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Molecular Application of Mass Spectrometry and Chromatography in Biomedicine

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Biophysics".

Deadline for manuscript submissions: 20 August 2025 | Viewed by 9215

Special Issue Editor

Dr. Giovanni Ventura

E-Mail Website
Guest Editor
Dipartimento di Chimica, Centro Interdipartimentale SMART, Università degli Studi di Bari, Via Orabona, 4-I-70126 Bari, Italy
Interests: mass spectrometry; liquid chromatography; lipidomics; proteomics; biomarker discovery
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Mass spectrometry and chromatography are revolutionizing medical research and diagnostics, delving deep into the intricate molecular landscapes of biological systems and uncovering crucial insights into the mechanisms of disease, the identification of biomarkers, drug metabolism, and personalized medicine.

In this Special Issue, by considering the field of Biomedicine, we wish to collect papers addressing the application of mass spectrometric techniques, whether used alone or in combination with chromatography, for the identification, quantification, or structural elucidation of biomolecules, including proteins, lipids, metabolites, and pharmaceutical compounds; this will enable the study of disease biomarkers, advance drug discovery, unveil potential health benefits, and enhance clinical diagnostics.

This Special Issue is supervised by Dr. Giovanni Ventura and assisted by our Topical Advisory Panel Member Dr. Mariachiara Bianco. We would like to invite you to contribute original articles or reviews related to approaches involving mass spectrometry and chromatography for biomedical application.

Dr. Giovanni Ventura
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 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. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. 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
  • chromatography
  • LC-MS
  • GC-MS
  • biomarker discovery
  • pharmaceuticals
  • metabolimics
  • proteomics
  • lipidomics

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Published Papers (6 papers)

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Research

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14 pages, 4659 KiB  
Article
Unlocking the Complexity of Antibody-Drug Conjugates: A Cutting-Edge LC-HRMS Approach to Refine Drug-to-Antibody Ratio Measurements with Highly Reactive Payloads
by Andrea Di Ianni, Kyra J. Cowan, Federico Riccardi Sirtori and Luca Barbero
Int. J. Mol. Sci. 2025, 26(7), 3080; https://doi.org/10.3390/ijms26073080 - 27 Mar 2025
Viewed by 570
Abstract
The complexity of therapeutic proteins like antibody–drug conjugates (ADCs) holds a tremendous analytical challenge. Complementary mass spectrometry approaches such as peptide mapping and intact mass analysis are required for the in-depth characterization of these bioconjugates. Cysteine-linked ADCs have shown a unique challenge for [...] Read more.
The complexity of therapeutic proteins like antibody–drug conjugates (ADCs) holds a tremendous analytical challenge. Complementary mass spectrometry approaches such as peptide mapping and intact mass analysis are required for the in-depth characterization of these bioconjugates. Cysteine-linked ADCs have shown a unique challenge for characterization, mainly when the conjugation is carried out on interchain cysteines, because their intact analysis requires native mass spectrometry conditions to preserve non-covalent binding between antibody chains. In this work, two different approaches were proposed. Specifically, a full scan data-independent all ion fragmentation (FS-AIF) and a full scan data-dependent targeted MS2 (FS-ddtMS2) were applied to generate complementary datasets for a cysteine-linked ADC characterization with a highly reactive payload. These two methods were applied to in vitro plasma stability and in vivo PK samples to calculate and refine mean drug-to-antibody ratio over time. Using this approach, we successfully characterized an ADC containing a hydrolysis-sensitive payload and refined the “active” drug-to-antibody ratio on in vitro stability and in vivo samples. These two methods allowed the confirmation of the different ADC species and potential metabolites of conjugated payload attached to the antibody backbone in a single analysis without needing a dedicated method for the conjugated payload metabolite identification. Full article
(This article belongs to the Special Issue Molecular Application of Mass Spectrometry and Chromatography in Biomedicine)
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8 pages, 1710 KiB  
Communication
The Glycosylation of Serum IgG Antibodies in Post-COVID-19 and Post-Vaccination Patients
by Csaba Váradi
Int. J. Mol. Sci. 2025, 26(2), 807; https://doi.org/10.3390/ijms26020807 - 18 Jan 2025
Viewed by 1108
Abstract
The signature of human serum IgG glycosylation is critical in the defense against pathogens. Alterations of IgG N-glycome were associated with COVID-19 (Coronavirus disease 2019) severity, although knowledge on the response to vaccination is limited. IgG N-glycome was analyzed in this study in [...] Read more.
The signature of human serum IgG glycosylation is critical in the defense against pathogens. Alterations of IgG N-glycome were associated with COVID-19 (Coronavirus disease 2019) severity, although knowledge on the response to vaccination is limited. IgG N-glycome was analyzed in this study in post-COVID-19 and post-vaccination patients to reveal potential glycosylation-based alterations using hydrophilic interaction liquid chromatography (HILIC-UPLC) with fluorescence (FLR) and mass-spectrometric (MS) detection. IgG antibodies were purified from serum samples through protein G affinity chromatography followed by PNGase F digestion-based deglycosylation. The released glycans were fluorescently derivatized by procainamide labeling and purified via solid-phase extraction. Higher levels of sialylation and afucosylation were identified in post-COVID-19 patients, which was further expanded by vaccination, but only in those who were previously SARS-CoV-2 (Severe acute respiratory syndrome coronavirus 2) infected. Full article
(This article belongs to the Special Issue Molecular Application of Mass Spectrometry and Chromatography in Biomedicine)
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16 pages, 3118 KiB  
Article
Comparative Pharmacokinetic Analysis of Aflibercept and Brolucizumab in Human Aqueous Humor Using Nano-Surface and Molecular-Orientation Limited Proteolysis
by Kosuke Nagaoka, Natsuka Kimura, Satoru Inoda, Takuya Takayama, Yusuke Arai, Yasuo Yanagi, Takashi Shimada, Ryozo Nagai, Hidenori Takahashi and Kenichi Aizawa
Int. J. Mol. Sci. 2025, 26(2), 556; https://doi.org/10.3390/ijms26020556 - 10 Jan 2025
Cited by 1 | Viewed by 1833
Abstract
Aflibercept and brolucizumab, two anti-VEGF agents used as intravitreal injections in ophthalmology, differ significantly in molecular weight (aflibercept—115 kDa and brolucizumab—26 kDa). Using aqueous humor samples collected after drug administration, we measured and performed a comparative analysis of pharmacokinetics and half-lives of these [...] Read more.
Aflibercept and brolucizumab, two anti-VEGF agents used as intravitreal injections in ophthalmology, differ significantly in molecular weight (aflibercept—115 kDa and brolucizumab—26 kDa). Using aqueous humor samples collected after drug administration, we measured and performed a comparative analysis of pharmacokinetics and half-lives of these drugs in the human eye. Since the quantification of monoclonal antibodies (mAbs) using antigen–antibody reactions, such as ELISA, is influenced by endogenous ligands or anti-drug antibodies, we employed nano-surface and molecular-orientation limited proteolysis (nSMOL), combined with liquid chromatography–tandem mass spectrometry (LC-MS/MS), for accurate measurements. Aqueous humor samples were collected from 59 eyes of 59 patients treated with aflibercept and 52 eyes of 52 patients treated with brolucizumab. Samples were obtained with a median post-injection period of 30 (range, 2–49) days for aflibercept and 28 (range, 4–60) days for brolucizumab. A population pharmacokinetic (PPK) analysis revealed that the half-life of aflibercept in human aqueous humor was significantly shorter than that of brolucizumab, 2.88 days versus 9.00 days, respectively (p = 1.16 × 10−7). Using the same mass spectrometry conditions, we calculated the half-lives of the two drugs. These results may be useful for optimizing the efficacy of these drugs in clinical practice. Full article
(This article belongs to the Special Issue Molecular Application of Mass Spectrometry and Chromatography in Biomedicine)
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17 pages, 1571 KiB  
Article
Tandem Mass Spectrometry in Untargeted Lipidomics: A Case Study of Peripheral Blood Mononuclear Cells
by Giovanni Ventura, Mariachiara Bianco, Cosima Damiana Calvano, Ilario Losito and Tommaso R. I. Cataldi
Int. J. Mol. Sci. 2024, 25(22), 12077; https://doi.org/10.3390/ijms252212077 - 10 Nov 2024
Cited by 1 | Viewed by 1617
Abstract
Peripheral blood mononuclear cells (PBMCs), including lymphocytes, are important components of the human immune system. These cells contain a diverse array of lipids, primarily glycerophospholipids (GPs) and sphingolipids (SPs), which play essential roles in cellular structure, signaling, and programmed cell death. This study [...] Read more.
Peripheral blood mononuclear cells (PBMCs), including lymphocytes, are important components of the human immune system. These cells contain a diverse array of lipids, primarily glycerophospholipids (GPs) and sphingolipids (SPs), which play essential roles in cellular structure, signaling, and programmed cell death. This study presents a detailed analysis of GP and SP profiles in human PBMC samples using tandem mass spectrometry (MS/MS). Hydrophilic interaction liquid chromatography (HILIC) and electrospray ionization (ESI) coupled with linear ion-trap MS/MS were employed to investigate the diagnostic fragmentation patterns that aided in determining regiochemistry in complex lipid extracts. Specifically, the study explored the fragmentation patterns of various lipid species, including phosphatidylcholines (PCs), phosphatidylethanolamines (PEs), their plasmalogen and lyso forms, phosphatidylserines (PSs), phosphatidylinositols (PIs), phosphatidylglycerols (PGs), sphingomyelins (SMs), and dihexosylceramides (Hex2Cer). Our comprehensive analysis led to the characterization of over 200 distinct lipid species, significantly expanding our understanding of PBMC lipidome complexity. A freely available spreadsheet tool for simulating MS/MS spectra of GPs is provided, enhancing the accessibility and reproducibility of this research. This study advances our knowledge of PBMC lipidomes and establishes a robust analytical framework for future investigations in lipidomics. Full article
(This article belongs to the Special Issue Molecular Application of Mass Spectrometry and Chromatography in Biomedicine)
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17 pages, 2220 KiB  
Article
Quantification of Letrozole, Palbociclib, Ribociclib, Abemaciclib, and Metabolites in Volumetric Dried Blood Spots: Development and Validation of an LC-MS/MS Method for Therapeutic Drug Monitoring
by Eleonora Cecchin, Marco Orleni, Sara Gagno, Marcella Montico, Elena Peruzzi, Rossana Roncato, Lorenzo Gerratana, Serena Corsetti, Fabio Puglisi, Giuseppe Toffoli, Erika Cecchin and Bianca Posocco
Int. J. Mol. Sci. 2024, 25(19), 10453; https://doi.org/10.3390/ijms251910453 - 27 Sep 2024
Cited by 2 | Viewed by 1433
Abstract
Therapeutic drug monitoring (TDM) may be beneficial for cyclin-dependent kinase 4/6 inhibitors (CDK4/6is), such as palbociclib, ribociclib, and abemaciclib, due to established exposure–toxicity relationships and the potential for monitoring treatment adherence. Developing a method for quantifying CDK4/6is, abemaciclib metabolites (M2, M20), and letrozole [...] Read more.
Therapeutic drug monitoring (TDM) may be beneficial for cyclin-dependent kinase 4/6 inhibitors (CDK4/6is), such as palbociclib, ribociclib, and abemaciclib, due to established exposure–toxicity relationships and the potential for monitoring treatment adherence. Developing a method for quantifying CDK4/6is, abemaciclib metabolites (M2, M20), and letrozole in dried blood spots (DBS) could be useful to enhance the feasibility of TDM. Thus, an optimized LC-MS/MS method was developed using the HemaXis DB10 device for volumetric (10 µL) DBS collection. Chromatographic separation was achieved using a reversed-phase XBridge BEH C18 column. Detection was performed with a triple quadrupole mass spectrometer, utilizing ESI source switching between negative and positive ionization modes and multiple reaction monitoring acquisition. Analytical validation followed FDA, EMA, and IATDMCT guidelines, demonstrating high selectivity, adequate sensitivity (LLOQ S/N ≥ 30), and linearity (r ≥ 0.997). Accuracy and precision met acceptance criteria (between-run: accuracy 95–106%, CV ≤ 10.6%). Haematocrit independence was confirmed (22–55%),with high recovery rates (81–93%) and minimal matrix effects (ME 0.9–1.1%). The stability of analytes under home-sampling conditions was also verified. Clinical validation supports DBS-based TDM as feasible, with conversion models developed for estimating plasma concentrations (the reference for TDM target values) of letrozole, abemaciclib, and its metabolites. Preliminary data for palbociclib and ribociclib are also presented. Full article
(This article belongs to the Special Issue Molecular Application of Mass Spectrometry and Chromatography in Biomedicine)
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Review

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25 pages, 748 KiB  
Review
Targeted Chiral Metabolomics of D-Amino Acids: Their Emerging Role as Potential Biomarkers in Neurological Diseases with a Focus on Their Liquid Chromatography–Mass Spectrometry Analysis upon Chiral Derivatization
by Cinzia Lella, Liam Nestor, Dimitri De Bundel, Yvan Vander Heyden and Ann Van Eeckhaut
Int. J. Mol. Sci. 2024, 25(22), 12410; https://doi.org/10.3390/ijms252212410 - 19 Nov 2024
Cited by 3 | Viewed by 1643
Abstract
In neuroscience research, chiral metabolomics is an emerging field, in which D-amino acids play an important role as potential biomarkers for neurological diseases. The targeted chiral analysis of the brain metabolome, employing liquid chromatography (LC) coupled to mass spectrometry (MS), is a pivotal [...] Read more.
In neuroscience research, chiral metabolomics is an emerging field, in which D-amino acids play an important role as potential biomarkers for neurological diseases. The targeted chiral analysis of the brain metabolome, employing liquid chromatography (LC) coupled to mass spectrometry (MS), is a pivotal approach for the identification of biomarkers for neurological diseases. This review provides an overview of D-amino acids in neurological diseases and of the state-of-the-art strategies for the enantioselective analysis of chiral amino acids (AAs) in biological samples to investigate their putative role as biomarkers for neurological diseases. Fluctuations in D-amino acids (D-AAs) levels can be related to the pathology of neurological diseases, for example, through their role in the modulation of N-methyl-D-aspartate receptors and neurotransmission. Because of the trace presence of these biomolecules in mammals and the complex nature of biological matrices, highly sensitive and selective analytical methods are essential. Derivatization strategies with chiral reagents are highlighted as critical tools for enhancing detection capabilities. The latest advances in chiral derivatization reactions, coupled to LC-MS/MS analysis, have improved the enantioselective quantification of these AAs and allow the separation of several chiral metabolites in a single analytical run. The enhanced performances of these methods can provide an accurate correlation between specific D-AA profiles and disease states, allowing for a better understanding of neurological diseases and drug effects on the brain. Full article
(This article belongs to the Special Issue Molecular Application of Mass Spectrometry and Chromatography in Biomedicine)
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