PyINETA: Open-Source Platform for INADEQUATE-JRES Integration in NMR Metabolomics

• Published in: Analytical chemistry (Washington) 2024-12, Vol.96 (48), p.19029-19037
• Main Authors: Taujale, Rahil, Uchimiya, Mario, Clendinen, Chaevien S., Borges, Ricardo M., Turck, Christoph W., Edison, Arthur S.
• Format: Article
• Language: English
• Subjects: Amino acids; Animals; Annotations; Carbon Isotopes - chemistry; Carbon Isotopes - metabolism; Experiments; Information processing; Magnetic Resonance Spectroscopy - methods; Metabolites; Metabolomics; Metabolomics - methods; Mice; Network analysis; NMR; Nuclear magnetic resonance; Open source software; Python; Software
• ISSN: 0003-2700; 1520-6882; 1520-6882
• DOI: 10.1021/acs.analchem.4c03966

Robust annotation of compounds is a critical element in metabolomics. The 13C-detection NMR experiment incredible natural abundance double-quantum transfer experiment (INADEQUATE) stands out as a powerful tool for structural elucidation, but this valuable experiment is not often included in metabolomics studies. This is partly due to the lack of a community platform that provides structural information based on INADEQUATE. Also, it is often the case that a single study uses various NMR experiments synergistically to improve the quality of information or balance total NMR experiment time, but there is no public platform that can integrate the outputs of INADEQUATE with other NMR experiments. Here, we introduce PyINETA, a Python-based INADEQUATE network analysis. PyINETA is an open-source platform that provides structural information on molecules using INADEQUATE, conducts database searches using an INADEQUATE library, and integrates information on INADEQUATE and a complementary NMR experiment 13C J-resolved experiment (13C-JRES). 13C-JRES was chosen because of its ability to efficiently provide relative quantification in a study of the 13C-enriched samples. Those steps are carried out automatically, and PyINETA keeps track of all the pipeline parameters and outputs, ensuring the transparency of annotation in metabolomics. Our evaluation of PyINETA using a model mouse study showed that PyINETA successfully integrated INADEQUATE and 13C-JRES. The results showed that 13C-labeled amino acids that were fed to mice were transferred to different tissues and were transformed to other metabolites. The distribution of those compounds was tissue-specific, showing enrichment of specific metabolites in the liver, spleen, pancreas, muscle, or lung. PyINETA is freely available on NMRbox.