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首页> 外文期刊>Journal of proteome research >Metagenomic Taxonomy-Guided Database-Searching Strategy for Improving Metaproteomic Analysis
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Metagenomic Taxonomy-Guided Database-Searching Strategy for Improving Metaproteomic Analysis

机译：梅毒语素分类 - 引导数据库搜索策略，用于改善元标分析

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摘要

Metaproteomics provides a direct measure of the functional information by investigating all proteins expressed by a microbiota. However, due to the complexity and heterogeneity of microbial communities, it is very hard to construct a sequence database suitable for a metaproteomic study. Using a public database, researchers might not be able to identify proteins from poorly characterized microbial species, while a sequencing-based metagenomic database may not provide adequate coverage for all potentially expressed protein sequences. To address this challenge, we propose a metagenomic taxonomy-guided database-search strategy (MT), in which a merged database is employed, consisting of both taxonomy-guided reference protein sequences from public databases and proteins from metagenome assembly. By applying our MT strategy to a mock microbial mixture, about two times as many peptides were detected as with the metagenomic database only. According to the evaluation of the reliability of taxonomic attribution, the rate of misassignments was comparable to that obtained using an a priori matched database. We also evaluated the MT strategy with a human gut microbial sample, and we found 1.7 times as many peptides as using a standard metagenomic database. In conclusion, our MT strategy allows the construction of databases able to provide high sensitivity and precision in peptide identification in metaproteomic studies, enabling the detection of proteins from poorly characterized species within the microbiota.
机译：Metaprootomics通过研究Microbiota表达的所有蛋白质来提供功能信息的直接测量功能信息。然而，由于微生物社区的复杂性和异质性，很难构建适合于元素研究的序列数据库。使用公共数据库，研究人员可能无法识别来自表征差的微生物物种的蛋白质，而基于测序的偏心组织数据库可能无法为所有可能表达的蛋白质序列提供足够的覆盖率。为了解决这一挑战，我们提出了一种偏见的分类分类标准数据库搜索策略（MT），其中采用合并的数据库，由来自公共数据库和来自梅塔群组件的蛋白质的分类作用引导蛋白序列组成。通过将MT策略应用于模拟微生物混合物，仅检测到许多肽的大约两倍仅与偏达蛋白数据库检测到。根据分类学归因的可靠性评估，误分析与使用先验匹配数据库获得的速率相当。我们还通过人体肠道微生物样品评估了MT策略，我们发现了肽的1.7倍，因为使用标准的偏心组织数据库。总之，我们的MT策略允许建设数据库，该数据库能够在肽鉴定方面提供高灵敏度和精确度，从而能够检测微生物群内的特征差的物种中的蛋白质。

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  • 来源
    《Journal of proteome research》 |2018年第4期|共10页
  • 作者

    Jinqiu Xiao; Alessandro Tanca; Ben Jia; Runqing Yang; Bo Wang; Yu Zhang; Jing Li;

  • 作者单位

    Department of Bioinformatics and Biostatistics School of Life Sciences and Biotechnology Shanghai Jiao Tong University Shanghai 200240 People’s Republic of China;

    Porto Conte Ricerche Science and Technology Park of Sardinia Tramariglio Alghero Italy;

    Department of Bioinformatics and Biostatistics School of Life Sciences and Biotechnology Shanghai Jiao Tong University Shanghai 200240 People’s Republic of China;

    College of Computer Science and Technology Zhejiang University Hangzhou 310027 People’s Republic of China;

    Department of Bioinformatics and Biostatistics School of Life Sciences and Biotechnology Shanghai Jiao Tong University Shanghai 200240 People’s Republic of China;

    Institute of Oceanography Shanghai Jiao Tong University Shanghai 200240 People’s Republic of China;

    Department of Bioinformatics and Biostatistics School of Life Sciences and Biotechnology Shanghai Jiao Tong University Shanghai 200240 People’s Republic of China;

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  • 原文格式 PDF
  • 正文语种 eng
  • 中图分类 分子生物学;蛋白质;
  • 关键词

    mass spectrometry; metagenomics; metaproteomics; microbial communities; taxonomy;

    机译：质谱;MetageNomics;metaprootomics;微生物社区;分类;

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