Search for Articles:
Title / Keyword
Author / Affiliation / Email
Journal
Article Type
 
 
Advanced Search
 
Section
Special Issue
Volume
Issue
Number
Page
 
10.3
5.1
Journals
Molecules
Special Issues
Application of Mass Spectrometry Techniques in Analytical Chemistry
molecules-logo
Submit to Special Issue Submit Abstract to Special Issue Review for Molecules Propose a Special Issue

Journal Menu

► Journal Menu

Journal Browser

► Journal Browser
share announcement

Application of Mass Spectrometry Techniques in Analytical Chemistry

A special issue of Molecules (ISSN 1420-3049). This special issue belongs to the section "Analytical Chemistry".

Deadline for manuscript submissions: 30 August 2026 | Viewed by 3066

Editors

Dr. Xiqing Bian

E-Mail Website
Guest Editor
Laboratory of Drug Discovery from Natural Resources and Industrialization, School of Pharmacy, Macau University of Science and Technology, Taipa, Macau, China
Interests: LC-MS; metabolomics; foodomics; derivatization; bioactive compounds; mechanism of action
Prof. Dr. Agata Kot-Wasik

E-Mail Website
Guest Editor
Department of Analytical Chemistry, Faculty of Chemistry, Gdańsk University of Technology, 11/12 Narutowicza St., 80-233 Gdańsk, Poland
Interests: liquid chromatography; mass spectrometry; hyphenated techniques sample preparation methods analysis of biomarkers; environmental analytics; lipidomics
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Mass spectrometry (MS) has become an indispensable cornerstone of modern analytical science, offering unparalleled sensitivity, specificity, and versatility. This Special Issue aims to showcase cutting-edge research and innovative applications of MS and its hyphenated techniques (e.g., GC-MS and LC-MS) across diverse fields. We welcome original research and reviews covering advancements in instrumentation, novel methodologies, and applications in areas such as proteomics/metabolomics, pharmaceutical development, food safety, and clinical diagnostics. Our goal is to highlight how MS technologies continue to push the boundaries of detection, quantification, and molecular characterization, addressing complex analytical challenges in science and industry.

Dr. Xiqing Bian
Prof. Dr. Agata Kot-Wasik
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 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-anonymized peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Molecules 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

  • mass spectrometry
  • analytical chemistry
  • omics analysis
  • pharmaceutical analysis
  • food safety
  • clinical diagnostics

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 (4 papers)

Download All Papers
Order results
Result details
Show export options expand_more Show export options expand_less
Select all
Export citation of selected articles as:

Research

16 pages, 2835 KB  
Article
Automated Peak Annotation in Time-of-Flight Secondary Ion Mass Spectrometry via a Physics-Informed Probabilistic Framework
by Jiahua Chen, Yujie Cao, Xingyu Jiang, Chunpeng Wu, Qing Hao, Yun Hu and Jiahui Liu
Molecules 2026, 31(13), 2388; https://doi.org/10.3390/molecules31132388 - 7 Jul 2026
Viewed by 422
Abstract
Peak annotation in Time-of-Flight Secondary Ion Mass Spectrometry (ToF-SIMS) is a persistent bottleneck that typically requires the manual assignment of chemical formulas to hundreds of fragment ion peaks per spectrum. This work describes a physics-informed probabilistic framework that automates this task by combining [...] Read more.
Peak annotation in Time-of-Flight Secondary Ion Mass Spectrometry (ToF-SIMS) is a persistent bottleneck that typically requires the manual assignment of chemical formulas to hundreds of fragment ion peaks per spectrum. This work describes a physics-informed probabilistic framework that automates this task by combining five chemically motivated constraints—Gaussian mass accuracy, element composition priors, isotope pattern matching, nitrogen rule parity, and graded valence bounds—into a multiplicative belief score. We evaluate the framework on 643 ground-truth peaks from 151 compounds spanning both positive and negative ion modes, and we explicitly distinguish two regimes. As a scoring task—when the correct formula is present in the candidate list—the framework attains 52.3% Top-1 and 76.4% Top-3 accuracy, a 4.9-fold improvement over mass-only scoring. In fully automated end-to-end deployment, where candidates are generated de novo, Top-1 accuracy is 26.3%; the limiting factor is candidate generation rather than scoring, as only 46.5% of ground-truth formulas are currently produced by the database and combinatorial generator. Leave-One-Compound-Out Cross-Validation (59 compounds, 525 peaks) yields 51.8% Top-1 accuracy with fixed domain-knowledge weights, confirming generalization stability. Ablation analysis identifies element composition priors as the dominant non-mass constraint (−27.7 percentage points when removed), followed by isotope matching (−10.3 pp) and the nitrogen rule (−5.3 pp). The framework requires no labeled training spectra—relying instead on physically motivated priors and curated fragment databases—provides interpretable per-constraint scores (which represent relative rankings rather than calibrated probabilities), and supports polarity-specific configurations, offering a practical computational foundation for automated ToF-SIMS spectrum interpretation. Full article
(This article belongs to the Special Issue Application of Mass Spectrometry Techniques in Analytical Chemistry)
►▼ Show Figures

Figure 1

17 pages, 7239 KB  
Article
Dual-Mode Native Mass Spectrometry Screening Identifies Ginsenoside Ligands of 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase (HPPK)
by Xinru Xue, Ronald J. Quinn, Bernd H. A. Rehm, Peter J. Myler and Miaomiao Liu
Molecules 2026, 31(12), 2065; https://doi.org/10.3390/molecules31122065 - 12 Jun 2026
Viewed by 513
Abstract
Identification of ligands targeting essential enzymes in Mycobacterium species remains an important strategy for anti-tuberculosis drug discovery. Here, a native mass spectrometry approach was employed using pooled 100-compound mixtures, enabling the direct detection of intact HPPK–ligand complexes in solution. Dual-mode MS acquisitions (low [...] Read more.
Identification of ligands targeting essential enzymes in Mycobacterium species remains an important strategy for anti-tuberculosis drug discovery. Here, a native mass spectrometry approach was employed using pooled 100-compound mixtures, enabling the direct detection of intact HPPK–ligand complexes in solution. Dual-mode MS acquisitions (low collision energy for complex detection and high collision energy for ligand confirmation), combined with an automated data analysis workflow, ensured robust identification of binding events from these complex samples. This strategy led to the identification of several HPPK-binding small molecules, all belonging to the dammarane triterpene glycoside (ginsenoside) class. Subsequent analysis of the hits revealed clear structure–affinity relationships, highlighting how specific aglycone modifications and glycosylation patterns influence binding to HPPK. Our findings expand the known chemical space of HPPK ligands and demonstrate the utility of native MS-based screening coupled with automated data analysis to uncover new ligand scaffolds for challenging enzyme targets. Full article
(This article belongs to the Special Issue Application of Mass Spectrometry Techniques in Analytical Chemistry)
►▼ Show Figures

Figure 1

23 pages, 14253 KB  
Article
Chemical Profiling of Aboveground and Underground Parts of Pterocephalus hookeri by Integrated FBMN, Untargeted LC-MS Metabolomics, and PAD-DESI-MSI
by Jiaxing Luo, Lanlan Fang, Muze Yu, Di Yang, Jing Zhang, Jia Yu, Ce Tang and Tingting Kuang
Molecules 2026, 31(11), 1868; https://doi.org/10.3390/molecules31111868 - 29 May 2026
Viewed by 474
Abstract
Pterocephalus hookeri (C.B.Clarke) Höeck is a classic traditional Tibetan medicinal herb with multiple pharmacological activities. The inconsistent usage of its medicinal parts (whole herb, aboveground part (AP), and underground part (UP)) in commercial circulation severely restricts its clinical safety and quality stability. Currently, [...] Read more.
Pterocephalus hookeri (C.B.Clarke) Höeck is a classic traditional Tibetan medicinal herb with multiple pharmacological activities. The inconsistent usage of its medicinal parts (whole herb, aboveground part (AP), and underground part (UP)) in commercial circulation severely restricts its clinical safety and quality stability. Currently, most existing chemical investigations focus on the whole herb, whereas the intraspecific chemical discrepancies between AP and UP remain poorly clarified. Herein, an integrated analytical strategy combining ultra-high-performance liquid chromatography–quadrupole time-of-flight mass spectrometry (UPLC-Q-TOF/MS)-based untargeted metabolomics, feature-based molecular networking (FBMN), and paper-based analytical device desorption electrospray ionization mass spectrometry imaging (PAD-DESI-MSI) was established to characterize differential metabolites and their spatial distribution in P. hookeri. A total of 101 compounds were annotated, and 12 vital differential metabolites were further screened with variable importance in projection (VIP) values > 1. The visualized distribution differences of these biomarkers were validated via heatmap and PAD-DESI-MSI analysis. Obvious differences in chemical accumulation characteristics were confirmed between AP and UP, which can guide reasonable clinical medication and rational dosage regulation referring to metabolite abundance. Moreover, optimized data filtering thresholds effectively eliminated metabolomic false positives, and FBMN exhibited excellent capacity for differential biomarker screening. This study provides a solid chemical basis for the quality evaluation and rational medicinal application of P. hookeri. Full article
(This article belongs to the Special Issue Application of Mass Spectrometry Techniques in Analytical Chemistry)
►▼ Show Figures

Graphical abstract

15 pages, 1223 KB  
Article
High-Throughput LC–MS/MS Quantification of Eighteen Cannabinoids in Hemp Flowers with Baseline Separation of Structural Isomers
by Na Liu, Maggie Schoener, Naima Jannath Rimi, Md Imon Hossain, Supraja Regunathan, Robert Powers and Liguo Song
Molecules 2026, 31(10), 1684; https://doi.org/10.3390/molecules31101684 - 16 May 2026
Viewed by 1041
Abstract
Following the passage of the Agriculture Improvement Act of 2018, demand for accurate cannabinoid quantification in hemp flowers has increased to ensure regulatory compliance. Liquid chromatography–tandem mass spectrometry (LC–MS/MS) using a triple-quadrupole mass spectrometer provides high sensitivity and selectivity and is well suited [...] Read more.
Following the passage of the Agriculture Improvement Act of 2018, demand for accurate cannabinoid quantification in hemp flowers has increased to ensure regulatory compliance. Liquid chromatography–tandem mass spectrometry (LC–MS/MS) using a triple-quadrupole mass spectrometer provides high sensitivity and selectivity and is well suited for this purpose; however, a review of the literature indicates that many published LC–MS/MS methods target only a limited number of cannabinoids, and reliable differentiation of structural isomers remains challenging. In this study, an LC–MS/MS method was developed for the simultaneous quantification of eighteen cannabinoids in hemp flowers. Baseline chromatographic separation of structural isomers enabled reliable differentiation of compounds with highly similar fragmentation patterns and allowed the use of the most sensitive multiple reaction monitoring (MRM) transitions for quantification. Both positive and negative ionization modes were employed to achieve optimal sensitivity using dynamic polarity switching within a single analytical run. Following validation in accordance with ISO/IEC 17025, the method was applied to a proficiency test hemp sample and six commercial hemp samples, demonstrating excellent time efficiency (11 min for 18 cannabinoids) and an exceptionally wide calibration range (8–5000 ng/mL, corresponding to 0.032–20% (w/w) for all cannabinoids). Full article
(This article belongs to the Special Issue Application of Mass Spectrometry Techniques in Analytical Chemistry)
►▼ Show Figures

Figure 1

Show export options expand_more Show export options expand_less
Select all
Export citation of selected articles as:
 
Displaying articles 1-4
Back to TopTop