An NGS-Independent Strategy for Proteome-Wide Identification of Single Amino Acid Polymorphisms by Mass Spectrometry.
An NGS-Independent Strategy for Proteome-Wide Identification of Single Amino Acid Polymorphisms by Mass Spectrometry.
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通过质谱法对单氨基酸多态性进行全蛋白质组鉴定的独立于 NGS 的策略。
DOI：
10.1021/acs.analchem.5b04417
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发表时间：
2016
影响因子：
7.4
通讯作者：
W. Shui
中科院分区：
文献类型：
--
作者：
Yun Xiong;Yufeng Guo;Weidi Xiao;Qichen Cao;Shanshan Li;Xianni Qi;Zhidan Zhang;Qinhong Wang;W. Shui
检测含有由非同义SNPs（nsSNPs）编码的单氨基酸多态性（SAP）的蛋白质可以帮助研究人员研究蛋白质变体的功能意义。大多数用于大规模SAP定位的蛋白基因组学方法需要构建包含从下一代测序（NGS）数据预测的蛋白变体的样品特异性数据库。针对这些NGS衍生的数据库搜索鸟枪蛋白质组数据集允许鉴定SAP肽，从而验证蛋白质组水平的序列变异。与传统方法相反，我们的研究提出了一种新的策略，用于蛋白质组范围的SAP检测，而不依赖于样品特异性NGS数据。通过使用我们的策略从工业耐热酵母菌株中搜索深度覆盖的蛋白质组数据集，与参考基因组相比，我们确定了337个推定的SAP。在用严格标准鉴定的SAP肽中，使用从该生物体获得的全基因组测序数据验证了85.2%的SAP位点，这表明用我们的策略鉴定SAP的准确性很高。更有趣的是，对于某些不能通过基因组测序预测的SAP肽，我们使用合成肽标准品来验证蛋白质组中肽变体的表达。我们的研究为蛋白质基因组学提供了一个独特的工具，可以在蛋白质组范围内直接鉴定SAP，并捕获与nsSNP无关的非遗传蛋白质变体。
Detection of proteins containing single amino acid polymorphisms (SAPs) encoded by nonsynonymous SNPs (nsSNPs) can aid researchers in studying the functional significance of protein variants. Most proteogenomic approaches for large-scale SAPs mapping require construction of a sample-specific database containing protein variants predicted from the next-generation sequencing (NGS) data. Searching shotgun proteomic data sets against these NGS-derived databases allowed for identification of SAP peptides, thus validating the proteome-level sequence variation. Contrary to the conventional approaches, our study presents a novel strategy for proteome-wide SAP detection without relying on sample-specific NGS data. By searching a deep-coverage proteomic data set from an industrial thermotolerant yeast strain using our strategy, we identified 337 putative SAPs compared to the reference genome. Among the SAP peptides identified with stringent criteria, 85.2% of SAP sites were validated using whole-genome sequencing data obtained for this organism, which indicates high accuracy of SAP identification with our strategy. More interestingly, for certain SAP peptides that cannot be predicted by genomic sequencing, we used synthetic peptide standards to verify expression of peptide variants in the proteome. Our study has provided a unique tool for proteogenomics to enable proteome-wide direct SAP identification and capture nongenetic protein variants not linked to nsSNPs.
影响因子：
4.4
作者：
Dasari, Surendra;Chambers, Matthew C.;Slebos, Robbert J.;Zimmerman, Lisa J.;Ham, Amy-Joan L.;Tabb, David L.
通讯作者：
Tabb, David L.
影响因子：
4.4
作者：
Sheynkman GM;Shortreed MR;Frey BL;Scalf M;Smith LM
通讯作者：
Smith LM