Protomix：一个用于氢核磁共振代谢组学数据预处理的Python软件包。

Protomix: a Python package for H-NMR metabolomics data preprocessing.

作者信息

Zniber Mohammed, Fatihi Youssef, Huynh Tan-Phat

机构信息

Laboratory of Molecular Science and Engineering, Åbo Akademi University, Henrikinkatu 2, Turku 20500, Finland.

Department of Computer Science, Ibn Tofail University, Kenitra 14000, Morocco.

出版信息

Bioinform Adv. 2024 Nov 27;5(1):vbae192. doi: 10.1093/bioadv/vbae192. eCollection 2025.

DOI:10.1093/bioadv/vbae192

PMID:39735575

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC11671038/

Abstract

MOTIVATION

NMR-based metabolomics is a field driven by technological advancements, necessitating the use of advanced preprocessing tools. Despite this need, there is a remarkable scarcity of comprehensive and user-friendly preprocessing tools in Python. To bridge this gap, we have developed Protomix-a Python package designed for metabolomics research. Protomix offers a set of automated, efficient, and user-friendly signal-preprocessing steps, tailored to streamline and enhance the preprocessing phase in metabolomics studies.

RESULTS

This package presents a comprehensive preprocessing pipeline compatible with various data analysis tools. It encompasses a suite of functionalities for data extraction, preprocessing, and interactive visualization. Additionally, it includes a tutorial in the form of a Python Jupyter notebook, specifically designed for the analysis of 1D H-NMR metabolomics data related to prostate cancer and benign prostatic hyperplasia.

AVAILABILITY AND IMPLEMENTATION

Protomix can be accessed at https://github.com/mzniber/protomix and https://protomix.readthedocs.io/en/latest/index.html.

摘要

动机

基于核磁共振的代谢组学是一个由技术进步驱动的领域，需要使用先进的预处理工具。尽管有此需求，但Python中全面且用户友好的预处理工具却极为匮乏。为了填补这一空白，我们开发了Protomix——一个专为代谢组学研究设计的Python软件包。Protomix提供了一套自动化、高效且用户友好的信号预处理步骤，旨在简化和加强代谢组学研究中的预处理阶段。