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New Insights into Proteomics and Applications in Molecular Diagnostics and Systems Biology

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

Deadline for manuscript submissions: closed (20 October 2024) | Viewed by 6793

Special Issue Editor

Dr. Paulo Marcelo

E-Mail Website
Guest Editor
Plateforme d’Ingénierie Cellulaire & Analyses des Protéines ICAP, FR CNRS 3085 ICP, Université de Picardie Jules Verne, 80039 Amiens, France
Interests: tandem mass spectrometry; quantitative proteomics; shotgun proteomics; functional proteomics; systems biology; small molecules; biomarker discovery; data analysis

Special Issue Information

Dear Colleagues,

In recent years, proteomics has revolutionizing our understanding of cellular processes, disease mechanisms and drug development. Some of the recent advances in proteomics approaches have propelled this field to the forefront of modern biology and medicine. Proteomics plays an essential role in deciphering the complex molecular machinery of living organisms. It explores the identity, structure, function and interactions of proteins, shedding light on their crucial roles in cellular functions and signaling pathways. Recent technological advancements include those in mass spectrometry, such as isobaric stable isotope labelling. The multiplexing capability of these reagents enables achieving deep proteome coverage for multiple samples. These innovations have paved the way for the discovery of novel biomarkers for diseases, providing valuable insights into early diagnosis and personalized medicine.

Furthermore, proteomics has been instrumental in elucidating the mechanisms underlying various diseases, including cancer, neurodegenerative disorders and infectious diseases. By identifying specific protein alterations associated with these conditions, researchers are now better equipped to develop targeted therapies and therapeutic interventions. Additionally, proteomics has fostered the emergence of systems biology, allowing scientists to integrate proteomic data with genomics, transcriptomics and metabolomics, creating a holistic view of biological systems. The application of proteogenomics helps elucidate the complex landscape of cancer mutations and potential therapeutic targets. Moreover, single-cell proteomics has also emerged as a cutting-edge approach, enabling the study of heterogeneity within cell populations and shedding light on developmental processes and disease pathogenesis.

In conclusion, proteomics has undergone transformative developments in recent years, empowering researchers with the tools and knowledge needed to unravel the complexities of life at the molecular level. As we delve into the remarkable progress and potential of proteomics, we gain a deeper appreciation for its significance in driving advancements in medicine, diagnostics and our overall comprehension of the biological world.

Dr. Paulo Marcelo
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
  • liquid chromatography
  • tandem mass spectrometry (MS/MS)
  • quantitative proteomics
  • shotgun proteomics
  • label-free quantification
  • post-translational modifications
  • protein–protein interactions
  • proteogenomics
  • single-cell proteomics
  • data analysis
  • bioinformatics
  • functional proteomics
  • phosphoproteomics
  • glycoproteomics
  • biomarker discovery
  • top–down proteomics
  • clinical applications
  • disease proteomics
  • systems biology

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Published Papers (3 papers)

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20 pages, 526 KiB  
Article
Follicular Fluid Proteomic Analysis to Identify Predictive Markers of Normal Embryonic Development
by Janusz Przewocki, Dominik Kossiński, Adam Łukaszuk, Grzegorz Jakiel, Izabela Wocławek-Potocka, Stanisław Ołdziej and Krzysztof Łukaszuk
Int. J. Mol. Sci. 2024, 25(15), 8431; https://doi.org/10.3390/ijms25158431 - 1 Aug 2024
Cited by 1 | Viewed by 1941
Abstract
Ageing populations, mass “baby-free” policies and children born to mothers at the age at which they are biologically expected to become grandmothers are growing problems in most developed societies. Therefore, any opportunity to improve the quality of infertility treatments seems important for the [...] Read more.
Ageing populations, mass “baby-free” policies and children born to mothers at the age at which they are biologically expected to become grandmothers are growing problems in most developed societies. Therefore, any opportunity to improve the quality of infertility treatments seems important for the survival of societies. The possibility of indirectly studying the quality of developing oocytes by examining their follicular fluids (hFFs) offers new opportunities for progress in our understanding the processes of final oocyte maturation and, consequently, for predicting the quality of the resulting embryos and personalising their culture. Using mass spectrometry, we studied follicular fluids collected individually during in vitro fertilisation and compared their composition with the quality of the resulting embryos. We analysed 110 follicular fluids from 50 oocyte donors, from which we obtained 44 high-quality, 39 medium-quality, and 27 low-quality embryos. We identified 2182 proteins by Sequential Window Acquisition of all Theoretical Mass Spectra (SWATH-MS) using a TripleTOF 5600+ hybrid mass spectrometer, of which 484 were suitable for quantification. We were able to identify several proteins whose concentrations varied between the follicular fluids of different oocytes from the same patient and between patients. Among them, the most important appear to be immunoglobulin heavy constant alpha 1 (IgA1hc) and dickkopf-related protein 3. The first one is found at higher concentrations in hFFs from which oocytes develop into poor-quality embryos, the other one exhibits the opposite pattern. None of these have, so far, had any specific links to fertility disorders. In light of these findings, these proteins should be considered a primary target for research aimed at developing a diagnostic tool for oocyte quality control and pre-fertilisation screening. This is particularly important in cases where the fertilisation of each egg is not an option for ethical or other reasons, or in countries where it is prohibited by law. Full article
(This article belongs to the Special Issue New Insights into Proteomics and Applications in Molecular Diagnostics and Systems Biology)
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19 pages, 3169 KiB  
Article
The Bee Gut Microbiota: Bridging Infective Agents Potential in the One Health Context
by Bruno Tilocca, Viviana Greco, Cristian Piras, Carlotta Ceniti, Mariachiara Paonessa, Vincenzo Musella, Roberto Bava, Ernesto Palma, Valeria Maria Morittu, Anna Antonella Spina, Fabio Castagna, Andrea Urbani, Domenico Britti and Paola Roncada
Int. J. Mol. Sci. 2024, 25(7), 3739; https://doi.org/10.3390/ijms25073739 - 27 Mar 2024
Cited by 4 | Viewed by 3008
Abstract
The bee gut microbiota plays an important role in the services the bees pay to the environment, humans and animals. Alongside, gut-associated microorganisms are vehiculated between apparently remote habitats, promoting microbial heterogeneity of the visited microcosms and the transfer of the microbial genetic [...] Read more.
The bee gut microbiota plays an important role in the services the bees pay to the environment, humans and animals. Alongside, gut-associated microorganisms are vehiculated between apparently remote habitats, promoting microbial heterogeneity of the visited microcosms and the transfer of the microbial genetic elements. To date, no metaproteomics studies dealing with the functional bee microbiota are available. Here, we employ a metaproteomics approach to explore a fraction of the bacterial, fungal, and unicellular parasites inhabiting the bee gut. The bacterial community portrays a dynamic composition, accounting for specimens of human and animal concern. Their functional features highlight the vehiculation of virulence and antimicrobial resistance traits. The fungal and unicellular parasite fractions include environment- and animal-related specimens, whose metabolic activities support the spatial spreading of functional features. Host proteome depicts the major bee physiological activities, supporting the metaproteomics strategy for the simultaneous study of multiple microbial specimens and their host-crosstalks. Altogether, the present study provides a better definition of the structure and function of the bee gut microbiota, highlighting its impact in a variety of strategies aimed at improving/overcoming several current hot topic issues such as antimicrobial resistance, environmental pollution and the promotion of environmental health. Full article
(This article belongs to the Special Issue New Insights into Proteomics and Applications in Molecular Diagnostics and Systems Biology)
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Other

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12 pages, 1216 KiB  
Opinion
From Proteomics to the Analysis of Single Protein Molecules
by Elena A. Ponomarenko, Yuri D. Ivanov, Anastasia A. Valueva, Tatyana O. Pleshakova, Victor G. Zgoda, Nikita E. Vavilov, Ekaterina V. Ilgisonis, Andrey V. Lisitsa and Alexander I. Archakov
Int. J. Mol. Sci. 2024, 25(19), 10308; https://doi.org/10.3390/ijms251910308 - 25 Sep 2024
Viewed by 1274
Abstract
Limit of detection (LoD) is a term that is used to characterize the sensitivity of an analytical method. The existing limitation of the sensitivity of analysis using modern mass spectrometry methods has been experimentally shown to be a limiting factor in the application [...] Read more.
Limit of detection (LoD) is a term that is used to characterize the sensitivity of an analytical method. The existing limitation of the sensitivity of analysis using modern mass spectrometry methods has been experimentally shown to be a limiting factor in the application of proteomic technologies in medicine. This article proposes a concept of a new technology that will set a new vector of development in the development of systems for solving problems of medical diagnostics and deals with theoretical and practical aspects of creating a new technology for the detection of single biomacromolecules (in particular, proteins) in biological samples. Such technology should be based on the principle of signal registration similar to that used in a Geiger counter (also known as a Geiger–Müller counter or G-M counter), a device that automatically counts the number of ionizing particles that hit it. This counter is free from probabilistic components; it registers a signal if there is at least one target molecule in the analysis chamber. Predictive medical diagnostics require technology based on methods where sensitivity allows for the detection of single marker molecules in a biological sample volume of 1–10 µL, the smallest volume of biomaterial used in laboratory diagnostics. Creation of a detector with a sensitivity of 10−18 M would allow for the detection of one molecule in 1 µL of the sample, which fundamentally makes this approach analogous to a G-M counter for solutions. To date, bioanalytical methods are limited to a sensitivity of 10−12 M (which is approximately 1 million molecules per 1 μL), which is insufficient to capture the early stages of pathological processes. Full article
(This article belongs to the Special Issue New Insights into Proteomics and Applications in Molecular Diagnostics and Systems Biology)
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