PubChemLite for Exposomics + predicted CCS from CCSbase - 5 Sept. 2025

PubChemLite is a subset of PubChem (https://pubchem.ncbi.nlm.nih.gov/) selected from major categories of the Table of Contents page at the PubChem Classification Browser (https://pubchem.ncbi.nlm.nih.gov/classification/#hid=72). This version of PubChemLite for Exposomics has predicted collision cross section (CCS) values for 11 adducts provided by Libin Xu and team at CCSbase (https://ccsbase.net/) calculated from the latest c3sdb code. PubChemLite exposomics is compiled from 11 categories: AgroChemInfo, BioPathway, DrugMedicInfo, FoodRelated, PharmacoInfo, SafetyInfo, ToxicityInfo, KnownUse, DisorderDisease, Identification, ChemClass. CCS adducts provided are: [M+H]+, [M-H]-, [M+Na]+, [M+K]+, [M+NH4]+, [M+H-H2O]+, [M+HCOO]-, [M+CH3COO]-, [M+Na-2H]-, [M]+, [M]- Details on the CCS prediction are given here: Ross et al. (2020) Analytical Chemistry, DOI: 10.1021/acs.analchem.9b05772 PubChemLite is described in Schymanski et al. (2021) J. Cheminformatics, DOI: 10.1186/s13321-021-00489-0 An article describing these joint efforts is available: Elapavalore et al. (2025) ES&T Letters, DOI: 10.1021/acs.estlett.4c01003 PubChemCIDs have been collapsed by InChIKey first block, reporting the structure from the most annotated CID, plus related CIDs. Entries that will be ignored by MetFrag (salts, disconnected substances) or cause errors (e.g. transition metals) have been removed. The Patent and PubMed ID counts are extracted from files on the PubChem FTP site. The "AnnoTypeCount" term counts how many of the categories are represented, the subsequent column (named per category) counts the number of annotation categories available in the next sub-category of the TOC entry. These files can be used "as is" as localCSV for MetFrag Command Line (https://ipb-halle.github.io/MetFrag/) - please do NOT upload these files directly to the web interface, they are too large and will be available in a drop-down menu. Further details are described in Schymanski et al. (2021) DOI:10.1186/s13321-021-00489-0 and Elapavalore et al. (2025) DOI: 10.1021/acs.estlett.4c01003 NOTE: The latest PubChemLite for Exposomics version can be downloaded at DOI:10.5281/zenodo.5995885 (currently updating monthly). This file will be updated shortly after. Please cite this data source and Elapavalore et al. (2025) DOI: 10.1021/acs.estlett.4c01003 when using this dataset.PubChemLite是PubChem（https://pubchem.ncbi.nlm.nih.gov/）的子集，其数据选自PubChem分类浏览器（PubChem Classification Browser，https://pubchem.ncbi.nlm.nih.gov/classification/#hid=72）目录页面的主要分类类别。本次发布的暴露组学专用PubChemLite包含由CCSbase（https://ccsbase.net/）的Libin Xu团队提供的11种加合物的预测碰撞截面（collision cross section, CCS）数值，这些数值基于最新的c3sdb代码计算得到。 暴露组学专用PubChemLite数据集包含11个类别的数据：AgroChemInfo、BioPathway、DrugMedicInfo、FoodRelated、PharmacoInfo、SafetyInfo、ToxicityInfo、KnownUse、DisorderDisease、Identification、ChemClass。 本次提供的CCS加合物包括：[M+H]+、[M-H]-、[M+Na]+、[M+K]+、[M+NH4]+、[M+H-H2O]+、[M+HCOO]-、[M+CH3COO]-、[M+Na-2H]-、[M]+、[M]-。 关于CCS预测的详细方法可参考：Ross等人（2020）发表于《Analytical Chemistry》的研究，DOI: 10.1021/acs.analchem.9b05772。 PubChemLite数据集的相关介绍可参见Schymanski等人（2021）发表于《Journal of Cheminformatics》的论文，DOI: 10.1186/s1332-021-00489-0。 关于本次联合研究的相关文章可参见：Elapavalore等人（2025）发表于《ES&T Letters》的研究，DOI: 10.1021/acs.estlett.4c01003。 PubChem化合物标识（CID）已通过InChIKey的第一个区块进行合并，以注释最丰富的CID的结构作为代表，并关联相关CID。已移除会被MetFrag忽略的条目（如盐类、非共价连接物质）或会引发错误的条目（如过渡金属）。专利与PubMed ID的统计信息提取自PubChem FTP站点的文件。其中"AnnoTypeCount"字段用于统计条目所归属的分类数量，后续以分类名称命名的列则用于统计目录条目下一子分类下可用的注释类别数目。 本数据集文件可直接用作MetFrag命令行工具（https://ipb-halle.github.io/MetFrag/）的本地CSV文件——请注意请勿直接将这些文件上传至网页端界面，因文件体积过大，它们将以下拉菜单的形式提供调用。 更多详细信息可参考Schymanski等人（2021，DOI:10.1186/s1332-021-00489-0）与Elapavalore等人（2025，DOI:10.1021/acs.estlett.4c01003）的相关研究。 注意：最新版暴露组学专用PubChemLite数据集可通过DOI:10.5281/zenodo.5995885下载（当前更新频率为每月一次），本文件将紧随其更新。 使用本数据集时，请引用该数据源及Elapavalore等人（2025，DOI:10.1021/acs.estlett.4c01003）的研究。