的聚糖和肽结构，而不需要从糖肽中释放聚糖。我们的湿实验室的原始数据代表了一系列的MS/MS质谱从反相液相色谱运行的尺寸排阻富集胰蛋白酶消化的糖肽从糖蛋白。首先分析MS/MS光谱，以鉴别各糖肽上存在的糖基化肽和N-聚糖单糖组成。我们进一步开发了一种分支定界算法来从头搜索N-聚糖结构，即，单糖组成和它们的有序序列。我们的从头算法是基于迭代生长和选择的群体聚糖结构，它不使用已知的聚糖结构的数据库。我们使用（i）计算机生成的光谱（有或没有恶化的缺失），（ii）纯化的糖蛋白转铁蛋白，以及（iii）从人血浆中富集的N-糖肽的复杂混合物来验证该算法。我们的分支定界算法描述了来自所有上述三种输入数据类型的聚糖结构。由于聚糖结构的多样性很大，结果通常包含几种与光谱几乎同样匹配的拟定结构。总之，该算法从MS/MS谱自动识别糖肽及其结构，从而大大减少了大量潜在聚糖结构中可能的聚糖结构的数量。
The aim of our study is to automatically analyze the glycan and peptide structures of N-glycopeptides without a need to release glycans from the glycopeptides. Our wet laboratory raw data represent a series of MS/MS mass spectra obtained from a reverse-phase liquid chromatography run of size-exclusion-enriched tryptic-digested glycopeptides from glycoproteins. The MS/MS spectra are first analyzed in order to identify glycosylated peptides and N-glycan monosaccharide compositions present on each glycopeptide. We further developed a Branch-and-Bound algorithm to search de novo N-glycan structures, i.e., monosaccharide compositions and their ordered sequences from native glycopeptides. Our de novo algorithm is based on iterative growth and selection of a population of glycan structures and it does not use databases of known glycan structures. We validate the algorithm with (i) in silico-generated spectra, with or without deteriorating deletions, (ii) with a purified glycoprotein transferrin, and (iii) with a complex mixture of N-glycopeptides enriched from human plasma. Our Branch-and-Bound algorithm depicted glycan structures from all the above-mentioned three input data types. Due to the large diversity of glycan structures, the results typically contained several proposed structures matching almost equally well to the spectra. In conclusion, this algorithm automatically identifies glycopeptides and their structures from the MS/MS spectra and thus greatly reduces the number of possible glycan structures from the vast amount of potential ones.