Elapavalore Anjana, Ross Dylan H, Grouès Valentin, Aurich Dagny, Krinsky Allison M, Kim Sunghwan, Thiessen Paul A, Zhang Jian, Dodds James N, Baker Erin S, Bolton Evan E, Xu Libin, Schymanski Emma L
Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 6 Avenue du Swing, 4367 Belvaux, Luxembourg.
Department of Medicinal Chemistry, University of Washington, Seattle, Washington 98195, United States.
Environ Sci Technol Lett. 2025 Jan 24;12(2):166-174. doi: 10.1021/acs.estlett.4c01003. eCollection 2025 Feb 11.
Finding relevant chemicals in the vast (known) chemical space is a major challenge for environmental and exposomics studies leveraging nontarget high resolution mass spectrometry (NT-HRMS) methods. Chemical databases now contain hundreds of millions of chemicals, yet many are not relevant. This article details an extensive collaborative, open science effort to provide a dynamic collection of chemicals for environmental, metabolomics, and exposomics research, along with supporting information about their relevance to assist researchers in the interpretation of candidate hits. The PubChemLite for Exposomics collection is compiled from ten annotation categories within PubChem, enhanced with patent, literature and annotation counts, predicted partition coefficient (logP) values, as well as predicted collision cross section (CCS) values using CCSbase. Monthly versions are archived on Zenodo under a CC-BY license, supporting reproducible research, and a new interface has been developed, including historical trends of patent and literature data, for researchers to browse the collection. This article details how PubChemLite can support researchers in environmental and exposomics studies, describes efforts to increase the availability of experimental CCS values, and explores known limitations and potential for future developments. The data and code behind these efforts are openly available. PubChemLite can be browsed at https://pubchemlite.lcsb.uni.lu.
在利用非靶向高分辨率质谱（NT-HRMS）方法进行的环境和暴露组学研究中，在广阔的（已知）化学空间中找到相关化学物质是一项重大挑战。化学数据库现在包含数亿种化学物质，但许多并不相关。本文详细介绍了一项广泛的合作性开放科学工作，旨在为环境、代谢组学和暴露组学研究提供一个动态的化学物质集合，以及关于它们相关性的支持信息，以帮助研究人员解释候选命中物。暴露组学专用的PubChemLite集合是从PubChem中的十个注释类别编译而来的，通过专利、文献和注释计数、预测的分配系数（logP）值以及使用CCSbase预测的碰撞截面（CCS）值进行了增强。每月版本在CC-BY许可下存档于Zenodo，支持可重复研究，并且已经开发了一个新界面，包括专利和文献数据的历史趋势，供研究人员浏览该集合。本文详细介绍了PubChemLite如何支持环境和暴露组学研究中的研究人员，描述了增加实验性CCS值可用性的努力，并探讨了已知的局限性和未来发展的潜力。这些努力背后的数据和代码是公开可用的。可在https://pubchemlite.lcsb.uni.lu浏览PubChemLite。
