Strategies for metagenomic-guided whole-community proteomics of complex microbial environments.
Strategies for metagenomic-guided whole-community proteomics of complex microbial environments.
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DOI：
10.1371/journal.pone.0027173
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发表时间：
2011
期刊：
影响因子：
3.7
通讯作者：
Hettich RL
中科院分区：
文献类型：
--
作者：
Cantarel BL;Erickson AR;VerBerkmoes NC;Erickson BK;Carey PA;Pan C;Shah M;Mongodin EF;Jansson JK;Fraser-Liggett CM;Hettich RL
大规模蛋白质组学实验中准确的蛋白质鉴定依赖于详细、准确的蛋白质目录，该目录源自基于基因组序列数据的开放阅读框的预测。由于蛋白质组数据集和相应的短读核苷酸序列数据之间的可变重叠，基于质谱的蛋白质组数据与环境宏基因组序列的计算蛋白质组预测的整合一直具有挑战性。在这项研究中，我们使用来自相同人类粪便样本的匹配宏基因组序列生成的蛋白质预测，对几种增加宏蛋白质组数据集中微生物肽光谱匹配的策略进行了基准测试。此外，我们还研究了基于质谱的过滤器（高质量精度、增量相关性）和从头肽测序对这些复杂数据集中肽谱分配的数量和鲁棒性的影响。总之，我们发现，针对相同样品的 DNA 测序中的非组装读数搜索高质量准确的肽测量值，可显着增加可识别的蛋白质，而不会牺牲准确性。
Accurate protein identification in large-scale proteomics experiments relies upon a detailed, accurate protein catalogue, which is derived from predictions of open reading frames based on genome sequence data. Integration of mass spectrometry-based proteomics data with computational proteome predictions from environmental metagenomic sequences has been challenging because of the variable overlap between proteomic datasets and corresponding short-read nucleotide sequence data. In this study, we have benchmarked several strategies for increasing microbial peptide spectral matching in metaproteomic datasets using protein predictions generated from matched metagenomic sequences from the same human fecal samples. Additionally, we investigated the impact of mass spectrometry-based filters (high mass accuracy, delta correlation), and de novo peptide sequencing on the number and robustness of peptide-spectrum assignments in these complex datasets. In summary, we find that high mass accuracy peptide measurements searched against non-assembled reads from DNA sequencing of the same samples significantly increased identifiable proteins without sacrificing accuracy.
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4.1
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States, David J.