{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"bioRxiv"}],"indexed":{"date-parts":[[2026,1,15]],"date-time":"2026-01-15T21:25:29Z","timestamp":1768512329415,"version":"3.49.0"},"posted":{"date-parts":[[2024,7,13]]},"group-title":"Systems Biology","reference-count":35,"publisher":"openRxiv","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2024,7,13]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                <jats:p>\n                  Annotating compounds with high confidence is a critical element in metabolomics.\n                  <jats:sup>13<\/jats:sup>\n                  C-detection NMR experiment INADEQUATE (incredible natural abundance double-quantum transfer experiment) stands out as a powerful tool for structural elucidation, whereas this valuable experiment is not often included in metabolomics studies. This is partly due to the lack of community platform that provides structural information based 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 and other NMR experiments either. Here, we introduce PyINETA, Python-based INADEQUATE network analysis. PyINETA is an open-source platform that provides structural information of molecules using INADEQUATE, conducts database search, and integrates information of INADEQUATE and a complementary NMR experiment\n                  <jats:sup>13<\/jats:sup>\n                  C\n                  <jats:italic>J<\/jats:italic>\n                  -resolved experiment (\n                  <jats:sup>13<\/jats:sup>\n                  C-JRES). 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 our pipeline successfully integrated INADEQUATE and\n                  <jats:sup>13<\/jats:sup>\n                  C-JRES. The results showed that\n                  <jats:sup>13<\/jats:sup>\n                  C-labeled amino acids that were fed to mice were transferred to different tissues, and, also, they were transformed to other metabolites. The distribution of those compounds was tissue-specific, showing enrichment of particular metabolites in liver, spleen, pancreas, muscle, or lung. The value of PyINETA was not limited to those known compounds; PyINETA also provided fragment information for unknown compounds. PyINETA is available on NMRbox.\n                <\/jats:p>","DOI":"10.1101\/2024.07.10.601875","type":"posted-content","created":{"date-parts":[[2024,7,13]],"date-time":"2024-07-13T22:05:15Z","timestamp":1720908315000},"source":"Crossref","is-referenced-by-count":0,"title":["PyINETA: Open-source platform for INADEQUATE-JRES integration in NMR metabolomics"],"prefix":"10.64898","author":[{"given":"Rahil","family":"Taujale","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mario","family":"Uchimiya","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Chaevien S.","family":"Clendinen","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ricardo M.","family":"Borges","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Christoph W.","family":"Turck","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Arthur S.","family":"Edison","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"54368","reference":[{"issue":"1","key":"2024071612301322000_2024.07.10.601875v1.1","doi-asserted-by":"crossref","first-page":"47","DOI":"10.1021\/ac403520j","article-title":"Multidimensional approaches to NMR-based metabolomics","volume":"86","year":"2014","journal-title":"Anal Chem"},{"key":"2024071612301322000_2024.07.10.601875v1.2","doi-asserted-by":"publisher","DOI":"10.1021\/acs.analchem.6b03724"},{"issue":"47","key":"2024071612301322000_2024.07.10.601875v1.3","doi-asserted-by":"crossref","first-page":"16308","DOI":"10.1021\/acs.analchem.2c02902","article-title":"Leveraging the HMBC to Facilitate Metabolite Identification","volume":"94","year":"2022","journal-title":"Anal Chem"},{"key":"2024071612301322000_2024.07.10.601875v1.4","doi-asserted-by":"crossref","first-page":"69","DOI":"10.1007\/978-1-4939-9690-2_5","article-title":"Practical guidelines for 13C-based NMR metabolomics","volume":"2037","year":"2019","journal-title":"Methods Mol Biol"},{"key":"2024071612301322000_2024.07.10.601875v1.5","first-page":"611","article-title":"An overview of methods using 13C for improved compound identification in metabolomics and natural products","volume":"6","year":"2015","journal-title":"Front Plant Sci"},{"issue":"18","key":"2024071612301322000_2024.07.10.601875v1.6","doi-asserted-by":"crossref","first-page":"9242","DOI":"10.1021\/ac502346h","article-title":"13C NMR metabolomics: Applications at natural abundance","volume":"86","year":"2014","journal-title":"Anal Chem"},{"issue":"21","key":"2024071612301322000_2024.07.10.601875v1.7","doi-asserted-by":"crossref","first-page":"9006","DOI":"10.1021\/ja3033058","article-title":"Carbon backbone topology of the metabolome of a cell","volume":"134","year":"2012","journal-title":"J Am Chem Soc"},{"issue":"11","key":"2024071612301322000_2024.07.10.601875v1.8","doi-asserted-by":"crossref","first-page":"5698","DOI":"10.1021\/acs.analchem.5b00867","article-title":"13C NMR metabolomics: INADEQUATE network Analysis","volume":"87","year":"2015","journal-title":"Anal Chem"},{"key":"2024071612301322000_2024.07.10.601875v1.9","doi-asserted-by":"publisher","DOI":"10.1021\/ja00534a056"},{"key":"2024071612301322000_2024.07.10.601875v1.10","doi-asserted-by":"publisher","DOI":"10.1021\/ac4007254"},{"key":"2024071612301322000_2024.07.10.601875v1.11","doi-asserted-by":"crossref","unstructured":"Uchimiya, M. ; Olofsson, M. ; Powers, M. 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