PepArML: A Meta-Search Peptide Identification Platform for Tandem Mass Spectra.
PepArML: A Meta-Search Peptide Identification Platform for Tandem Mass Spectra.
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DOI：
10.1002/0471250953.bi1323s44
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发表时间：
2013-12
影响因子：
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通讯作者：
Edwards, Nathan J
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文献类型：
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作者：
Edwards, Nathan J
PepArML元搜索多肽识别平台为七个搜索引擎提供了统一的搜索接口；用于大规模搜索的强大的集群、网格和云计算调度器；以及无监督、无模型、基于机器学习的结果组合器，它为每个光谱选择最佳的多肽识别，估计错误发现率，并输出PepXML格式的识别。元搜索平台支持Mascot；同时支持原生、k-Score和S-Score评分；OMSSA；MyriMatch；以及使用MS-GF频谱概率分数进行检查-重新格式化频谱数据并为每个搜索引擎动态构建搜索配置。组合器基于搜索引擎结果和特征为每个光谱选择最佳的多肽识别，这些特征对酶消化、保留时间、前体同位素簇、质量准确度和蛋白质组学多肽属性进行建模，不需要特征效用或权重的先验知识。PepArML元搜索多肽识别平台在10%的FDR下识别的光谱通常是单个搜索引擎的2-3倍。
The PepArML meta-search peptide identification platform provides a unified search interface to seven search engines; a robust cluster, grid, and cloud computing scheduler for large-scale searches; and an unsupervised, model-free, machine-learning-based result combiner, which selects the best peptide identification for each spectrum, estimates false-discovery rates, and outputs pepXML format identifications. The meta-search platform supports Mascot; Tandem with native, k-score, and s-score scoring; OMSSA; MyriMatch; and InsPecT with MS-GF spectral probability scores — reformatting spectral data and constructing search configurations for each search engine on the fly. The combiner selects the best peptide identification for each spectrum based on search engine results and features that model enzymatic digestion, retention time, precursor isotope clusters, mass accuracy, and proteotypic peptide properties, requiring no prior knowledge of feature utility or weighting. The PepArML meta-search peptide identification platform often identifies 2–3 times more spectra than individual search engines at 10% FDR.