Submit to Special Issue Submit Abstract to Special Issue Review for Plants Propose a Special Issue

Journal Menu

Journal Browser

► Journal Browser

Mass Spectrometry-Based Approaches in Natural Products Research

Special Issue Editors
Special Issue Information
Keywords
Benefits of Publishing in a Special Issue
Published Papers

A special issue of Plants (ISSN 2223-7747). This special issue belongs to the section "Phytochemistry".

Deadline for manuscript submissions: 31 December 2025 | Viewed by 4704

Share This Special Issue

Special Issue Editors

Prof. Dr. Felipe Moura Araújo da Silva

E-Mail Website
Guest Editor

Centro de Apoio Multidisciplinar (CAM), Universidade Federal do Amazonas (UFAM), Manaus, AM, Brazil
Interests: natural products chemistry; mass spectrometry; phytochemistry; analytical instrumentation

Dr. Rita De Cássia Saraiva Nunomura

E-Mail Website
Guest Editor

Departamento de Química (DQ), Universidade Federal do Amazonas (UFAM), Manaus, AM, Brazil
Interests: natural products chemistry; organic chemistry; organic synthesis; pharmacology biochemistry

Special Issue Information

Dear Colleagues,

Nowadays, mass spectrometry-based approaches constitute the primary strategy for rapid advancements in natural products research, as they allow for the dereplication and quantification of bioactive compounds in plants. These compounds, including alkaloids, flavonoids, terpenoids, and others, play essential roles in various biological processes and are of great interest across fields such as plant biochemistry, molecular biology, plant biotechnology, food sciences, agriculture, horticulture, and beyond.

This upcoming special issue will focus on currently used mass spectrometry-based strategies in natural products research. These strategies involve normally hyphenated techniques, such as liquid chromatography coupled with mass spectrometry (LC-MS) and gas chromatography coupled with mass spectrometry (GC-MS), which are powerful systems in the search for chemical knowledge about biological samples. Emphasis will be placed on modern strategies based on GC-MS and LC-MS to investigate bioactive compounds in plants. Other analytical approaches are also encouraged, as well as studies investigating samples with promising biological activity.

We invite researchers to contribute articles that explore the use of these analytical techniques in various applications within natural products research, from identifying known metabolites to developing innovative methodologies for complex plant matrix analysis.

This issue provides an excellent opportunity for researchers to share their latest findings and insights, furthering our collective understanding of the potential of mass spectrometry-based approaches in natural products research.

In this Special Issue, original research articles and reviews are welcome.

I look forward to receiving your contributions

Prof. Dr. Felipe Moura Araújo da Silva
Dr. Rita De Cássia Saraiva Nunomura
Guest Editors

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 100 words) can be sent to the Editorial Office for announcement on this website.

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. Plants is an international peer-reviewed open access semimonthly 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

phytochemistry
dereplication
LC-MS
GC-MS

Benefits of Publishing in a Special Issue

Ease of navigation: Grouping papers by topic helps scholars navigate broad scope journals more efficiently.
Greater discoverability: Special Issues support the reach and impact of scientific research. Articles in Special Issues are more discoverable and cited more frequently.
Expansion of research network: Special Issues facilitate connections among authors, fostering scientific collaborations.
External promotion: Articles in Special Issues are often promoted through the journal's social media, increasing their visibility.
Reprint: MDPI Books provides the opportunity to republish successful Special Issues in book format, both online and in print.

Further information on MDPI's Special Issue policies can be found here.

Published Papers (8 papers)

Download All Papers

Order results

Result details

Show export options Show export options

Select all

Export citation of selected articles as:

Research

14 pages, 1409 KB

Open AccessArticle

SIRT1 Activation by Lignans Identified via UPLC-qTOF-MS/MS-Based Metabolomic Profiling of Piper longum L. Fruit (Long Pepper)

by Van-Hieu Mai, Jun-Li Yang, Thi-Kim-Quy Ha, Jorge-Eduardo Ponce-Zea, Minh Thi Tuyet Le, Ba-Wool Lee, Jin-Pyo An and Won Keun Oh

Plants 2025, 14(20), 3186; https://doi.org/10.3390/plants14203186 - 16 Oct 2025

Abstract

The fruits of Piper longum L. (long pepper), a spice and medicinal plant of the family Piperaceae, are widely used in South and Southeast Asian cuisine and traditional medicine, valued for their pungent flavor and aroma. The metabolomic profiling of P. longum using UPLC-qTOF-MS/MS provided a comprehensive chemical characterization of this traditional medicinal plant, revealing that lignans and amide alkaloids are the major classes of secondary metabolites. To further investigate its pharmacological potential, the bioactive ethyl acetate fraction was subjected to a SIRT1-targeted chemical investigation. This led to the isolation and structural elucidation of three previously undescribed compounds, a cadinene-type sesquiterpene (1) and two oxo-neolignan (2 and 5), along with four known compounds 3, 4, 6, and 7. Compounds (1–7) were evaluated for their ability to modulate p53-dependent transcriptional activity via SIRT1 activation using a luciferase reporter cell-based assay. SIRT1, a NAD⁺-dependent deacetylase, is a crucial regulator of longevity, metabolism, and cellular stress resistance, making it a key target for the treatment of age-related diseases. Compounds 2–7 exhibited significant SIRT1 activation, with compound 6 displaying particularly high efficacy, comparable to resveratrol, the most well-known natural SIRT1 activator. This study demonstrates that the discovery of novel chemical scaffolds through bioactivity-guided screening highlights the value of combining advanced metabolomics with pharmacological evaluation. The results support the traditional medicinal use of long pepper and its potential for development into functional foods or pharmaceuticals for healthy aging. Full article

(This article belongs to the Special Issue Mass Spectrometry-Based Approaches in Natural Products Research)

► Show Figures

Figure 1

27 pages, 9212 KB

Open AccessArticle

Optimization of the Extraction of Bioactive Compounds and Metabolomic Profile of Licaria armeniaca

by Lanalice R. Ferreira, Bianca R. Abelém, José Diogo E. Reis, Christelle Anne N. P. Herman, Pablo Luis B. Figueiredo, Laine Celestino Pinto, Luiza Helena Martins, Milton Nascimento da Silva, Paulo Wender P. Gomes and Joyce Kelly R. da Silva

Plants 2025, 14(20), 3158; https://doi.org/10.3390/plants14203158 - 14 Oct 2025

Viewed by 270

Abstract

The ultrasound-assisted extraction (UAE) method was optimized to extract bioactive compounds from Licaria armeniaca tissues. Extraction time, solid–liquid ratio (m/v), and ethanol percentage were investigated using a central composite rotational design and response surface methodology (RSM). Antioxidant activity (DPPH) and total phenolic content (TPC) served as the response variables. Most efficient extraction conditions were obtained for leaves (64.88% ethanol, 26.07 min, 6.23% m/v; R² = 0.93) and thin branches (73.81% ethanol, 31.34 min, 11% m/v; R² = 0.74). For thick branches, no significant predictive model was obtained, and optimal points were defined based on the best observed TPC and DPPH results (50% ethanol, 35 min, 11% m/v). The optimized extracts were analyzed by liquid chromatography–tandem mass spectrometry associated with molecular networking, GNPS (Global Natural Products Social Molecular Network) library searching, and machine learning tools. Metabolomic profiling indicated that leaves contained mainly alkaloids (46.34%), amino acids and peptides (19.51%), and shikimate derivatives and phenylpropanoids (12.20%). Thin branches showed predominance of alkaloids (35.97%), amino acids and peptides (20.86%), and carbohydrates (12.23%), while thick branches contained alkaloids (46.34%), amino acids and peptides (25.00%), and fatty acids (14.26%). Additionally, the extracts displayed significant cytotoxic activity against cancer cell lines of AGP-01 (malignant gastric ascites), AHOL (Human glioblastoma) and A549 (lung cancer) with IC50 values less than 50 μg/mL. Full article

(This article belongs to the Special Issue Mass Spectrometry-Based Approaches in Natural Products Research)

► Show Figures

Figure 1

16 pages, 887 KB

Open AccessArticle

Analysis of the Phenolic Compounds, Volatile Profile, and Evaluation of the Antioxidant Activity of 18 Different Varieties of Honey from the Italian Market

by Doaa Abouelenein, Laura Acquaticci, Eleonora Spinozzi, Agnese Santanatoglia, Gulzhan Khamitova, Ahmed M. Mustafa, Marco Cespi, Silvia Preziuso, Luca Bianchi, Filippo Maggi and Giovanni Caprioli

Plants 2025, 14(19), 3109; https://doi.org/10.3390/plants14193109 - 9 Oct 2025

Viewed by 479

Abstract

The aim of this study was to present a comprehensive analysis of honey varieties from different botanical origins, focusing on their phenolic compounds’ composition, volatile profiles, and antioxidant activity. We simultaneously identified and quantified 37 bioactive compounds, including anthocyanins, flavonols, flavones, flavan-3-ols, proanthocyanidins, and phenolic acids, across various honey samples by HPLC-MS/MS. Total phenolic content (TPC), total flavonoid content (TFC), and antioxidant activity (AOA) were determined using UV-Vis spectrophotometric analysis. The content of phenolic compounds quantified by HPLC-MS/MS ranged from 19.56 to 243.94 mg·kg⁻¹, highlighting a high presence of these antioxidant compounds (mainly phenolic acids), confirmed also by the positive correlation between TPC and DPPH values. Among volatiles compounds, analyzed by HS-SPME-GC-MS, benzene acetaldehyde and furfural resulted specific for two types of honey samples (H-7 and H-9), highlighting the possibility of searching for chemical markers to characterize honeys of different specie/origin. This study enhances our understanding of the bioactive potential of honey from different botanical origins and provides a foundation for future research on its health benefits. Full article

(This article belongs to the Special Issue Mass Spectrometry-Based Approaches in Natural Products Research)

► Show Figures

Figure 1

17 pages, 997 KB

Open AccessArticle

Cultivar-Specific Differences in C6 and C7 Sugar Metabolism During Avocado Ripening: Comparative Insights from Bacon, Fuerte, and Hass

by María Gemma Beiro-Valenzuela, Romina P. Monasterio, Irene Serrano-García, Elena Hurtado-Fernández, Carmen María Sánchez-Arévalo, Jorge Fernando Fernández-Sánchez, Romina Pedreschi, Lucía Olmo-García and Alegría Carrasco-Pancorbo

Plants 2025, 14(18), 2856; https://doi.org/10.3390/plants14182856 - 12 Sep 2025

Viewed by 486

Abstract

Avocado is a unique fruit in which of seven-carbon (C7) sugars (notably D-mannoheptulose and perseitol) dominate the carbohydrate profile at harvest. Despite growing interest in sugar-mediated ripening processes, limited comparative data exist across cultivars. This work characterises the dynamic changes in non-structural carbohydrates in the mesotecarp of three commercially relevant avocado varieties—Bacon, Fuerte, and Hass—across four defined ripening stages, from unripe to overripe, with five biological replicates per stage. Using a validated hydrophilic interaction liquid chromatography–mass spectrometry (HILIC–MS) method, we quantified five key sugars and assessed their evolution through ripening. Concentrations varied among the studied samples within the following ranges: D-mannoheptulose, 0.4–49 mg/g dry weight (DW); perseitol, 0.5–23 mg/g DW; glucose, 0.8–5.3 mg/g DW; fructose, 0.6–4.5 mg/g DW; and sucrose, 0.5–3.4 mg/g DW. C7 sugar levels consistently declined, while C6 sugars increased—primarily between the intermediate and ready-to-eat stages—with distinct cultivar-specific patterns. Bacon maintained elevated C7 concentrations for a longer period; Fuerte exhibited a rapid transition from C7 to C6 sugars; and Hass displayed a more gradual and balanced shift. Multivariate analysis (partial least squares discriminant analysis, PLS-DA) effectively discriminated between cultivars at each ripening stage, confirming cultivar-specific metabolic signatures. These findings offer new insights into avocado carbohydrate metabolism, emphasising variety-dependent pathways that could inform breeding strategies, optimise postharvest ripening protocols, and support the nutritional characterisation of different avocado cultivars. Full article

(This article belongs to the Special Issue Mass Spectrometry-Based Approaches in Natural Products Research)

► Show Figures

Figure 1

21 pages, 3406 KB

Open AccessArticle

Antiproliferative and Anti-Migratory Activities of an Extract from Fridericia platyphylla Leaves and Its Molecular Profile

by Jhonathas Aparecido R. Brito, Amanda de Jesus A. Miranda, Victor Antonio S. Lima, Samuel dos Santos S. Buna, Marcelino S. do Rosário, Rafael F. Lima, Monique M. Martins, Marcelo S. de Andrade, Maria D. S. B. Nascimento, Vanderlan da Silva Bolzani, Ana Paula Silva de Azevedo-Santos, Josélia Alencar Lima, Júlia Karla de A. M. Xavier and Cláudia Quintino da Rocha

Plants 2025, 14(17), 2693; https://doi.org/10.3390/plants14172693 - 28 Aug 2025

Viewed by 636

Abstract

Fridericia platyphylla, a member of the Bignoniaceae family, is widely recognized as a rich source of flavonoids with significant biopharmacological potential. This study aimed to perform a chemical annotation of its metabolites and to evaluate the antitumor activity of the hydroalcoholic extract from its leaves. The chemical diversity of this specimen was analyzed using liquid chromatography coupled with tandem mass spectrometry and Molecular Networking. Fifteen significant phenolic compounds were annotated, including phenolic acid derivatives, flavonoid glycosides, and flavone aglycones. Furthermore, the antiproliferative activities against human cervical cell lines, adenocarcinoma HPV 18 positive (HeLa) and carcinoma HPV 16 positive (SiHa), in vitro, exhibited distinct inhibitory effects, with IC₅₀ values of 44.78 and 66.97 µg mL⁻¹, respectively. The extract inhibited cell migration and exhibited cytotoxic effects by reducing the viability of HeLa and SiHa cells, suggesting its potential as a therapeutic candidate for cervical cancer. Therefore, given the significant antiproliferative and anti-migratory activity, these results open up prospects for investigating F. platyphylla leaf extract in the development of alternative therapies for cervical cancer. Full article

(This article belongs to the Special Issue Mass Spectrometry-Based Approaches in Natural Products Research)

► Show Figures

Figure 1

11 pages, 1113 KB

Open AccessArticle

Identification of Daphnane Diterpenoids from Flower Buds and Blooming Flowers of Daphne odora Using UHPLC-Q-Exactive-Orbitrap MS

by Kouharu Otsuki, Kousei Miyamoto, Mami Goto, Mi Zhang, Takashi Kikuchi and Wei Li

Plants 2025, 14(17), 2616; https://doi.org/10.3390/plants14172616 - 22 Aug 2025

Viewed by 558

Abstract

Daphne odora is an evergreen shrub belonging to the Thymelaeaceae family that is widely cultivated as an ornamental garden plant. Its roots, leaves, and flowers have traditionally been used in Chinese medicine to treat pain, skin diseases, and rheumatism. While previous phytochemical studies have reported the presence of phenols, coumarins, biflavonoids, lignans, and daphnane diterpenoids in D. odora, its flowers remain largely unexplored. In the present study, the first comprehensive investigation of daphnane diterpenoids contained in the flower buds and blooming flowers of D. odora was conducted using ultra-high-performance liquid chromatography coupled with Q-Exactive-Orbitrap high-resolution mass spectrometry (UHPLC-Q-Exactive-Orbitrap MS). A total of 30 daphnane diterpenoids were identified, including 12 previously unreported compounds, through detailed analysis of their retention times and MS/MS fragmentation patterns. Comparative profiling revealed that flower buds contained a higher abundance and greater diversity of daphnane diterpenoids than flowers. Furthermore, LC–MS-guided isolation enabled the purification of a novel compound, daphneodorin I (16), and its structure was elucidated through extensive physicochemical and spectroscopic analyses. Compound 16 represents the first daphnane diterpenoid with a Z-configured phenolic acyl moiety isolated from plants of the Thymelaeaceae family. Full article

(This article belongs to the Special Issue Mass Spectrometry-Based Approaches in Natural Products Research)

► Show Figures

Figure 1

21 pages, 613 KB

Open AccessArticle

Nutritional Composition, Volatile Profiles, and Biological Evaluation of Honeys from Melipona interrupta and Melipona seminigra from Amazonas State, Brazil

by Emilly J. S. P. de Lima, Carlos V. A. da Silva, Fernanda A. S. Rocha, Aline de M. Rodrigues, Samuel C. Costa, Rebeca S. França, Raiana S. Gurgel, Bárbara N. Batista, Patrícia M. Albuquerque, Waldireny R. Gomes, Hector H. F. Koolen and Giovana A. Bataglion

Plants 2025, 14(14), 2106; https://doi.org/10.3390/plants14142106 - 9 Jul 2025

Viewed by 1025

Abstract

Honey is a natural product produced by bees from the nectar of plants and has been widely used as a sweetener for centuries. In addition to its traditional use, it is also employed for other purposes due to its biological and nutraceutical properties. Although honey production is mostly associated with bees of the genus Apis, species from other genera, such as Melipona, also produce it, albeit on a smaller scale. The honey produced by these two genera shows significant differences in its composition. Moreover, distinct geographical localizations, which, consequently, have different flora, guide the chemical compositions of these samples. Regarding the Amazon region, the amount of knowledge about the honey samples from Melipona species is still scarce. In this context, the present study aimed to characterize the volatile compositions of honey from Melipona interrupta and Melipona seminigra, as well as from the floral sources available, in addition to evaluating their nutritional aspects, antioxidant activity, and antibacterial activity. The analysis of chemical composition was performed using gas chromatography coupled to mass spectrometry (GC-MS). Antioxidant activity was determined by DPPH and ABTS assays, while antimicrobial activity was tested against Escherichia coli, Staphylococcus aureus, Klebsiella pneumoniae, Pseudomonas aeruginosa, Proteus mirabilis, Staphylococcus epidermidis, Enterococcus faecalis, Salmonella enterica, Serratia marcescens, Bacillus subtilis, Candida albicans, Candida tropicalis, and Candida parapsilosis. The results allowed the identification of volatiles present in the honey and floral sources. The samples displayed moderate antioxidant activity and slightly antibacterial activity (MIC) of 75 μg/mL against two bacterial strains tested, demonstrating potential antimicrobial activity. Full article

(This article belongs to the Special Issue Mass Spectrometry-Based Approaches in Natural Products Research)

► Show Figures

Figure 1

14 pages, 982 KB

Open AccessArticle

Botanical Authenticity of Miraruira Sold in the Amazonas State, Brazil, Based on Chemical Profiling Using DI-MS and Chemometric Analyses

by Shelson M. da R. Braga, Felipe M. A. da Silva, Giovana A. Bataglion, Marcia G. A. de Almeida, Larissa O. de Souza, Rebeca dos S. França, Cesar A. S. de Souza, Francinaldo A. da Silva-Filho, Afonso D. L. de Souza, Hector H. F. Koolen and Maria L. B. Pinheiro

Plants 2025, 14(13), 2012; https://doi.org/10.3390/plants14132012 - 1 Jul 2025

Viewed by 448

Abstract

Miraruira is a medicinal plant-based product (MPBP) that is widely used in the state of Amazonas for the treatment of diabetes, though its botanical identity remains unclear, which raises concerns about authenticity and therapeutic consistency. One solution to this problem is the use of mass spectrometry-based approaches, which have emerged as powerful tools for verifying botanical origin based on chemical composition. Thus, to confirm the botanical authenticity of miraruira, direct-injection mass spectrometry (DI-MS) and chemometric analyses (PCA and HCA) were conducted on methanol fractions of Salacia impressifolia and Connarus ruber, both suspected sources of miraruira, as well as commercial samples obtained in street markets in Manaus, Brazil. Additionally, the hexane extracts of C. ruber and the commercial samples were screened for benzoquinones using DI-MS, as these compounds are recurrent in the genus Connarus. The DI-MS and PCA analyses revealed distinct chemical profiles for each species, and identified mangiferin and epicatechin as chemical markers for S. impressifolia and C. ruber, respectively. Furthermore, PCA demonstrated that all the commercial samples exhibited chemical profiles closely aligned with C. ruber. However, the HCA indicated variability among these samples, suggesting C. ruber or related Connarus species are the primary sources of miraruira. Moreover, embelin, rapanone, and suberonone were identified as the main compounds in the hexane extracts of C. ruber and the commercial products. This study successfully confirmed the botanical authenticity of miraruira, identified key bioactive compounds related to its traditional use in the treatment of diabetes symptoms, and demonstrated the effectiveness of DI-MS as a valuable tool for addressing authenticity issues in MPBPs. Full article

(This article belongs to the Special Issue Mass Spectrometry-Based Approaches in Natural Products Research)

► Show Figures

Journal Menu

Journal Browser

Mass Spectrometry-Based Approaches in Natural Products Research

Share This Special Issue

Special Issue Editors

Special Issue Information

Keywords

Benefits of Publishing in a Special Issue

Published Papers (8 papers)

Research

Further Information

Guidelines

MDPI Initiatives

Follow MDPI