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 1H-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.

Details

Title
Protomix: a Python package for 1H-NMR metabolomics data preprocessing
Author
Zniber, Mohammed 1 ; Youssef Fatihi 2 ; Tan-Phat Huynh 1   VIAFID ORCID Logo 

1  Laboratory of Molecular Science and Engineering, Åbo Akademi University , Henrikinkatu 2, Turku 20500, Finland 
2  Department of Computer Science, Ibn Tofail University , Kenitra 14000, Morocco 
Publication year
2025
Publication date
2025
Publisher
Oxford University Press
e-ISSN
26350041
Source type
Scholarly Journal
Language of publication
English
DOI
https://doi.org/10.1093/bioadv/vbae192
ProQuest document ID
3191362943
Copyright
© The Author(s) 2024. Published by Oxford University Press. This work is published under http://creativecommons.org/licenses/by/4.0/ (the “License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.