MetaboLabPy—An Open-Source Software Package for Metabolomics NMR Data Processing and Metabolic Tracer Data Analysis
<b>Introduction:</b> NMR spectroscopy is a powerful technique for studying metabolism, either in metabolomics settings or through tracing with stable isotope-enriched metabolic precursors. MetaboLabPy (version 0.9.66) is a free and open-source software package used to process 1D- and 2D-...
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| description | <b>Introduction:</b> NMR spectroscopy is a powerful technique for studying metabolism, either in metabolomics settings or through tracing with stable isotope-enriched metabolic precursors. MetaboLabPy (version 0.9.66) is a free and open-source software package used to process 1D- and 2D-NMR spectra. The software implements a complete workflow for NMR data pre-processing to prepare a series of 1D-NMR spectra for multi-variate statistical data analysis. This includes a choice of algorithms for automated phase correction, segmental alignment, spectral scaling, variance stabilisation, export to various software platforms, and analysis of metabolic tracing data. The software has an integrated help system with tutorials that demonstrate standard workflows and explain the capabilities of MetaboLabPy. <b>Materials and Methods:</b> The software is implemented in Python and uses numerous Python toolboxes, such as numpy, scipy, pandas, etc. The software is implemented in three different packages: metabolabpy, qtmetabolabpy, and metabolabpytools. The metabolabpy package contains classes to handle NMR data and all the numerical routines necessary to process and pre-process 1D NMR data and perform multiplet analysis on 2D-<sup>1</sup>H, <sup>13</sup>C HSQC NMR data. The qtmetabolabpy package contains routines related to the graphical user interface. <b>Results:</b> PySide6 is used to produce a modern and user-friendly graphical user interface. The metabolabpytools package contains routines which are not specific to just handling NMR data, for example, routines to derive isotopomer distributions from the combination of NMR multiplet and GC-MS data. A deep-learning approach for the latter is currently under development. MetaboLabPy is available via the Python Package Index or via GitHub. |
| format | Article |
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| institution | Kabale University |
| issn | 2218-1989 |
| language | English |
| publishDate | 2025-01-01 |
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| spelling | doaj-art-cc61795a936f4d998a6658fa23996ed12025-01-24T13:41:17ZengMDPI AGMetabolites2218-19892025-01-011514810.3390/metabo15010048MetaboLabPy—An Open-Source Software Package for Metabolomics NMR Data Processing and Metabolic Tracer Data AnalysisChristian Ludwig0Department of Metabolism and Systems Sciences, School of Medical Sciences, College of Medicine and Health, University of Birmingham, Birmingham B15 2TT, UK<b>Introduction:</b> NMR spectroscopy is a powerful technique for studying metabolism, either in metabolomics settings or through tracing with stable isotope-enriched metabolic precursors. MetaboLabPy (version 0.9.66) is a free and open-source software package used to process 1D- and 2D-NMR spectra. The software implements a complete workflow for NMR data pre-processing to prepare a series of 1D-NMR spectra for multi-variate statistical data analysis. This includes a choice of algorithms for automated phase correction, segmental alignment, spectral scaling, variance stabilisation, export to various software platforms, and analysis of metabolic tracing data. The software has an integrated help system with tutorials that demonstrate standard workflows and explain the capabilities of MetaboLabPy. <b>Materials and Methods:</b> The software is implemented in Python and uses numerous Python toolboxes, such as numpy, scipy, pandas, etc. The software is implemented in three different packages: metabolabpy, qtmetabolabpy, and metabolabpytools. The metabolabpy package contains classes to handle NMR data and all the numerical routines necessary to process and pre-process 1D NMR data and perform multiplet analysis on 2D-<sup>1</sup>H, <sup>13</sup>C HSQC NMR data. The qtmetabolabpy package contains routines related to the graphical user interface. <b>Results:</b> PySide6 is used to produce a modern and user-friendly graphical user interface. The metabolabpytools package contains routines which are not specific to just handling NMR data, for example, routines to derive isotopomer distributions from the combination of NMR multiplet and GC-MS data. A deep-learning approach for the latter is currently under development. MetaboLabPy is available via the Python Package Index or via GitHub.https://www.mdpi.com/2218-1989/15/1/48NMRmetabolomicstracingstable isotopedeep learningPython |
| spellingShingle | Christian Ludwig MetaboLabPy—An Open-Source Software Package for Metabolomics NMR Data Processing and Metabolic Tracer Data Analysis Metabolites NMR metabolomics tracing stable isotope deep learning Python |
| title | MetaboLabPy—An Open-Source Software Package for Metabolomics NMR Data Processing and Metabolic Tracer Data Analysis |
| title_full | MetaboLabPy—An Open-Source Software Package for Metabolomics NMR Data Processing and Metabolic Tracer Data Analysis |
| title_fullStr | MetaboLabPy—An Open-Source Software Package for Metabolomics NMR Data Processing and Metabolic Tracer Data Analysis |
| title_full_unstemmed | MetaboLabPy—An Open-Source Software Package for Metabolomics NMR Data Processing and Metabolic Tracer Data Analysis |
| title_short | MetaboLabPy—An Open-Source Software Package for Metabolomics NMR Data Processing and Metabolic Tracer Data Analysis |
| title_sort | metabolabpy an open source software package for metabolomics nmr data processing and metabolic tracer data analysis |
| topic | NMR metabolomics tracing stable isotope deep learning Python |
| url | https://www.mdpi.com/2218-1989/15/1/48 |
| work_keys_str_mv | AT christianludwig metabolabpyanopensourcesoftwarepackageformetabolomicsnmrdataprocessingandmetabolictracerdataanalysis |