Wilmarth Phillip A, Riviere Michael A, David Larry L
Department of Biochemistry and Molecular Biology, School of Medicine, Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239 USA.
J Ocul Biol Dis Infor. 2009 Dec 12;2(4):223-234. doi: 10.1007/s12177-009-9042-6.
Analysis of shotgun proteomics datasets requires techniques to distinguish correct peptide identifications from incorrect identifications, such as linear discriminant functions and target/decoy protein databases. We report an efficient, flexible proteomic analysis workflow pipeline that implements these techniques to control both peptide and protein false discovery rates. We demonstrate its performance by analyzing two-dimensional liquid chromatography separations of lens proteins from human, mouse, bovine, and chicken lenses. We compared the use of International Protein Index databases to UniProt databases and no-enzyme SEQUEST searches to tryptic searches. Sequences present in the International Protein Index databases allowed detection of several novel crystallins. An alternate start codon isoform of betaA4 was found in human lens. The minor crystallin gammaN was detected for the first time in bovine and chicken lenses. Chicken gammaS was identified and is the first member of the gamma-crystallin family observed in avian lenses. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s12177-009-9042-6) contains supplementary material, which is available to authorized users.
鸟枪法蛋白质组学数据集的分析需要一些技术来区分正确的肽段鉴定和错误的鉴定，例如线性判别函数和目标/诱饵蛋白质数据库。我们报告了一种高效、灵活的蛋白质组学分析工作流程管道，该管道实施这些技术以控制肽段和蛋白质的错误发现率。我们通过分析来自人、小鼠、牛和鸡晶状体的晶状体蛋白的二维液相色谱分离来证明其性能。我们比较了国际蛋白质索引数据库与UniProt数据库的使用情况，以及无酶SEQUEST搜索与胰蛋白酶搜索的情况。国际蛋白质索引数据库中存在的序列使得能够检测到几种新的晶状体蛋白。在人晶状体中发现了βA4的一种替代起始密码子异构体。首次在牛和鸡晶状体中检测到次要的晶状体蛋白γN。鉴定出鸡γS，它是在鸟类晶状体中观察到的γ-晶状体蛋白家族的首个成员。电子补充材料：本文的在线版本（doi:10.1007/s12177-009-9042-6）包含补充材料，授权用户可以获取。
