PPIP: Automated Software for Identification of Bioactive Endogenous Peptides

Endogenous peptides play an important role in multiple biological processes in many species. Liquid chromatography coupled to tandem mass spectrometry (LC–MS/MS) is an important technique for detecting these peptides on a large scale. We present PPIP, which is a dedicated peptidogenomics software for identifying endogenous peptides based on peptidomics and RNA-Seq data. This software automates the de novo transcript assembly based on RNA-Seq data, construction of a protein reference database based on the de novo assembled transcripts, peptide identification, function analysis, and HTML-based report generation. Different function components are integrated using Docker technology. The Docker image of PPIP is available at https://hub.docker.com/r/shawndp/ppip, and the source code under GPL-3 license is available at https://github.com/Shawn-Xu/PPIP. A user manual of PPIP is available at https://shawn-xu.github.io/PPIP.内源性肽（Endogenous peptides）在诸多物种的多种生物学过程中发挥着重要作用。液相色谱-串联质谱联用技术（Liquid chromatography coupled to tandem mass spectrometry, LC–MS/MS）是大规模检测此类肽类的关键实验技术。本研究推出PPIP，这是一款专为基于肽组学（peptidomics）与RNA测序（RNA-Seq）数据鉴定内源性肽而开发的专用肽基因组学软件。该软件可自动化完成基于RNA-Seq数据的从头转录本组装、基于从头组装转录本的蛋白质参考数据库构建、肽段鉴定、功能分析以及基于HTML格式的报告生成全流程。软件的各项功能组件均通过Docker技术实现集成。PPIP的Docker镜像可从https://hub.docker.com/r/shawndp/ppip获取，遵循GPL-3开源许可协议的源代码可从https://github.com/Shawn-Xu/PPIP获取，其用户手册则可通过https://shawn-xu.github.io/PPIP查阅。