School of Life Science and Technology, Shanghai Tech University, Shanghai 201210, China; Shanghai Center for Bioinformation Technology, Shanghai Academy of Science and Technology, Shanghai 201203, China.
School of Life Science and Technology, Shanghai Tech University, Shanghai 201210, China; Shanghai Center for Bioinformation Technology, Shanghai Academy of Science and Technology, Shanghai 201203, China; Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China.
J Genet Genomics. 2018 Jul 20;45(7):381-388. doi: 10.1016/j.jgg.2018.07.005. Epub 2018 Jul 19.
Protein phosphorylation, one of the most important protein post-translational modifications, is involved in various biological processes, and the identification of phosphorylation peptides (phosphopeptides) and their corresponding phosphorylation sites (phosphosites) will facilitate the understanding of the molecular mechanism and function of phosphorylation. Mass spectrometry (MS) provides a high-throughput technology that enables the identification of large numbers of phosphosites. PhoPepMass is designed to assist human phosphopeptide identification from MS data based on a specific database of phophopeptide masses and a multivariate hypergeometric matching algorithm. It contains 244,915 phosphosites from several public sources. Moreover, the accurate masses of peptides and fragments with phosphosites were calculated. It is the first database that provides a systematic resource for the query of phosphosites on peptides and their corresponding masses. This allows researchers to search certain proteins of which phosphosites have been reported, to browse detailed phosphopeptide and fragment information, to match masses from MS analyses with defined threshold to the corresponding phosphopeptide, and to compare proprietary phosphopeptide discovery results with results from previous studies. Additionally, a database search software is created and a "two-stage search strategy" is suggested to identify phosphopeptides from tandem mass spectra of proteomics data. We expect PhoPepMass to be a useful tool and a source of reference for proteomics researchers. PhoPepMass is available at https://www.scbit.org/phopepmass/index.html.
蛋白质磷酸化是最重要的蛋白质翻译后修饰之一，参与各种生物过程，鉴定磷酸化肽（磷酸肽）及其相应的磷酸化位点（磷酸化位点）将有助于理解磷酸化的分子机制和功能。质谱（MS）提供了一种高通量技术，能够基于磷酸肽质量的特定数据库和多元超几何匹配算法从 MS 数据中鉴定大量磷酸肽。PhoPepMass 旨在基于磷酸肽质量的特定数据库和多元超几何匹配算法，从 MS 数据中辅助人类磷酸肽的鉴定。它包含来自多个公共来源的 244,915 个磷酸化位点。此外，还计算了带有磷酸化位点的肽和片段的精确质量。这是第一个提供查询肽上磷酸化位点及其相应质量的系统资源的数据库。这允许研究人员搜索已报道磷酸化位点的特定蛋白质，浏览详细的磷酸肽和片段信息，将 MS 分析中定义阈值的质量与相应的磷酸肽匹配，并将专有的磷酸肽发现结果与以前的研究结果进行比较。此外，还创建了数据库搜索软件，并提出了“两阶段搜索策略”，以从蛋白质组学数据的串联质谱中鉴定磷酸肽。我们希望 PhoPepMass 能成为蛋白质组学研究人员的有用工具和参考来源。PhoPepMass 可在 https://www.scbit.org/phopepmass/index.html 上获取。
