Investigating protein isoforms via proteomics: a feasibility study.
Investigating protein isoforms via proteomics: a feasibility study.
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DOI：
10.1002/pmic.200900445
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发表时间：
2010-03
期刊：
影响因子：
3.4
通讯作者：
Hubbard, Simon J.
中科院分区：
文献类型：
--
作者：
Blakeley, Paul;Siepen, Jennifer A.;Lawless, Craig;Hubbard, Simon J.
选择性剪接 (AS) 和前信使 RNA 的加工解释了多细胞真核生物中基因数量和蛋白质组复杂性之间的差异。然而，通过实验鉴定出的替代蛋白质亚型相对较少，特别是在蛋白质水平上。在这项研究中，我们评估了蛋白质组学了解人类和其他四种模型真核生物中不同剪接的蛋白质亚型的能力。存在可告知可变剪接的蛋白质组学数据的 Ensembl 注释基因的数量超过人类和线虫基因组中可变剪接基因的 33%。首次检查鸡的 AS，我们发现了 600 多个基因的蛋白质组学支持。然而，尽管肽鉴定仅支持 Ensembl 中注释的一小部分替代蛋白质亚型，但更多的变体适合蛋白质组学鉴定。这些现有的鉴定（AS 基因的 10-51%）与理论上可行的鉴定（90-99%）之间仍然存在相当大的差距。我们还比较了 Swiss-Prot 和 Ensembl 之间的注释，建议使用两者来最大程度地覆盖 AS。我们建议使用选定的反应和标准进行有针对性的蛋白质组实验对于发现更多替代亚型并讨论围绕这些策略的问题至关重要。
Alternative splicing (AS) and processing of pre-messenger RNAs explains the discrepancy between the number of genes and proteome complexity in multicellular eukaryotic organisms. However, relatively few alternative protein isoforms have been experimentally identified, particularly at the protein level. In this study, we assess the ability of proteomics to inform on differently spliced protein isoforms in human and four other model eukaryotes. The number of Ensembl-annotated genes for which proteomic data exists that informs on alternative splicing exceeds 33% of the alternately spliced genes in the human and worm genomes. Examining AS in chicken for the first time, we find proteomic support for over 600 genes. However, although peptide identifications support only a small fraction of alternative protein isoforms that are annotated in Ensembl, many more variants are amenable to proteomic identification. There remains a sizeable gap between these existing identifications (10-51% of AS genes) and those that are theoretically feasible (90-99%). We also compare annotations between Swiss-Prot and Ensembl, recommending use of both to maximise coverage of AS. We propose that targeted proteomic experiments using selected reactions and standards are essential to uncover further alternative isoforms and discuss the issues surrounding these strategies.
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影响因子：
14.9
作者：
UniProt Consortium
通讯作者：
UniProt Consortium
影响因子：
4.8
作者：
Kirkpatrick, DS;Gerber, SA;Gygi, SP
通讯作者：
Gygi, SP
影响因子：
4.7
作者：
Jiao, Yuxia;Robison, A. J.;Colbran, Roger J.
通讯作者：
Colbran, Roger J.
影响因子：
7
作者：
Gupta, Nitin;Tanner, Stephen;Pevzner, Pavel A.
通讯作者：
Pevzner, Pavel A.
DOI：
10.1073/pnas.0811066106
发表时间：
2008-12-30
影响因子：
11.1
作者：
Castellana, Natalie E.;Payne, Samuel H.;Briggs, Steven P.
通讯作者：
Briggs, Steven P.