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Proteomes
Special Issues
Clinical Proteomics: Third Edition
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Clinical Proteomics: Third Edition

A special issue of Proteomes (ISSN 2227-7382).

Deadline for manuscript submissions: closed (30 June 2023) | Viewed by 6976

Special Issue Editors

Dr. Edwin Lasonder

E-Mail Website
Guest Editor
Department of Applied Sciences, Faculty of Life and Health Sciences, Northumbria University, Newcastle-Upon-Tyne NE1 8ST, UK
Interests: mass spectrometry-based proteomics; malaria; Plasmodium falciparum; red blood cells; cancer; phosphorylation; signalling pathways; clinical proteomics
Special Issues, Collections and Topics in MDPI journals
Dr. Vikram Sharma

E-Mail Website
Guest Editor
School of Biomedical Sciences, University of Plymouth, Plymouth PL4 8AA, UK
Interests: proteomics; mass spectrometry; signaling pathways; cancer; phosphorylation
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

In the post-genome era, ‘omics’ technologies are key to our understanding of human disease because these technologies provide a global approach rather than studying single genes/proteins by traditional biochemical approaches. This Special Issue is dedicated to covering the area of clinical proteomics and translational mass-spectrometry-based proteomics research. This typically involves protein profiling of human cells and tissues in health and disease state for the detection of diagnostic and prognostic biomarkers, or for developing mechanistic insights into disease pathogenicity. An important advantage of the global proteome approach is that it provides an overall catalogue of differentially expressed proteins in body fluids, cells, and tissues that define disease phenotypes in patients, which can contribute to individualized treatments. Recent advancements in modern mass spectrometers regarding sensitivity, sequencing methods (DDA, DIA), and quantification approaches of clinical samples (label-free quantification, multiplex quantitation via isobaric chemical tags, and absolute quantification via SRM/MRM technology) enable deep proteome coverage of clinical samples, which is an important prerequisite for personalized medicine.

In this Special Issue of Proteomes, we are looking forward to original research studies on proteome analysis of disease-related samples and welcome the submission of review articles covering recent developments in clinical proteomics.

Dr. Edwin Lasonder
Dr. Vikram Sharma
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. Proteomes is an international peer-reviewed open access quarterly 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 1800 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

  • Clinical proteomics 
  • Disease 
  • Body fluids and tissue 
  • Personalized medicine 
  • Quantitative proteomics

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Published Papers (2 papers)

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14 pages, 879 KiB  
Article
Urine Peptidome Analysis Identifies Common and Stage-Specific Markers in Early Versus Advanced CKD
by Sam Hobson, Emmanouil Mavrogeorgis, Tianlin He, Justyna Siwy, Thomas Ebert, Karolina Kublickiene, Peter Stenvinkel and Harald Mischak
Proteomes 2023, 11(3), 25; https://doi.org/10.3390/proteomes11030025 - 23 Aug 2023
Cited by 1 | Viewed by 1898
Abstract
Given the pathophysiological continuum of chronic kidney disease (CKD), different molecular determinants affecting progression may be associated with distinct disease phases; thus, identification of these players are crucial for guiding therapeutic decisions, ideally in a non-invasive, repeatable setting. Analyzing the urinary peptidome has [...] Read more.
Given the pathophysiological continuum of chronic kidney disease (CKD), different molecular determinants affecting progression may be associated with distinct disease phases; thus, identification of these players are crucial for guiding therapeutic decisions, ideally in a non-invasive, repeatable setting. Analyzing the urinary peptidome has been proven an efficient method for biomarker determination in CKD, among other diseases. In this work, after applying several selection criteria, urine samples from 317 early (stage 2) and advanced (stage 3b–5) CKD patients were analyzed using capillary electrophoresis coupled to mass spectrometry (CE-MS). The entire two groups were initially compared to highlight the respective pathophysiology between initial and late disease phases. Subsequently, slow and fast progressors were compared within each group in an attempt to distinguish phase-specific disease progression molecules. The early vs. late-stage CKD comparison revealed 929 significantly different peptides, most of which were downregulated and 268 with collagen origins. When comparing slow vs. fast progressors in early stage CKD, 42 peptides were significantly altered, 30 of which were collagen peptide fragments. This association suggests the development of structural changes may be reversible at an early stage. The study confirms previous findings, based on its multivariable-matched progression groups derived from a large initial cohort. However, only four peptide fragments differed between slow vs. fast progressors in late-stage CKD, indicating different pathogenic processes occur in fast and slow progressors in different stages of CKD. The defined peptides associated with CKD progression at early stage might potentially constitute a non-invasive approach to improve patient management by guiding (personalized) intervention. Full article
(This article belongs to the Special Issue Clinical Proteomics: Third Edition)
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Review

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27 pages, 2271 KiB  
Review
Proteomic Research of Extracellular Vesicles in Clinical Biofluid
by Shipan Fan and Ansgar Poetsch
Proteomes 2023, 11(2), 18; https://doi.org/10.3390/proteomes11020018 - 6 May 2023
Cited by 4 | Viewed by 4306
Abstract
Extracellular vesicles (EVs), the lipid bilayer membranous structures of particles, are produced and released from almost all cells, including eukaryotes and prokaryotes. The versatility of EVs has been investigated in various pathologies, including development, coagulation, inflammation, immune response modulation, and cell–cell communication. Proteomics [...] Read more.
Extracellular vesicles (EVs), the lipid bilayer membranous structures of particles, are produced and released from almost all cells, including eukaryotes and prokaryotes. The versatility of EVs has been investigated in various pathologies, including development, coagulation, inflammation, immune response modulation, and cell–cell communication. Proteomics technologies have revolutionized EV studies by enabling high-throughput analysis of their biomolecules to deliver comprehensive identification and quantification with rich structural information (PTMs, proteoforms). Extensive research has highlighted variations in EV cargo depending on vesicle size, origin, disease, and other features. This fact has sparked activities to use EVs for diagnosis and treatment to ultimately achieve clinical translation with recent endeavors summarized and critically reviewed in this publication. Notably, successful application and translation require a constant improvement of methods for sample preparation and analysis and their standardization, both of which are areas of active research. This review summarizes the characteristics, isolation, and identification approaches for EVs and the recent advances in EVs for clinical biofluid analysis to gain novel knowledge by employing proteomics. In addition, the current and predicted future challenges and technical barriers are also reviewed and discussed. Full article
(This article belongs to the Special Issue Clinical Proteomics: Third Edition)
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