The Arabidopsis PeptideAtlas: Harnessing worldwide proteomics data to create a comprehensive community proteomics resource
The Arabidopsis PeptideAtlas: Harnessing worldwide proteomics data to create a comprehensive community proteomics resource
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DOI：
10.1093/plcell/koab211
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发表时间：
2021-08-19
期刊：
影响因子：
11.6
通讯作者：
Deutsch，Eric W.
中科院分区：
文献类型：
--
作者：
van Wijk，Klaas J.;Leppert，Tami;Deutsch，Eric W.
我们开发了一个资源，拟南芥肽图谱（www.peptideatlas.org/builds/arabidopsis/），以解决有关拟南芥蛋白质组的核心问题，如蛋白质剪接形式和翻译后修饰（PTMs）的意义，或简单地获得有关特定蛋白质的可靠信息。PeptideAtlas基于ProteomeXchange收集的已发表的质谱（MS）数据，并通过统一的处理和元数据注释管道进行重新分析。所有匹配的ms衍生肽数据都与光谱、技术和生物元数据相关联。在1.43亿个MS/MS（串联质谱）光谱中，有近4000万个与参考基因组Araport11相匹配，在最高置信度（错误发现率0.0004；2个非嵌套肽每个≥9个氨基酸）下鉴定出约50万个独特的肽和17,858个独特鉴定的蛋白质（每个基因只有同种异构体），指定的典型蛋白和3,543个低置信度蛋白质。对未观察到的蛋白质的物理化学性质进行了评估。目前在Araport11中未发现的其他蛋白质和同种异构体被鉴定出来，这些蛋白质和异构体是由假基因、可选择的开始、停止和/或剪接变异体和小的开放阅读框架产生的；在更新拟南芥基因组时应考虑这些特征。磷酸化可以通过复杂的PTM查看器检查。PeptideAtlas集成了社区资源，包括TAIR， JBrowse中的曲目，PPDB和UniProtKB。随后的PeptideAtlas构建将包含数百万个MS/MS数据。
We developed a resource, the Arabidopsis PeptideAtlas (www.peptideatlas.org/builds/arabidopsis/), to solve central questions about theArabidopsis thalianaproteome, such as the significance of protein splice forms and post-translational modifications (PTMs), or simply to obtain reliable information about specific proteins. PeptideAtlas is based on published mass spectrometry (MS) data collected through ProteomeXchange and reanalyzed through a uniform processing and metadata annotation pipeline. All matched MS-derived peptide data are linked to spectral, technical, and biological metadata. Nearly 40 million out of ∼143 million MS/MS (tandem MS) spectra were matched to the reference genome Araport11, identifying ∼0.5 million unique peptides and 17,858 uniquely identified proteins (only isoform per gene) at the highest confidence level (false discovery rate 0.0004; 2 non-nested peptides ≥9 amino acid each), assigned canonical proteins, and 3,543 lower-confidence proteins. Physicochemical protein properties were evaluated for targeted identification of unobserved proteins. Additional proteins and isoforms currently not in Araport11 were identified that were generated from pseudogenes, alternative start, stops, and/or splice variants, and small Open Reading Frames; these features should be considered when updating the Arabidopsis genome. Phosphorylation can be inspected through a sophisticated PTM viewer. PeptideAtlas is integrated with community resources including TAIR, tracks in JBrowse, PPDB, and UniProtKB. Subsequent PeptideAtlas builds will incorporate millions more MS/MS data.