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Metabolites
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LC-MS/MS Analysis for Plant Secondary Metabolites, 2nd Edition
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LC-MS/MS Analysis for Plant Secondary Metabolites, 2nd Edition

A special issue of Metabolites (ISSN 2218-1989). This special issue belongs to the section "Plant Metabolism".

Deadline for manuscript submissions: 30 September 2026 | Viewed by 3629

Special Issue Editor

Dr. Tiantian Ye

E-Mail Website
Guest Editor
School of Bioengineering and Health, Wuhan Textile University, Wuhan 430200, China
Interests: LC-MS analysis; metabolomics; nucleic acid modifications
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues，

We are pleased to announce the launch of a new Special Issue, “LC-MS/MS Analysis for Plant Secondary Metabolites, 2nd Edition”, a continuation of a previously successful Special Issue.

Plant secondary metabolites encompass a diverse group of molecules that play a critical role, yet they are not directly involved in plant growth, development, and stress response. An accurate and reliable analysis of the secondary metabolites would enhance our comprehension of their physiological status and deepen our understanding of specific biochemical processes in plants. Liquid chromatography–tandem mass spectrometry (LC-MS/MS) has emerged as a powerful and essential technique for metabolomics analysis. Advancements in LC-MS/MS have facilitated the simultaneous measurement of numerous metabolites. Nevertheless, obtaining high-quality metabolomics datasets as well as ef-fectively integrating and interpreting the data still present challenges.

In this Special Issue entitled "LC-MS/MS Analysis for Plant Secondary Metabolites, 2nd Edition”, we aim to showcase the wide range of research and applications of LC-MS/MS analysis in the field of plant secondary metabolites. We invite submissions covering various aspects of LC-MS/MS analysis, including applications, method and instrumentation development, and advancements in bioinfor-matic methodology. Original research papers as well as review articles are welcomed for submission.

Dr. Tiantian Ye
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 250 words) can be sent to the Editorial Office for assessment.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Metabolites is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • liquid chromatography
  • mass spectrometry
  • secondary metabolites
  • metabolomics
  • abiotic and biotic stress
  • plant development

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Related Special Issue

Published Papers (5 papers)

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Research

17 pages, 5036 KB  
Article
HR-LCMS/MS-Based Dereplication of Plant-Derived Autophagy Inducers Revealed Astragalus dasyanthus as a New Glabrol Producer
by Anastasiia K. Bolikhova, Vera A. Alferova, Anton R. Izzi, Arina A. Nikandrova, Gulnara K. Kudryakova, Mikhail Y. Zhitlov, Ekaterina A. Guseva, Dmitry S. Karpov, Dmitrii A. Lukianov, Olga A. Dontsova and Petr V. Sergiev
Metabolites 2026, 16(5), 311; https://doi.org/10.3390/metabo16050311 - 1 May 2026
Viewed by 262
Abstract
Background/Objectives: Autophagy is an important cellular self-cleansing process whose normal functioning is essential for preventing many age-related diseases. The search for and study of new autophagy activators allows the proposal of novel therapeutic approaches for the treatment of age-related diseases. Medical plants are [...] Read more.
Background/Objectives: Autophagy is an important cellular self-cleansing process whose normal functioning is essential for preventing many age-related diseases. The search for and study of new autophagy activators allows the proposal of novel therapeutic approaches for the treatment of age-related diseases. Medical plants are a rich source of bioactive compounds with variable functions. In this study, we propose an HR-LCMS/MS-based technique for identifying the principal autophagy activators in plant extracts. Methods: We performed a Western blot analysis of the autophagy-inducing activity of plant extract HPLC fractions on a model of SH-SY5Y cells. The composition of the fractions showing autophagy-activating potential was determined via HR-LCMS/MS. Results: We analyzed five plants known to produce autophagy activators and proved the ability of the method to detect the main bioactive compounds. Additional screening demonstrated for the first time that Astragalus dasyanthus is a producer of the autophagy-inducer glabrol. Conclusions: The described HR-LCMS/MS-based method for identifying autophagy activators in multicomponent plant extracts is effective and could be used for further high-throughput screening. Full article
(This article belongs to the Special Issue LC-MS/MS Analysis for Plant Secondary Metabolites, 2nd Edition)
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15 pages, 5939 KB  
Article
Deep Learning-Based and Python-Driven Construction and Application of a Mass Spectrometry Data Analysis Workflow: Taking Glucosinolates as an Example
by Shangshen Yang, Siyu Jia, Peiyu Jia, Wenyu Xie and Xiaoming Wang
Metabolites 2026, 16(4), 274; https://doi.org/10.3390/metabo16040274 - 17 Apr 2026
Viewed by 301
Abstract
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 [...] Read more.
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. Full article
(This article belongs to the Special Issue LC-MS/MS Analysis for Plant Secondary Metabolites, 2nd Edition)
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18 pages, 1566 KB  
Article
Comparative Metabolomics Analysis of Gastrodia elata Blume Different Growth Stages: Insights into Chemical Composition and Bioactivities
by Guoqiang Zhou, Jiayi An, Yi Li, Zunhan Zhang, Yaru Chang and Guanxiu Xiao
Metabolites 2026, 16(4), 223; https://doi.org/10.3390/metabo16040223 - 30 Mar 2026
Viewed by 592
Abstract
Background: Gastrodia elata Blume (GE) is a valuable traditional Chinese medicine with a wide range of clinical applications, yet the relationship between its developmental stages, phytochemical profiles, and functional properties remains poorly characterized. Methods: In this study, an integrated approach combining [...] Read more.
Background: Gastrodia elata Blume (GE) is a valuable traditional Chinese medicine with a wide range of clinical applications, yet the relationship between its developmental stages, phytochemical profiles, and functional properties remains poorly characterized. Methods: In this study, an integrated approach combining chemical assays and UHPLC–Orbitrap–MS/MS-based untargeted metabolomics was employed to characterize three growth stages: Mima (MT, seed tubers), Baima (BT, immature tubers), and Jianma (JT, mature tubers). Results: Multivariate statistical analyses demonstrated clear stage-dependent discrimination in metabolic profiles. A total of 31 differential metabolites were identified, including parishin derivatives, phenolics, amino acids, and organic acids. Specifically, Parishin E, Parishin G, total phenolics, and total flavonoids predominated in the early stage (MT), whereas gastrodin and Parishin C progressively accumulated and peaked in the mature stage (JT). Bioactivity assays revealed that GE extracts exhibited significant antioxidant and hypoglycemic (α-glucosidase and α-amylase inhibitory) effects, which followed an initial decrease followed by a subsequent recovery during development. Correlation analysis further established a strong relationship between phenolic-associated metabolites (particularly Parishin E/G/H) and the observed bioactivities. Conclusions: In summary, these findings elucidate the metabolic dynamics of GE across developmental stages and provide a scientific basis for optimizing harvest timing and raw-material grading to enhance the functional properties of GE-derived products. Full article
(This article belongs to the Special Issue LC-MS/MS Analysis for Plant Secondary Metabolites, 2nd Edition)
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15 pages, 8769 KB  
Article
Transcriptomic Analysis of the Regulatory Mechanism of Tea Polyphenol Biosynthesis in Chionanthus retusus and Functional Characterization of CrHSP70-14 in Terms of Its Effect on Tea Polyphenols
by Liyang Guo, Yuzhu Wu, Jihong Li, Haiyan Wang, Muge Niu, Mengmeng Wang, Shicong Zhao, Wenjing Song, Jiaxun Liu, Jingyu Wang and Jinnan Wang
Metabolites 2026, 16(1), 26; https://doi.org/10.3390/metabo16010026 - 25 Dec 2025
Viewed by 541
Abstract
Background: Chionanthus retusus Lindl. et Paxt., a deciduous tree of the genus Chionanthus (Oleaceae), represents a significant native species and a widely cultivated ornamental. Its tender leaves can be processed into tea, traditionally consumed in southern China under the common name [...] Read more.
Background: Chionanthus retusus Lindl. et Paxt., a deciduous tree of the genus Chionanthus (Oleaceae), represents a significant native species and a widely cultivated ornamental. Its tender leaves can be processed into tea, traditionally consumed in southern China under the common name “Nuomi Cha”. Methods: Our team quantified the tea polyphenol content across 150 individual trees of C. retusus and selected three low-polyphenol (ZB_D_14, AQ_2, AQ_1) and three high-polyphenol (SX_3, SXG_D_8, TS_D_13) lines for transcriptome sequencing of their young leaves. The resulting data were analyzed to screen for candidate genes. Subsequently, transgenic plants were constructed, and their tea polyphenol content was determined. Results: A significant difference in tea polyphenol content was confirmed between the high- and low-polyphenol lines. Weighted Gene Co-expression Network Analysis (WGCNA) pinpointed a key module strongly associated with tea polyphenol synthesis, encompassing 432 DEGs, which were predominantly enriched in pathways like phenylpropanoid biosynthesis. A comparative transcriptomic analysis further yielded 84 DEGs (40 up- and 44 down-regulated). Enrichment analysis showed these were primarily involved in flavonoid and phenylpropanoid biosynthesis pathways. Expression profiling of genes in the tea polyphenol biosynthetic pathway indicated that several key genes (e.g., 4CL, CHS, DFR) were highly expressed in the high-content lines. A gene interaction network related to this synthesis identified 20 hub genes (e.g., CrHSP70-14, CrMYB44, CrbHLH92). Functional validation of four hubs (CrMYB44, CrHSP70-14, CrCDC6B, CrRAE1) via tobacco transient transformation assays demonstrated that all four significantly elevated tea polyphenol levels, with CrHSP70-14 overexpression yielding the highest content. Furthermore, stable CrHSP70-14 overexpression transgenic tobacco lines were generated, exhibiting significantly higher leaf tea polyphenol content versus controls. Conclusions: This study identifies multiple regulatory genes involved in C. retusus tea polyphenol biosynthesis, provides initial mechanistic insights, and establishes a molecular foundation for breeding specialized tea cultivars of this species. Full article
(This article belongs to the Special Issue LC-MS/MS Analysis for Plant Secondary Metabolites, 2nd Edition)
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22 pages, 1349 KB  
Article
Fruit Quality Characterization and Comprehensive Evaluation of 30 Chionanthus retusus Accessions
by Muge Niu, Jinnan Wang, Baoqiang Huang, Hui Tian, Maotong Sun, Jihong Li, Jing Ren and Cuishuang Liu
Metabolites 2025, 15(9), 588; https://doi.org/10.3390/metabo15090588 - 3 Sep 2025
Viewed by 1159
Abstract
Objectives: Research on kernel oil content and secondary metabolites in Chionanthus retusus was conducted to evaluate its potential as an oil crop. Methods: Fruits from 30 individual trees were collected to analyze morphological traits, oil content, and the composition of fatty acids, phytosterols, [...] Read more.
Objectives: Research on kernel oil content and secondary metabolites in Chionanthus retusus was conducted to evaluate its potential as an oil crop. Methods: Fruits from 30 individual trees were collected to analyze morphological traits, oil content, and the composition of fatty acids, phytosterols, and tocopherols. Correlation, cluster, and principal component analyses were performed on the resulting data. Results: The mean fresh fruit weight, dry fruit weight, dry kernel weight, and kernel percentage were 77.02 g, 24.33 g, 12.22 g, and 51.14%, respectively. Kernel oil content averaged 35.83%, comprising seven fatty acids with oleic acid as the predominant component. Total phytosterol content reached 279.58 mg/100 g oil, with β-sitosterol being the major constituent among seven detected sterols. Total tocopherols were 571.13 μg/g oil, dominated by γ-tocopherol, indicating a potential antioxidant capacity. These components may reduce the demand for synthetic antioxidant food additives. A significant positive correlation was observed between kernel dry weight and oil content (r = 0.760, p < 0.01), supporting kernel dry weight as a key phenotypic indicator for high-oil breeding. Fruit quality traits did not cluster by geographic origin, whereas secondary metabolite profiles showed origin-based clustering. For breeding oil-producing C. retusus, select seeds with superior provenances based on secondary metabolites and cultivate them under optimal conditions to develop varieties with plump fruit, thereby boosting yield. Accessions WS-4 and WS-3 were identified as promising germplasm resources for oil production. Conclusions: The abundant oleic acid, β-sitosterol, and γ-tocopherol in C. retusus kernels highlight its potential as a woody oilseed crop. Full article
(This article belongs to the Special Issue LC-MS/MS Analysis for Plant Secondary Metabolites, 2nd Edition)
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