Determining Alternative Protein Isoform Expression Using RNA Sequencing and Mass Spectrometry.
Determining Alternative Protein Isoform Expression Using RNA Sequencing and Mass Spectrometry.
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DOI：
10.1016/j.xpro.2020.100138
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发表时间：
2020-12-18
期刊：
影响因子：
--
通讯作者：
Lam MPY
中科院分区：
文献类型：
--
作者：
Han Y;Wright JM;Lau E;Lam MPY
选择性剪接极大地扩展了人类基因组的编码能力，但有多少选择性转录本被翻译成蛋白质或具有功能重要性仍然未知，有待实验验证。在这里，我们描述了一个协议，结合转录组学（RNA-seq）和蛋白质组学（质谱[MS]）分析，以确定蛋白质组中的替代异构体。此工作流程适用于匹配样本的定制生成的RNA-seq和MS数据，以及公共存储库中现有转录组学和蛋白质组学数据集的重新分析。有关本方案使用和执行的完整详细信息，请参阅。多组学工作流程用于识别替代蛋白质异构体适用于公开可用或内部生成的RNA-seq和蛋白质组学数据JCAST管道用于创建样品特异性蛋白质序列数据库能够重新分析现有数据集以识别差异调节的异构体选择性剪接极大地扩展了人类基因组的编码能力，但有多少替代转录物被翻译成蛋白质或具有功能重要性仍是未知的，有待实验验证。在这里，我们描述了一个协议，结合转录组学（RNA-seq）和蛋白质组学（质谱[MS]）分析，以确定蛋白质组中的替代异构体。此工作流程适用于匹配样本的定制生成的RNA-seq和MS数据，以及公共存储库中现有转录组学和蛋白质组学数据集的重新分析。
Alternative splicing greatly expands the coding capacity of the human genome, but how many alternative transcripts are translated as proteins or carry functional importance remains unknown and awaits experimental verification. Here, we describe a protocol that combines transcriptomics (RNA-seq) and proteomics (mass spectrometry [MS]) analyses to identify alternative isoforms in proteomes. This workflow is applicable to custom-generated RNA-seq and MS data from matching samples, as well as the reanalysis of existing transcriptomics and proteomics datasets in public repositories. For complete details on the use and execution of this protocol, please refer to. Multi-omics workflow for identification of alternative protein isoforms Applicable to publicly available or in-house generated RNA-seq and proteomics data JCAST pipeline for creation of sample-specific protein sequence databases Enables reanalysis of existing datasets to identify differentially regulated isoforms Alternative splicing greatly expands the coding capacity of the human genome, but how many alternative transcripts are translated as proteins or carry functional importance remains unknown and awaits experimental verification. Here, we describe a protocol that combines transcriptomics (RNA-seq) and proteomics (mass spectrometry [MS]) analyses to identify alternative isoforms in proteomes. This workflow is applicable to custom-generated RNA-seq and MS data from matching samples, as well as the reanalysis of existing transcriptomics and proteomics datasets in public repositories.
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DOI：
10.1093/bioinformatics/btt543
发表时间：
2013-12-15
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Wang X;Zhang B
通讯作者：
Zhang B
影响因子：
64.8
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Tran, John C.;Zamdborg, Leonid;Ahlf, Dorothy R.;Lee, Ji Eun;Catherman, Adam D.;Durbin, Kenneth R.;Tipton, Jeremiah D.;Vellaichamy, Adaikkalam;Kellie, John F.;Li, Mingxi;Wu, Cong;Sweet, Steve M. M.;Early, Bryan P.;Siuti, Nertila;LeDuc, Richard D.;Compton, Philip D.;Thomas, Paul M.;Kelleher, Neil L.
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Kelleher, Neil L.
影响因子：
12.3
作者：
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通讯作者：
Pertea, Mihaela
影响因子：
12.3
作者：
Kim D;Pertea G;Trapnell C;Pimentel H;Kelley R;Salzberg SL
通讯作者：
Salzberg SL
DOI：
10.1073/pnas.1419161111
发表时间：
2014-12-23
影响因子：
11.1
作者：
Shen, Shihao;Park, Juw Won;Xing, Yi
通讯作者：
Xing, Yi