{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,30]],"date-time":"2026-07-30T12:45:53Z","timestamp":1785415553905,"version":"3.56.0"},"reference-count":35,"publisher":"MDPI AG","issue":"4","license":[{"start":{"date-parts":[[2026,4,17]],"date-time":"2026-04-17T00:00:00Z","timestamp":1776384000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100007129","name":"Natural Science Foundation of Shandong Province","doi-asserted-by":"crossref","award":["ZR2024MH003"],"award-info":[{"award-number":["ZR2024MH003"]}],"id":[{"id":"10.13039\/501100007129","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100007129","name":"Natural Science Foundation of Shandong Province","doi-asserted-by":"crossref","award":["ZR2020QH323"],"award-info":[{"award-number":["ZR2020QH323"]}],"id":[{"id":"10.13039\/501100007129","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["82003917"],"award-info":[{"award-number":["82003917"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"award":["82003917"],"award-info":[{"award-number":["82003917"]}],"id":[{"id":"https:\/\/ror.org\/01h0zpd94","id-type":"ROR","asserted-by":"publisher"}]},{"name":"Shandong Province Higher Education Institutions Youth Creative Technology Support Program","award":["2023KJ190"],"award-info":[{"award-number":["2023KJ190"]}]},{"name":"2025 Shandong Provincial Key R&D Program","award":["2025CXGC020304"],"award-info":[{"award-number":["2025CXGC020304"]}]},{"name":"Jinan Municipal School-Enterprise Integration Development Strategic Engineering Project","award":["JNSX2024018"],"award-info":[{"award-number":["JNSX2024018"]}]},{"name":"General Project of Shandong Provincial Traditional Chinese Medicine Science and Technology Program","award":["M20251722"],"award-info":[{"award-number":["M20251722"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Metabolites"],"abstract":"<jats:p>Background: Radish seeds are our model on glucosinolates (GSLs), which is a class of secondary metabolites in medicinal plants of the Brassicaceae family. Multilayer perceptron (MLP) network is highly effective in the study of complex plants. This study came up with a smart plan through the Python language. Methods: First, we used the MLP network to pick out GSL precursor ions, running them through a deep learning filter. Next, we set up an automated screening system and looked at how standard chemicals break down. To speed things up, we created a scoring system that flagged promising compounds. After that, we built a tracer molecular network, basically connecting compounds according to how the plant makes them, which helped us label everything accurately. Finally, we brought in a math-based tool that pieces together different chemical parts to predict new GSL structures. Results: With this workflow, we annotated 195 glucosinolate-related compounds in radish seeds. That includes 86 regular GSLs, 34 malonyl products, 40 sinapoyl compounds, and 35 diglycosides. Among them, eight compounds were confirmed by comparison with authentic standards (retention time and MS\/MS data), whereas the remaining compounds were tentatively annotated based on accurate mass measurements, diagnostic fragment ions, Tracer Molecular Nnetworking, and literature\/database matching. In addition, 36 compounds were considered putatively novel derivatives pending further structural confirmation. Conclusions: This new approach reduces the time spent on determining chemicals in complicated samples. This can be done with other vegetables and medicinal herbs by researchers. It assists us in knowing the chemistry of plants in a deeper manner.<\/jats:p>","DOI":"10.3390\/metabo16040274","type":"journal-article","created":{"date-parts":[[2026,4,17]],"date-time":"2026-04-17T14:24:51Z","timestamp":1776435891000},"page":"274","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Deep Learning-Based and Python-Driven Construction and Application of a Mass Spectrometry Data Analysis Workflow: Taking Glucosinolates as an Example"],"prefix":"10.3390","volume":"16","author":[{"given":"Shangshen","family":"Yang","sequence":"first","affiliation":[{"name":"Innovation Institute of Chinese Medicine and Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan 250355, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Siyu","family":"Jia","sequence":"additional","affiliation":[{"name":"Innovation Institute of Chinese Medicine and Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan 250355, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Peiyu","family":"Jia","sequence":"additional","affiliation":[{"name":"Grade 2023 of Academy of Basic Medicine, Jining Medical University, Jining 272000, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wenyu","family":"Xie","sequence":"additional","affiliation":[{"name":"Innovation Institute of Chinese Medicine and Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan 250355, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiaoming","family":"Wang","sequence":"additional","affiliation":[{"name":"Experimental Center, Shandong University of Traditional Chinese Medicine, Jinan 250355, China"},{"name":"Shandong Key Laboratory of Digital Traditional Chinese Medicine, Jinan 250355, China"},{"name":"Shandong Province Cardiovascular Disease TCM Precision Treatment Engineering Research Centre, Jinan 250355, China"},{"name":"Key Laboratory of Traditional Chinese Medicine Classical Theory, Ministry of Education, Jinan 250355, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,4,17]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"112873","DOI":"10.1016\/j.foodres.2023.112873","article-title":"Identification of glucosinolates and volatile odor compounds in microwaved radish (Raphanus sativus L.) seeds and the corresponding oils by UPLC-IMS-QTOF-MS and GC \u00d7 GC-qMS analysis","volume":"169","author":"Jia","year":"2023","journal-title":"Food Res. Int."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"136864","DOI":"10.1016\/j.foodchem.2023.136864","article-title":"Micro-grinding\u2013based production for sulforaphene-enriched radish seeds extract via facilitating glucosinolates-myrosinase reaction, and evaluation of its anti-adipogenic effects","volume":"429","author":"Lee","year":"2023","journal-title":"Food Chem."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"134088","DOI":"10.1016\/j.foodchem.2022.134088","article-title":"Effect of LED lights on the growth, nutritional quality and glucosinolate content of broccoli, cabbage and radish microgreens","volume":"401","author":"Demir","year":"2023","journal-title":"Food Chem."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"5","DOI":"10.1016\/S0031-9422(00)00316-2","article-title":"The chemical diversity and distribution of glucosinolates and isothiocyanates among plants","volume":"56","author":"Fahey","year":"2001","journal-title":"Phytochemistry"},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"16","DOI":"10.1016\/j.phytochem.2012.02.005","article-title":"Glucosinolate structures in evolution","volume":"77","author":"Agerbirk","year":"2012","journal-title":"Phytochemistry"},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"112100","DOI":"10.1016\/j.phytochem.2019.112100","article-title":"Glucosinolate structural diversity, identification, chemical synthesis and metabolism in plants","volume":"169","author":"Montaut","year":"2020","journal-title":"Phytochemistry"},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"10","DOI":"10.1016\/j.phytochem.2011.01.034","article-title":"Isoferuloyl derivatives of five seed glucosinolates in the crucifer genus Barbarea","volume":"72","author":"Agerbirk","year":"2011","journal-title":"Phytochemistry"},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"103904","DOI":"10.1016\/j.jfca.2021.103904","article-title":"Irrigation timing as a glucosinolate alteration factor in radish (Raphanus sativus L.) (Gya Labuk and Tsentay Labuk) in the Indian Trans-Himalayan region of Ladakh","volume":"100","author":"Chorol","year":"2021","journal-title":"J. Food Compos. Anal."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"104270","DOI":"10.1016\/j.jff.2020.104270","article-title":"Glucosinolate-rich hydrolyzed extract from Moringa oleifera leaves decreased the production of TNF-\u03b1 and IL-1\u03b2 cytokines and induced ROS and apoptosis in human colon cancer cells","volume":"75","author":"Berhow","year":"2020","journal-title":"J. Funct. Foods"},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"118","DOI":"10.1016\/j.tox.2011.09.034","article-title":"The chemopreventive properties of cruciferous vegetables: Is oxidative stress in cancer cell cytotoxicity induced by glucosinolate hydrolysis products?","volume":"290","author":"Kadir","year":"2011","journal-title":"Toxicology"},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"1164","DOI":"10.1016\/j.foodchem.2010.11.152","article-title":"Glucosinolates fortification of cruciferous sprouts by sulphur supplementation during cultivation to enhance anti-cancer activity","volume":"126","author":"Kestwal","year":"2011","journal-title":"Food Chem."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"134965","DOI":"10.1016\/j.foodchem.2022.134965","article-title":"Correlations between flavor and glucosinolates and changes in quality-related physiochemical characteristics of Guizhou suancai during the fermentation process","volume":"405","author":"Di","year":"2023","journal-title":"Food Chem."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"5399","DOI":"10.1021\/acs.analchem.3c05057","article-title":"Advancing Natural Product Discovery: A Structure-Oriented Fractions Screening Platform for Compound Annotation and Isolation","volume":"96","author":"Ge","year":"2024","journal-title":"Anal. Chem."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"117478","DOI":"10.1016\/j.trac.2023.117478","article-title":"Best practices in NMR metabolomics: Current state","volume":"171","author":"Powers","year":"2024","journal-title":"Trends Analyt Chem."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"1459","DOI":"10.1039\/D4NP00065J","article-title":"Exploring microbial natural products through NMR-based metabolomics","volume":"42","author":"Wang","year":"2025","journal-title":"Nat. Prod. Rep."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"115120","DOI":"10.1016\/j.microc.2025.115120","article-title":"Comprehensive antioxidant profiling and TAC determination in Stevia rebaudiana leaves using on-line HPLC\u2013CUPRAC: Evaluation of three different post-column derivatization reactor workflows","volume":"217","author":"Acquaviva","year":"2025","journal-title":"Microchem. J."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"5465","DOI":"10.1007\/s00216-019-01920-0","article-title":"Preparation of a new benzylureido-\u03b2-cyclodextrin-based column and its application for the determination of phenylmercapturic acid and benzylmercapturic acid enantiomers in human urine by LC\/MS\/MS","volume":"411","author":"Li","year":"2019","journal-title":"Anal. Bioanal. Chem."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"116954","DOI":"10.1016\/j.trac.2023.116954","article-title":"Advances in high throughput LC\/MS based metabolomics: A review","volume":"160","author":"Plumb","year":"2023","journal-title":"Trends Analyt Chem."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"123803","DOI":"10.1016\/j.talanta.2022.123803","article-title":"Comparison of two azobenzene-based amino acid derivatization reagents for LC-MS\/MS analysis in positive and negative ESI modes","volume":"252","author":"Selberg","year":"2023","journal-title":"Talanta"},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"114780","DOI":"10.1016\/j.microc.2025.114780","article-title":"Comprehensive analytical approaches: The use of LC-MS and IC-MS in modern pharmaceutical and biomedical sciences","volume":"216","author":"Kaddah","year":"2025","journal-title":"Microchem. J."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"104298","DOI":"10.1016\/j.tifs.2023.104298","article-title":"Analytical opportunities and challenges for data handling with chemometrics strategies from LC-MS based food metabolomics","volume":"143","author":"Qin","year":"2024","journal-title":"Trends Food Sci. Tech."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"5085","DOI":"10.1016\/j.csbj.2022.09.004","article-title":"Strategies for structure elucidation of small molecules based on LC\u2013MS\/MS data from complex biological samples","volume":"20","author":"Tian","year":"2022","journal-title":"Comput. Struct. Biotechnol."},{"key":"ref_23","first-page":"900","article-title":"Advances in intelligent mass spectrometry data processing technology for in vivo analysis of natural medicines","volume":"22","author":"Chen","year":"2024","journal-title":"Chin. J. Nat. Med."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"465226","DOI":"10.1016\/j.chroma.2024.465226","article-title":"Advances in analytical technologies for emerging drug modalities and their separation challenges in LC-MS systems","volume":"1732","author":"Malarvannan","year":"2024","journal-title":"J. Chromatogr. A"},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"47","DOI":"10.1016\/j.jmsacl.2023.02.003","article-title":"Small molecule biomarker discovery: Proposed workflow for LC-MS-based clinical research projects","volume":"28","author":"Rischke","year":"2023","journal-title":"J. Mass. Spectrom. Adv. Clin. Lab."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"10985","DOI":"10.1021\/acs.jafc.4c12650","article-title":"Characterization, Target Isolation of Triterpenes in the Anti-inflammatory Fraction of Salvia rosmarinus via UPLC-Orbitrap MS\/MS Coupled with GNPS","volume":"73","author":"Xu","year":"2025","journal-title":"J. Agric. Food Chem."},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"1735","DOI":"10.1039\/D3NP00025G","article-title":"Machine learning-assisted structure annotation of natural products based on MS and NMR data","volume":"40","author":"Hu","year":"2023","journal-title":"Nat. Prod. Rep."},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"118243","DOI":"10.1016\/j.trac.2025.118243","article-title":"Application of machine learning in LC-MS-based non-targeted analysis","volume":"189","author":"Jin","year":"2025","journal-title":"TrAC Trends Anal. Chem."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"116034","DOI":"10.1016\/j.microc.2025.116034","article-title":"Modern analytical technology combined with machine learning to advance the genus Dendrobium Sw research: Current trends and future directions","volume":"219","author":"Ma","year":"2025","journal-title":"Microchem. J."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"1388","DOI":"10.1016\/j.jpha.2023.07.012","article-title":"Recent trends of machine learning applied to multi-source data of medicinal plants","volume":"13","author":"Zhang","year":"2023","journal-title":"J. Pharm. Anal."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"1671","DOI":"10.1016\/j.phytochem.2008.02.010","article-title":"Class targeted metabolomics: ESI ion trap screening methods for glucosinolates based on MSn fragmentation","volume":"69","author":"Rochfort","year":"2008","journal-title":"Phytochemistry"},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"792","DOI":"10.1016\/j.talanta.2017.12.019","article-title":"Chromatographic column evaluation for the untargeted profiling of glucosinolates in cauliflower by means of ultra-high performance liquid chroma-tography coupled to high resolution mass spectrometry","volume":"179","author":"Capriotti","year":"2018","journal-title":"Talanta"},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"115387","DOI":"10.1016\/j.jep.2022.115387","article-title":"Traditional uses, phytochemistry, transformation of ingredients and pharmacology of the dried seeds of Raphanus sativus L. (Raphani Semen), A comprehensive review","volume":"294","author":"Gao","year":"2022","journal-title":"J. Ethnopharmacol."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"7474","DOI":"10.1021\/jf301294h","article-title":"Investigation of Glucosinolate Profile and Qualitative Aspects in Sprouts and Roots of Horseradish (Armoracia rusticana) Using LC-ESI\u2013Hybrid Linear Ion Trap with Fourier Transform Ion Cyclotron Resonance Mass Spectrometry and Infrared Multiphoton Dissociation","volume":"60","author":"Agneta","year":"2012","journal-title":"J. Agric. Food Chem."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"462060","DOI":"10.1016\/j.chroma.2021.462060","article-title":"Current analytical methods for determination of glucosinolates in vegetables and human tissues","volume":"1643","author":"Almushayti","year":"2021","journal-title":"J. Chromatogr. A"}],"container-title":["Metabolites"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2218-1989\/16\/4\/274\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,4,25]],"date-time":"2026-04-25T04:20:16Z","timestamp":1777090816000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2218-1989\/16\/4\/274"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,4,17]]},"references-count":35,"journal-issue":{"issue":"4","published-online":{"date-parts":[[2026,4]]}},"alternative-id":["metabo16040274"],"URL":"https:\/\/doi.org\/10.3390\/metabo16040274","relation":{},"ISSN":["2218-1989"],"issn-type":[{"value":"2218-1989","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,4,17]]}}}