N-Terminal Peptide Detection with Optimized Peptide-Spectrum Matching and Streamlined Sequence Libraries.
N-Terminal Peptide Detection with Optimized Peptide-Spectrum Matching and Streamlined Sequence Libraries.
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DOI：
10.1021/acs.jproteome.5b00996
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发表时间：
2016-09-02
影响因子：
4.4
通讯作者：
Weir MP
中科院分区：
文献类型：
--
作者：
Lycette BE;Glickman JW;Roth SJ;Cram AE;Kim TH;Krizanc D;Weir MP
我们确定了酵母细胞裂解物中的胰蛋白酶肽映射到翻译起始位点的下游注释的起始位点使用肽谱匹配算法OMSSA和Mascot。为了提高肽谱匹配的准确性，使用几个标准化参数集运行两种算法，并且使用来自碰撞诱导解离的a、B和y离子运行Mascot。大部分（22%）的检测到的N-末端肽映射到翻译起始下游的注释的起始位点。通过蛋白质印迹分析验证了在与全长蛋白质（框1）相同的阅读框中来自下游起始的几种截短蛋白质的表达。为了便于对果蝇较大的染色体组进行分析，我们创建了一个精简的序列文库，其中所有重复的胰蛋白酶片段都已被删除。使用该“剥离”文库的OMSSA评估揭示了171个映射到下游翻译起始位点的肽，其中76%与全长注释的蛋白质在相同的阅读框中，尽管一些在不同的阅读框中，产生了不在注释的蛋白质组中的新蛋白质序列。下游AUG起始密码子周围的序列与核苷酸偏好相关，具有明显的三碱基周期N1^G2^A3。
We identified tryptic peptides in yeast cell lysates that map to translation initiation sites downstream of the annotated start sites using the peptide-spectrum matching algorithms OMSSA and Mascot. To increase the accuracy of peptide-spectrum matching, both algorithms were run using several standardized parameter sets, and Mascot was run utilizing a, b, and y ions from collision-induced dissociation. A large fraction (22%) of the detected N-terminal peptides mapped to translation initiation downstream of the annotated initiation sites. Expression of several truncated proteins from downstream initiation in the same reading frame as the full-length protein (frame 1) was verified by western analysis. To facilitate analysis of the larger nroteome of Drosophila, we created a streamlined sequence library from which all duplicated trypsin fragments had been removed. OMSSA assessment using this “stripped” library revealed 171 peptides that map to downstream translation initiation sites, 76% of which are in the same reading frame as the full-length annotated proteins, although some are in different reading frames creating new protein sequences not in the annotated proteome. Sequences surrounding implicated downstream AUG start codons are associated with nucleotide preferences with a pronounced three-base periodicity N1^G2^A3.
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遗传密码产生的mRNA二级结构的周期性模式。
影响因子：
14.9
作者：
Shabalina, Svetlana A.;Ogurtsov, Aleksey Y.;Spiridonov, Nikolay A.
通讯作者：
Spiridonov, Nikolay A.
影响因子：
4.4
作者：
Lin, Miin S.;Cherny, Justin J.;Fournier, Claire T.;Roth, Samuel J.;Krizanc, Danny;Weir, Michael P.
通讯作者：
Weir, Michael P.
DOI：
10.1073/pnas.1207846109
发表时间：
2012-09-11
影响因子：
11.1
作者：
Lee, Sooncheol;Liu, Botao;Qian, Shu-Bing
通讯作者：
Qian, Shu-Bing
影响因子：
4.4
作者：
Park, Christopher Y.;Klammer, Aaron A.;Noble, William S.
通讯作者：
Noble, William S.
影响因子：
20.3
作者：
Prudova, Anna;Serrano, Katherine;Overall, Christopher M.
通讯作者：
Overall, Christopher M.