GlycoMiner: a new software tool to elucidate glycopeptide composition
GlycoMiner: a new software tool to elucidate glycopeptide composition
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DOI：
10.1002/rcm.3731
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发表时间：
2008-10-01
影响因子：
2
通讯作者：
Drahos, Laszlo
中科院分区：
文献类型：
--
作者：
Ozohanics, Oliver;Krenyacz, Judit;Drahos, Laszlo
GlycoMiner是一种新的计算机软件，可以自动识别液相色谱/质谱（LC/MS）中获得的串联（MS/MS）光谱，这些光谱对应于n -糖肽。该程序补充了传统的蛋白质组学分析，可以在高通量环境中使用。该程序解释光谱并确定相应的糖肽的结构。GlycoMiner运行在Windows下，可以处理从各种仪器获得的光谱，可以从我们的网站（w3.chemres.hu/ms/ GlycoMiner）下载。该算法的工作原理与人类专家相似；评估低质量氧离子；从质子化分子中减少低聚糖的损失；并确定肽残基的质量。该程序已经在两种糖肽的胰蛋白酶消化上进行了测试：AGP（具有五个不同的n -糖基化位点）和转铁蛋白（具有两个n -糖基化位点）。结果已通过手动和GlycoMiner进行评估。3132个MS/MS谱图中有338个对应于糖肽；GlycoMiner鉴定假阳性率为0.1%，假阴性率为0.1%。从中可以手工识别出196个聚糖结构；GlycoMiner正确地识别了所有这些，没有假阳性。其余为低质量光谱，不适合进行结构鉴定。版权所有(C) 2008约翰威利父子有限公司
New computer software, GlycoMiner, has been developed to automatically identify tandem (MS/MS) spectra obtained in liquid chromatography/mass spectrometry (LC/MS) runs which correspond to N-glycopeptides. The program complements conventional proteomics analysis, and can be used in a high-throughput environment. The program interprets the spectra and determines the structure of the corresponding glycopeptides. GlycoMiner runs under Windows, can process spectra obtained oil various instruments, and can be downloaded from our website (w3.chemres.hu/ms/glycominer). The algorithm works similarly to a human expert; evaluates the low mass oxonium ions; deduces oligosaccharide losses from the protonated molecule; and identifies the mass of the peptide residue. The program has been tested on tryptic digests of two glycopeptides: AGP (which has five different N-glycosylation sites) and transferrin (with two N-glycosylation sites). Results have been evaluated both manually and by GlycoMiner. Out of 3132 MS/MS spectra 338 were found to correspond to glycopeptides; identification by GlycoMiner showed a 0.1% false positive and 0.1% false negative rate. From these it was possible to identify 196 glycan structures manually; GlycoMiner correctly identified all of these, with no false positives. The rest were low quality spectra, not suitable for structure assignment. Copyright (C) 2008 John Wiley & Sons, Ltd.