Flexible and Fast Mapping of Peptides to a Proteome with ProteoMapper.
Flexible and Fast Mapping of Peptides to a Proteome with ProteoMapper.
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使用 ProteoMapper 将肽灵活快速地映射到蛋白质组。
DOI：
10.1021/acs.jproteome.8b00544
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发表时间：
2018
影响因子：
4.4
通讯作者：
Moritz,RobertL
中科院分区：
文献类型：
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作者：
Mendoza,Luis;Deutsch,EricW;Sun,Zhi;Campbell,DavidS;Shteynberg,DavidD;Moritz,RobertL
自下而上的蛋白质组学依赖于蛋白质的蛋白水解或化学裂解成肽，通过质谱鉴定这些肽，并将鉴定的肽映射回参考蛋白质组以推断鉴定出哪些可能的蛋白质。当考虑到相似的蛋白质、蛋白质家族、剪接异构体、序列变异和可能的残基质量修饰，以及对蛋白质组的不完善和不完整的理解时，将肽可靠地映射到蛋白质仍然构成实质性挑战。ProteoMapper工具能够将肽全面快速地映射到参考蛋白质组。索引器组件为来自FASTA或PEFF文件的输入蛋白质组创建分段索引。ProMaST组件提供一个或多个输入肽相对于索引的超快映射。ProteoMapper允许考虑PEFF文件中编码的已知序列变异的搜索。它还使得模糊搜索能够找到具有残基顺序变化或在指定质量容限内的其他同量异位素或近同量异位素取代的高度相似的肽。我们展示了一个例子，一个命中奇迹识别PeptideAtlas，可以更好地解释了另一个高度观察到的蛋白质的编目和未编目序列变异的组合。ProteoMapper是一个免费的开源软件，下载后可在本地使用，嵌入其他应用程序，作为在线网络工具http：//www.peptideatlas.org/map，并作为网络服务。
Bottom-up proteomics relies on the proteolytic or chemical cleavage of proteins into peptides, the identification of those peptides via mass spectrometry, and the mapping of the identified peptides back to the reference proteome to infer which possible proteins are identified. Reliable mapping of peptides to proteins still poses substantial challenges when considering similar proteins, protein families, splice isoforms, sequence variation, and possible residue mass modifications, combined with an imperfect and incomplete understanding of the proteome. The ProteoMapper tool enables a comprehensive and rapid mapping of peptides to a reference proteome. The indexer component creates a segmented index for an input proteome from a FASTA or PEFF file. The ProMaST component provides ultrafast mapping of one or more input peptides against the index. ProteoMapper allows searches that take into account known sequence variation encoded in PEFF files. It also enables fuzzy searches to find highly similar peptides with residue order changes or other isobaric or near-isobaric substitutions within a specified mass tolerance. We demonstrate an example of a one-hit-wonder identification in PeptideAtlas that may be better explained by a combination of catalogued and uncatalogued sequence variation in another highly observed protein. ProteoMapper is a free and open source, available for local use after downloading, embedding in other applications, as an online web tool at http://www.peptideatlas.org/map, and as a web service.