Critical steps in an environmental metaproteomics workflow,Environmental Microbiology

当前位置： X-MOL 学术 › Environ. Microbiol. › 论文详情

Our official English website, www.x-mol.net, welcomes your feedback! (Note: you will need to create a separate account there.)

Critical steps in an environmental metaproteomics workflow
Environmental Microbiology ( IF 4.3 ) Pub Date : 2024-05-18 , DOI: 10.1111/1462-2920.16637
Daniel J Nebauer _{1,

2} , Leanne A Pearson _{1,

2} , Brett A Neilan _{1,

2}

Affiliation

Environmental metaproteomics is a rapidly advancing field that provides insights into the structure, dynamics, and metabolic activity of microbial communities. As the field is still maturing, it lacks consistent workflows, making it challenging for non‐expert researchers to navigate. This review aims to introduce the workflow of environmental metaproteomics. It outlines the standard practices for sample collection, processing, and analysis, and offers strategies to overcome the unique challenges presented by common environmental matrices such as soil, freshwater, marine environments, biofilms, sludge, and symbionts. The review also highlights the bottlenecks in data analysis that are specific to metaproteomics samples and provides suggestions for researchers to obtain high‐quality datasets. It includes recent benchmarking studies and descriptions of software packages specifically built for metaproteomics analysis. The article is written without assuming the reader's familiarity with single‐organism proteomic workflows, making it accessible to those new to proteomics or mass spectrometry in general. This primer for environmental metaproteomics aims to improve accessibility to this exciting technology and empower researchers to tackle challenging and ambitious research questions. While it is primarily a resource for those new to the field, it should also be useful for established researchers looking to streamline or troubleshoot their metaproteomics experiments.

中文翻译：

环境宏蛋白质组学工作流程中的关键步骤

环境宏蛋白质组学是一个快速发展的领域，它提供了对微生物群落的结构、动态和代谢活动的见解。由于该领域仍处于成熟阶段，因此缺乏一致的工作流程，这使得非专业研究人员难以驾驭。本综述旨在介绍环境宏蛋白质组学的工作流程。它概述了样品采集、处理和分析的标准实践，并提供了克服常见环境基质（如土壤、淡水、海洋环境、生物膜、污泥和共生体）所带来的独特挑战的策略。该综述还强调了宏蛋白质组样本特有的数据分析瓶颈，并为研究人员获得高质量数据集提供了建议。它包括最近的基准测试研究和专为宏蛋白质组分析而构建的软件包的描述。本文的撰写并未假设读者熟悉单一生物体蛋白质组学工作流程，因此一般来说，蛋白质组学或质谱学的新手也可以轻松理解。这本环境宏蛋白质组学入门书旨在提高这项令人兴奋的技术的可及性，并使研究人员能够解决具有挑战性和雄心勃勃的研究问题。虽然它主要是为该领域的新手提供的资源，但对于寻求简化宏蛋白质组学实验或解决其问题的知名研究人员来说，它也应该很有用。

更新日期：2024-05-18

点击分享查看原文

点击收藏

公开下载

阅读更多本刊新发论文本刊介绍/投稿指南