HyPep: An Open-Source Software for Identification and Discovery of Neuropeptides Using Sequence Homology Search.
HyPep: An Open-Source Software for Identification and Discovery of Neuropeptides Using Sequence Homology Search.
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DOI：
10.1021/acs.jproteome.2c00597
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发表时间：
2023-02-03
影响因子：
4.4
通讯作者：
Li, Lingjun
中科院分区：
文献类型：
--
作者：
Vu, Nhu Q.;Yen, Hsu-Ching;Fields, Lauren;Cao, Weifeng;Li, Lingjun
神经肽是一类在生物化学、生理和行为过程中具有关键调节作用的内源性肽。神经肽的质谱分析通常依赖于用于数据库搜索和肽鉴定的蛋白质信息学工具。由于神经肽数据库通常是通过实验建立的，并且由彼此具有高序列相似性的短序列组成，因此我们开发了一种新的数据库搜索工具HyPep，该工具利用序列同源性搜索进行肽鉴定。HyPep将通过PEAKS软件生成的无数据库、从头测序的肽序列与神经肽数据库序列进行比对，以基于比对评分鉴定神经肽。使用来自各种C.并与商业数据库检索软件PEAKS DB进行比较。在1%的错误发现率下，HyPep比PEAKS DB从每种组织类型中鉴定出更多的神经肽，两种程序的错误匹配率均为2%。除了鉴定，本报告还描述了HyPep如何帮助发现新的神经肽。
Neuropeptides are a class of endogenous peptides that have key regulatory roles in biochemical, physiological, and behavioral processes. Mass spectrometry analyses of neuropeptides often rely on protein informatics tools for database searching and peptide identification. As neuropeptide databases are typically experimentally built and comprised of short sequences with high sequence similarity to each other, we developed a novel database searching tool, HyPep, which utilizes sequence homology searching for peptide identification. HyPep aligns database-free, de novo sequenced peptide sequences generated through PEAKS software with neuropeptide database sequences to identify neuropeptides based on an alignment score. HyPep performance was optimized using LC-MS/MS measurements of peptide extracts from various C. sapidus neuronal tissue types and compared with a commercial database searching software, PEAKS DB. HyPep identified more neuropeptides from each tissue type than PEAKS DB at 1% false discovery rate and the false match rate from both programs was 2%. In addition to identification, this report describes how HyPep can aid in the discovery of novel neuropeptides.
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影响因子：
5.7
作者：
Dickinson PS;Qu X;Stanhope ME
通讯作者：
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影响因子：
11.1
作者：
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通讯作者：
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影响因子：
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作者：
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作者：
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DOI：
10.3791/1207
发表时间：
2009-03-23
期刊：
Journal of visualized experiments : JoVE
影响因子：
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作者：
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通讯作者：
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