Detecting Modifications in Proteomics Experiments with Param-Medic
Detecting Modifications in Proteomics Experiments with Param-Medic
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DOI：
10.1021/acs.jproteome.8b00954
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发表时间：
2019-04-01
影响因子：
4.4
通讯作者：
Noble, William S.
中科院分区：
文献类型：
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作者：
May, Damon H.;Tamura, Kaipo;Noble, William S.
在多肽数据库中搜索串联质谱图需要准确了解各种实验参数，包括机器设置和样品制备方案的细节。在某些情况下，例如在重新分析公共数据集时，这种实验性元数据可能丢失或不准确。我们描述了一种方法，用于直接从给定的一组质谱图中自动推断各种类型修饰的存在，包括稳定同位素和等压标记和串联质量标记以及磷酸化肽的浓缩。我们展示了所提出的方法的敏感性和特异性，并在新版本的软件工具Param-Medic中提供了开源的Python和C++实现。
Searching tandem mass spectra against a peptide database requires accurate knowledge of various experimental parameters, including machine settings and details of the sample preparation protocol. In some cases, such as in reanalysis of public data sets, this experimental metadata may be missing or inaccurate. We describe a method for automatically inferring the presence of various types of modifications, including stable-isotope and isobaric labeling and tandem mass tags as well as the enrichment of phosphorylated peptides, directly from a given set of mass spectra. We demonstrate the sensitivity and specificity of the proposed approach, and we provide open-source Python and C++ implementations in a new version of the software tool Param-Medic.