Metaproteomics allows to decipher the structure and functionality of microbial communities. Despite its rapid development, crucial steps such as the creation of standardized protein search databases and reliable protein annotation remain challenging. To overcome those critical steps, we developed a new program named mPies (metaProteomics in environmental sciences). mPies allows the creation of protein databases derived from assembled or unassembled metagenomes, and/or public repositories based on taxon IDs, gene or protein names. For the first time, mPies facilitates the automatization of reliable taxonomic and functional consensus annotations at the protein group level, minimizing the well-known protein inference issue, which is commonly encountered in metaproteomics. mPies' workflow is highly customizable with regards to input data, workflow steps, and parameter adjustment. mPies is implemented in Python 3/Snakemake and freely available on GitHub: https://github.com/johanneswerner/mPies/. REVIEWER: This article was reviewed by Dr. Wilson Wen Bin Goh.

中文翻译：

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mPies：一种新型的元蛋白质组学工具，用于创建相关的蛋白质数据库和自动化的蛋白质注释。

元蛋白质组学允许破译微生物群落的结构和功能。尽管其发展迅速，但关键步骤（如创建标准化蛋白质搜索数据库和可靠的蛋白质注释）仍然具有挑战性。为了克服这些关键步骤，我们开发了一个名为mPies（环境科学中的元蛋白质组学）的新程序。mPies允许基于分类群ID，基因或蛋白质名称创建由组装或未组装的元基因组和/或公共存储库衍生的蛋白质数据库。mPies首次在蛋白质组水平上促进了可靠的分类学和功能共识注释的自动化，从而最大程度地减少了在元蛋白质组学中经常遇到的众所周知的蛋白质推断问题。对于输入数据，mPies的工作流程是高度可定制的，工作流程步骤和参数调整。mPies在Python 3 / Snakemake中实现，可在GitHub上免费使用：https：//github.com/johanneswerner/mPies/。审稿人：本文由Wilson Wen Bin Goh博士审阅。