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Cancers
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Mass Spectrometry-Based “Omics” Approaches in Cancer Research
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Mass Spectrometry-Based “Omics” Approaches in Cancer Research

A special issue of Cancers (ISSN 2072-6694). This special issue belongs to the section "Methods and Technologies Development".

Deadline for manuscript submissions: closed (30 May 2025) | Viewed by 8044

Special Issue Editors

Dr. Rita Casadonte

E-Mail Website
Guest Editor
Proteopath GmbH, Max-Planck-Str. 17, 54296 Trier, Germany
Interests: cancer; diagnostics; mass spectrometry; molecular pathology; “omics”
Special Issues, Collections and Topics in MDPI journals
Dr. Kristina Schwamborn

E-Mail Website
Guest Editor
Institute of Pathology, School of Medicine, Technical University of Munich, Trogerstr. 18, 81675 Munich, Germany
Interests: immunohistochemistry; hemato-oncology; uro-oncology; mass spectrometry
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Over the past two decades, the words "omics" has expanded from the initial "genomics" to a wide range of biomolecular disciplines directed toward the study of RNA species (transcriptomics), proteins (proteomics), lipids (lipidomics), glycans (glycomics), and metabolites (metabolomics). The spread of omics disciplines has been possible mainly through the development of novel and high-throughput mass spectrometry technologies and informatics tools capable of generating large amounts of data related to different levels of biological complexity (DNA, mRNA, proteins, metabolites, etc.).

Emerging omics technologies are likely to influence the development of omics-based analysis of cancer in the future, as both the types and numbers of molecular measurements continue to increase. Furthermore, the combination of different omics approaches generates more comprehensive information, ultimately leading to a deeper understanding of cancer. There is a strong interest to push “omics” technologies in the direction of highly personalized medicine to achieve targeted therapies capable of halting tumor progression.

The purpose of this Special Issue is to deliver recent advances of mass spectrometry‐based “omics” application in cancer helping in biomarker discovery for early diagnosis, prognosis, and appropriate therapeutics.

Dr. Rita Casadonte
Dr. Kristina Schwamborn
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 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. Cancers 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 2900 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

  • biomarker discovery
  • cancer
  • mass spectrometry
  • “omics”

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Published Papers (2 papers)

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20 pages, 2506 KB  
Article
Urinary Metabolome Study for Monitoring Prostate Cancer Recurrence Following Radical Prostatectomy
by Sabur Badmos, Elizabeth Noriega Landa, Kiana L. Holbrook, George E. Quaye, Xiaogang Su and Wen-Yee Lee
Cancers 2025, 17(17), 2756; https://doi.org/10.3390/cancers17172756 - 24 Aug 2025
Viewed by 971
Abstract
Background/objectives: Prostate cancer (PCa) is the most common cancer among males. Approximately 20–40% of patients with clinically localized PCa will present with a biochemical recurrence after a radical prostatectomy (RP), while some will present with recurrent metastasis. Monitoring the disease post-treatment is crucial [...] Read more.
Background/objectives: Prostate cancer (PCa) is the most common cancer among males. Approximately 20–40% of patients with clinically localized PCa will present with a biochemical recurrence after a radical prostatectomy (RP), while some will present with recurrent metastasis. Monitoring the disease post-treatment is crucial for detecting a potential cancer recurrence early. Urinary volatile organic compounds (VOCs) have shown potential to detect PCa. However, their application in disease monitoring remains unexplored. Methods: A total of 165 urine samples were collected from male adults with biopsy-designated PCa-positive results before (n = 55) and after a RP (n = 55), and with biopsy-designated PCa-negative diagnosis (n = 55). The post-RP cohort was subdivided into three groups based on their health status after surgery as recovered healthy, biochemical recurrence, and recurrent metastasis. VOCs in the urine samples were extracted by stir bar sorptive extraction and analyzed using gas chromatography and mass spectrometry. We explored the use of metabolomics and a machine learning algorithm tool to investigate the potential of using VOCs for differentiating PCa diagnoses before and after the RP procedure with different outcomes. Results: Over 100 potential VOCs were identified to differentiate PCa patients before and after a RP, and those with biochemical recurrence and recurrent metastasis. Conclusions: Urinary VOCs are promising biomarkers that could be used to differentiate PCa patients pre- and post-RP. The findings from this research provide preliminary insights and could aid future investigations in developing tools for PCa patients after treatment. The absence of a validation cohort limits the reproducibility and translational impact of these findings; therefore, the results should be considered exploratory and require confirmation in larger, independent cohorts. Full article
(This article belongs to the Special Issue Mass Spectrometry-Based “Omics” Approaches in Cancer Research)
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Review

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23 pages, 11223 KB  
Review
Proximity Labeling: Precise Proteomics Technology for Mapping Receptor Protein Neighborhoods at the Cancer Cell Surface
by Saman Rahmati and Andrew Emili
Cancers 2025, 17(2), 179; https://doi.org/10.3390/cancers17020179 - 8 Jan 2025
Cited by 1 | Viewed by 6330
Abstract
Cell surface receptors are pivotal to cancer cell transformation, disease progression, metastasis, early detection, targeted therapy, drug responses, and clinical outcomes. Since they coordinate complex signaling communication networks in the tumor microenvironment, mapping the physical interaction partners of cell surface receptors in vivo [...] Read more.
Cell surface receptors are pivotal to cancer cell transformation, disease progression, metastasis, early detection, targeted therapy, drug responses, and clinical outcomes. Since they coordinate complex signaling communication networks in the tumor microenvironment, mapping the physical interaction partners of cell surface receptors in vivo is vital for understanding their roles, functional states, and suitability as therapeutic targets. Yet traditional methods like immunoprecipitation and affinity purification–mass spectrometry often fail to detect key but weak or transient receptor–protein interactions. Proximity labeling, a cutting-edge proteomics technology, addresses these technical challenges by enabling precise mapping of protein neighborhoods around a receptor target on the cell surface of cancer cells. This technique has been successfully applied in vitro and in vivo for proteomic mapping across various model systems. This review explores the fundamental principles, technologies, advantages, limitations, and applications of proximity labeling in cancer biology, focusing on mapping receptor microenvironments. By advancing mechanistic insights into cancer cell receptor signaling mechanisms, proximity labeling is poised to transform cancer research, improve targeted therapies, and illuminate avenues to overcome drug resistance. Full article
(This article belongs to the Special Issue Mass Spectrometry-Based “Omics” Approaches in Cancer Research)
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