Faculty of Life Sciences, Michael Smith Building, University of Manchester, Manchester, UK.
Proteomics. 2010 Mar;10(6):1127-40. doi: 10.1002/pmic.200900445.
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 AS exceeds 33% of the alternately spliced genes in the human and worm genomes. Examining AS in chicken via proteomics for the first time, we find support for over 600 AS 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 (10-52% 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 maximize 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.
可变剪接 (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，相对较少的可变蛋白异构体已被实验鉴定，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在人类和其他四种模式真核生物中不同剪接蛋白异构体的信息提供能力。在人类和蠕虫基因组中，有超过 33%的交替剪接基因具有可提供 AS 信息的蛋白质组数据。首次通过蛋白质组学研究鸡的 AS，我们发现超过 600 个 AS 基因得到支持。然而，尽管肽鉴定仅支持注释在 Ensembl 中的一小部分可变蛋白异构体，但许多更多的变体可通过蛋白质组学鉴定。这些现有鉴定（10-52%的 AS 基因）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，建议同时使用这两种方法以最大限度地覆盖 AS。我们提出，使用选定反应和标准的靶向蛋白质组学实验对于揭示更多的可变异构体是必不可少的，并讨论了这些策略所面临的问题。
