Hu Han, Huang Yu, Mao Yang, Yu Xiang, Xu Yongmei, Liu Jian, Zong Chengli, Boons Geert-Jan, Lin Cheng, Xia Yu, Zaia Joseph
From the ‡Bioinformatics Program, Boston University, Boston, Massachusetts 02215, USA; §Center for Biomedical Mass Spectrometry, Department of Biochemistry, Boston University School of Medicine, Boston University, Boston, Massachusetts 02118, USA;
§Center for Biomedical Mass Spectrometry, Department of Biochemistry, Boston University School of Medicine, Boston University, Boston, Massachusetts 02118, USA;
Mol Cell Proteomics. 2014 Sep;13(9):2490-502. doi: 10.1074/mcp.M114.039560. Epub 2014 Jun 12.
Heparan sulfate (HS) is a linear polysaccharide expressed on cell surfaces, in extracellular matrices and cellular granules in metazoan cells. Through non-covalent binding to growth factors, morphogens, chemokines, and other protein families, HS is involved in all multicellular physiological activities. Its biological activities depend on the fine structures of its protein-binding domains, the determination of which remains a daunting task. Methods have advanced to the point that mass spectra with information-rich product ions may be produced on purified HS saccharides. However, the interpretation of these complex product ion patterns has emerged as the bottleneck to the dissemination of these HS sequencing methods. To solve this problem, we designed HS-SEQ, the first comprehensive algorithm for HS de novo sequencing using high-resolution tandem mass spectra. We tested HS-SEQ using negative electron transfer dissociation (NETD) tandem mass spectra generated from a set of pure synthetic saccharide standards with diverse sulfation patterns. The results showed that HS-SEQ rapidly and accurately determined the correct HS structures from large candidate pools.
硫酸乙酰肝素（HS）是一种线性多糖，存在于后生动物细胞的细胞表面、细胞外基质和细胞颗粒中。通过与生长因子、形态发生素、趋化因子和其他蛋白质家族的非共价结合，HS参与了所有多细胞生理活动。其生物学活性取决于其蛋白质结合结构域的精细结构，而确定这些结构仍然是一项艰巨的任务。目前的方法已经发展到可以对纯化的HS糖进行产生具有丰富信息的产物离子的质谱分析。然而，这些复杂产物离子模式的解释已成为这些HS测序方法推广的瓶颈。为了解决这个问题，我们设计了HS-SEQ，这是第一个使用高分辨率串联质谱进行HS从头测序的综合算法。我们使用从一组具有不同硫酸化模式的纯合成糖标准品产生的负电子转移解离（NETD）串联质谱对HS-SEQ进行了测试。结果表明，HS-SEQ能够从大量候选池中快速准确地确定正确的HS结构。
