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

IF 1.3 4区化学 Q3 CHEMISTRY, MULTIDISCIPLINARY

Journal of the Brazilian Chemical Society Pub Date : 2023-06-23 DOI:10.21577/0103-5053.20230016

P. Sanches, Danilo de Oliveira, Ivan dos Reis, A. Fernandes, Alex Silva, Marcos Eberlin, P. Carvalho, Gustavo Duarte, A. Porcari

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引用次数: 0

Abstract

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.

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将结构数据文件（.SDF）库与进化QI标识搜索拟合

Progenesis QI (PQI)是一个多平台的生物信息学工具，促进了代谢组学实验的鉴定工作流程。PQI使用北美MassBank (MoNA)库提供的碎片化数据进行代谢物注释。但是，PQI并不正式支持MoNA库和其他基于结构数据文件(.sdf)的库。本文介绍了一个名为MoNA的软件在Progenesis QI库转换器中的开发和应用，该软件通过校正库的碎片数据来实现PQI和MoNA，以提高Progenesis的可读性。我们评估了几个公开的实验数据集，包括人血浆、植物提取物、培养细胞、细菌、大鼠血清和大鼠海马。结果表明，为了使PQI能够从.msp(主谱文件)文件中访问碎片信息，必须对每个库进行文件转换。这一步骤被强烈推荐用于提高代谢物的鉴定水平。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Journal of the Brazilian Chemical Society 化学-化学综合

CiteScore

2.90

自引率

7.10%

发文量

审稿时长

3.4 months

期刊介绍： The Journal of the Brazilian Chemical Society embraces all aspects of chemistry except education, philosophy and history of chemistry. It is a medium for reporting selected original and significant contributions to new chemical knowledge.