Fitting Structure-Data Files (.SDF) Libraries to Progenesis QI Identification Searches

Progenesis QI (PQI) is a multiplatform bioinformatics tool that facilitates the identification workflow for metabolomics experiments. PQI uses fragmentation data provided by MassBank of North America (MoNA) libraries, among others, for metabolite annotation. However, PQI does not officially support MoNA libraries and other libraries based on structure-data files (.sdf). This paper describes the development and application of a software named MoNA to Progenesis QI Library Converter, allowing PQI and MoNA by correcting the fragmentation data of the library for Progenesis readability. We evaluated several public experimental datasets, including human plasma, plant extracts, cultured cells, bacteria, rat serum, and rat hippocampus. The results showed that it is mandatory to proceed with file conversion of each library to allow PQI to access fragmentation information from .msp (main spectra profile) files. This step is highly recommended to improve the identification level of the metabolites.Progenesis QI（PQI）是一款多平台生物信息学工具，可辅助代谢组学实验的化合物鉴定流程。PQI 依托北美质谱库（MassBank of North America, MoNA）等数据库提供的质谱碎裂数据开展代谢物注释工作。然而，PQI 官方并不支持 MoNA 数据库以及其他基于结构数据文件（.sdf）的数据库。本文介绍了一款名为“MoNA至Progenesis QI数据库转换器”的软件的开发与应用，该软件通过修正数据库的碎裂数据以适配PQI的读取规范，实现PQI与MoNA数据库的兼容。本研究评估了多套公开实验数据集，涵盖人类血浆、植物提取物、培养细胞、细菌、大鼠血清以及大鼠海马体样本。结果表明，必须对各数据库进行文件格式转换，才能使PQI读取.msp（质谱主谱文件，main spectra profile）中的碎裂信息。强烈建议执行该转换步骤，以提升代谢物的鉴定精度。