Use of shotgun proteomics for the identification, confirmation, and correction of C. elegans gene annotations
Use of shotgun proteomics for the identification, confirmation, and correction of C. elegans gene annotations
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DOI：
10.1101/gr.077644.108
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发表时间：
2008-10-01
期刊：
影响因子：
7
通讯作者：
MacCoss, Michael J.
中科院分区：
文献类型：
--
作者：
Merrihew, Gennifer E.;Davis, Colleen;MacCoss, Michael J.
我们描述了一种通用的基于质谱的方法，用于任何生物的基因注释，并利用秀丽隐杆线虫证明了其有效性。我们检测到6779个秀丽隐杆线虫蛋白（67,047个肽段），其中384个虽然在WormBase WS150中有注释，但缺乏cDNA或其他先前的实验支持。我们还发现了429个未在WS150中注释的新编码序列。近一半（192/ 429）的新编码序列被RT- PCR数据证实。新的编码序列中有33个（约8%）被预测为假基因，151个（约35%）在基因模型中显示出明显的错误，245个（57%）似乎是新基因。此外，我们在现有的WormBase基因模型中验证了6010个外显子-外显子剪接连接。我们的工作证实，质谱是一种强大的实验工具，用于注释测序基因组。此外，已鉴定肽的收集应该有助于未来针对感兴趣的特定蛋白质的蛋白质组学实验。
We describe a general mass spectrometry- based approach for gene annotation of any organism and demonstrate its effectiveness using the nematode Caenorhabditis elegans. We detected 6779 C. elegans proteins (67,047 peptides), including 384 that, although annotated in WormBase WS150, lacked cDNA or other prior experimental support. We also identified 429 new coding sequences that were unannotated in WS150. Nearly half (192/ 429) of the new coding sequences were confirmed with RT- PCR data. Thirty- three (similar to 8%) of the new coding sequences had been predicted to be pseudogenes, 151 (similar to 35%) reveal apparent errors in gene models, and 245 (57%) appear to be novel genes. In addition, we verified 6010 exon - exon splice junctions within existing WormBase gene models. Our work confirms that mass spectrometry is a powerful experimental tool for annotating sequenced genomes. In addition, the collection of identified peptides should facilitate future proteomics experiments targeted at specific proteins of interest.