The discovery of novel protein-coding features in mouse genome based on mass spectrometry data.
The discovery of novel protein-coding features in mouse genome based on mass spectrometry data.
复制标题
DOI：
10.1016/j.ygeno.2011.07.005
复制
发表时间：
2011-11
期刊：
影响因子：
4.4
通讯作者：
Xie L
中科院分区：
文献类型：
--
作者：
Xing XB;Li QR;Sun H;Fu X;Zhan F;Huang X;Li J;Chen CL;Shyr Y;Zeng R;Li YX;Xie L
后基因组时代，由于基因模型的复杂性，在真核生物基因组中识别蛋白质编码基因仍然是一个挑战。我们应用蛋白基因组学的策略来检测小鼠基因组中未注释的蛋白质编码区。来自不同小鼠样品的高准确度串联质谱（MS/MS）数据由内部LTQ-Orbitrap质谱仪生成。构建了两个可搜索的诊断蛋白质组数据集，一个包含所有可能的编码外显子连接，另一个包含所有推定的编码外显子，用于发现新的外显子剪接事件和新的不间断蛋白质编码区。总共鉴定了29，586个独特的肽。向后比对小鼠基因组，通过已知肽验证了4，471个注释基因的翻译;并且通过新肽在小鼠基因组中定义了172个基因事件。该方法为真核生物基因组编码基因的注释提供了重要依据。
Identifying protein-coding genes in eukaryotic genomes remains a challenge in post-genome era due to the complex gene models. We applied a proteogenomics strategy to detect un-annotated protein-coding regions in mouse genome. High-accuracy tandem mass spectrometry (MS/MS) data from diverse mouse samples were generated by LTQ-Orbitrap mass spectrometer in house. Two searchable diagnostic proteomic datasets were constructed, one with all possible encoding exon junctions, and the other with all putative encoding exons, for the discovery of novel exon splicing events and novel uninterrupted protein-coding regions. Altogether 29,586 unique peptides were identified. Aligning backwards to the mouse genome, the translation of 4,471 annotated genes were validated by the known peptides; and 172 genic events were defined in mouse genome by the novel peptides. The approach in the current work can provide substantial evidences for eukaryote genome annotation in encoding genes.
登录
查看更多内容
DOI：
10.1093/bioinformatics/btq033
发表时间：
2010-03-15
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Quinlan AR;Hall IM
通讯作者：
Hall IM
影响因子：
64.5
作者：
Huttlin EL;Jedrychowski MP;Elias JE;Goswami T;Rad R;Beausoleil SA;Villén J;Haas W;Sowa ME;Gygi SP
通讯作者：
Gygi SP
影响因子：
3.7
作者：
Bitton DA;Smith DL;Connolly Y;Scutt PJ;Miller CJ
通讯作者：
Miller CJ
影响因子：
14.9
作者：
Pruitt KD;Tatusova T;Klimke W;Maglott DR
通讯作者：
Maglott DR
影响因子：
12.3
作者：
Fermin, Damian;Allen, Baxter B.;Blackwell, Thomas W.;Menon, Rajasree;Adamski, Marcin;Xu, Yin;Ulintz, Peter;Omenn, Gilbert S.;States, David J.
通讯作者：
States, David J.