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Proteomes, Volume 13, Issue 3

2025 September - 21 articles

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Articles (21)

  • Systematic Review
  • Open Access
929 Views
12 Pages

19 September 2025

Neurogranin (NRGN), a synaptic protein essential for plasticity and memory function, is gaining recognition as a promising biomarker for mild traumatic brain injury (mTBI). This systematic review brings together findings from six studies that measure...

  • Article
  • Open Access
1 Citations
3,076 Views
20 Pages

Comparative Analysis of Plasma Extracellular Vesicle Isolation Methods for Purity Assessment and Biomarker Discovery

  • Alexandra T. Star,
  • Melissa Hewitt,
  • Amanpreet Badhwar,
  • Wen Ding,
  • Tammy-Lynn Tremblay,
  • Jennifer J. Hill,
  • William G. Willmore,
  • Jagdeep K. Sandhu and
  • Arsalan S. Haqqani

18 September 2025

Background: Extracellular vesicles (EVs) are an important source of blood biomarkers and are emerging as next-generation therapeutics. Demonstrating the purity of isolated EVs is essential for applications ranging from proteomics-based biomarker disc...

  • Article
  • Open Access
1,566 Views
22 Pages

Proteomic Analysis of Mechanical Injury Effects in Papaya Fruit at Two Maturity Stages

  • Francisco Antonio Reyes-Soria,
  • Eliel Ruiz-May,
  • Enrique Castaño,
  • Miguel Ángel Herrera-Alamillo,
  • José Miguel Elizalde-Contreras,
  • Samuel David Gamboa-Tuz,
  • Lidia F. E. Huerta-Nuñez,
  • Jesús Alejandro Zamora-Briseño and
  • Luis Carlos Rodríguez-Zapata

18 September 2025

Background: Mechanical damage to fruit during harvesting is nearly inevitable, with certain species, such as papaya, being particularly prone to spoilage. Postharvest handling can induce mechanical injuries that impair ripening and reduce shelf life,...

  • Article
  • Open Access
1,216 Views
15 Pages

Proteomic Analysis of Sputum from Patients with Active Tuberculosis

  • Endrei Marcantonio,
  • Amy M. Woron,
  • A. Christian Whelen and
  • Sladjana Prisic

12 September 2025

Background: Patients with pulmonary tuberculosis (TB) typically produce sputa, which are used to identify the pathogen. Sputum also contains host proteins that may aid in diagnosis. We hypothesized that sputa from TB patients will have unique proteom...

  • Article
  • Open Access
1,098 Views
13 Pages

Proteomic Analysis of the Periodontal Ligament During Orthodontic Movement: A Study in Rats

  • Camila Chierici Marcantonio,
  • Maria Eduarda Scordamaia Lopes,
  • Lélio Fernando Ferreira Soares,
  • Cristiane Ribeiro Salmon,
  • Francisco Humberto Nociti Junior,
  • James Deschner,
  • Andressa Vilas Boas Nogueira and
  • Joni Augusto Cirelli

11 September 2025

The periodontal ligament (PDL) is a dynamic connective tissue that absorbs and transmits mechanical forces, playing a critical role during orthodontic tooth movement (OTM). This study aimed to characterize the proteomic profile of rat PDLs subjected...

  • Article
  • Open Access
1,259 Views
27 Pages

Bidirectional Interaction Between PGE2-Preconditioned Mesenchymal Stem Cells and Myofibroblasts Mediates Anti-Fibrotic Effects: A Proteomic Investigation into Equine Endometrial Fibrosis Reversal

  • Lidice Méndez-Pérez,
  • Yat Sen Wong,
  • Belén O. Ibáñez,
  • Ioanna Martinez-Hormaza,
  • Lleretny Rodríguez-Álvarez and
  • Fidel Ovidio Castro

8 September 2025

Background: Endometrosis is a prevalent fibrotic condition in mares that impairs reproductive efficiency by inducing transdifferentiation of endometrial stromal cells into myofibroblasts, leading to excessive ECM deposition. Methods: To elucidate the...

  • Article
  • Open Access
1,163 Views
15 Pages

Background: Bradykinin (BK) is an inflammatory mediator. The degradation of labeled synthetic BK in biofluids can be used to report on the activity of angiotensin-converting enzyme (ACE) and basic carboxypeptidases N and CBP2, for which the neuropept...

  • Article
  • Open Access
3 Citations
2,167 Views
29 Pages

Adiposome Proteomics Uncover Molecular Signatures of Cardiometabolic Risk in Obese Individuals

  • Mohamed Saad Rakab,
  • Monica C. Asada,
  • Imaduddin Mirza,
  • Mohammed H. Morsy,
  • Amro Mostafa,
  • Francesco M. Bianco,
  • Mohamed M. Ali,
  • Chandra Hassan,
  • Mario A. Masrur and
  • Abeer M. Mahmoud
  • + 1 author

Background: Adipose-derived extracellular vesicles (adiposomes) are emerging as key mediators of inter-organ communication, yet their molecular composition and role in obesity-related pathophysiology remain underexplored. This study integrates clinic...

  • Article
  • Open Access
1,678 Views
13 Pages

Identification of Cancer-Associated Proteins in Colorectal Cancer Using Mass Spectrometry

  • Naoyuki Toyota,
  • Ryo Konno,
  • Shuhei Iwata,
  • Shin Fujita,
  • Yoshio Kodera,
  • Rei Noguchi,
  • Tadashi Kondo,
  • Yusuke Kawashima and
  • Yuki Yoshimatsu

Background: Colorectal cancer (CRC) is a leading cause of cancer-related mortality worldwide, with a multifactorial etiology involving genetic and environmental factors. Advanced proteomics offers valuable insights into the molecular mechanisms of ca...

  • Review
  • Open Access
1 Citations
2,366 Views
17 Pages

Post-translational modifications (PTMs) govern a multitude of protein functions within the cell, surpassing the basic function(s) encoded directly within the amino acid sequence. Despite the historical discovery of PTMs dating back over a century, re...

  • Article
  • Open Access
2,257 Views
18 Pages

Cell Surface Proteomics Reveals Hypoxia-Regulated Pathways in Cervical and Bladder Cancer

  • Faris Alanazi,
  • Ammar Sharif,
  • Melissa Kidd,
  • Emma-Jayne Keevill,
  • Vanesa Biolatti,
  • Richard D. Unwin,
  • Peter Hoskin,
  • Ananya Choudhury,
  • Tim A. D. Smith and
  • Conrado G. Quiles

Background Plasma membrane proteins (PMPs) play key roles in cell signalling, adhesion, and trafficking, and are attractive therapeutic targets in cancer due to their surface accessibility. However, their typically low abundance limits detection by c...

  • Article
  • Open Access
1 Citations
2,232 Views
48 Pages

Multiplex Targeted Proteomic Analysis of Cytokine Ratios for ICU Mortality in Severe COVID-19

  • Rúben Araújo,
  • Cristiana P. Von Rekowski,
  • Tiago A. H. Fonseca,
  • Cecília R. C. Calado,
  • Luís Ramalhete and
  • Luís Bento

Background: Accurate and timely prediction of mortality in intensive care unit (ICU) patients, particularly those with COVID-19, remains clinically challenging due to complex immune responses. Proteomic cytokine profiling holds promise for refining m...

  • Article
  • Open Access
1,912 Views
19 Pages

Molecular Remodeling of the Sperm Proteome Following Varicocele Sclero-Embolization: Implications for Semen Quality Improvement

  • Domenico Milardi,
  • Edoardo Vergani,
  • Francesca Mancini,
  • Fiorella Di Nicuolo,
  • Emanuela Teveroni,
  • Emanuele Pierpaolo Vodola,
  • Alessandro Oliva,
  • Giuseppe Grande,
  • Alessandro Cina and
  • Alfredo Pontecorvi
  • + 6 authors

Background: Varicocele is a common condition involving the dilation of veins in the scrotum, often linked to male infertility and testicular dysfunction. This study aimed to elucidate the molecular effects of successful varicocele treatment on sperm...

  • Article
  • Open Access
1,546 Views
21 Pages

Background: The reproductive ability of equine species is a critical component of equine breeding programs, with sperm quality serving as a primary determinant of reproductive success. In this study, we perform an integrative analysis of proteomics a...

  • Article
  • Open Access
1 Citations
2,266 Views
24 Pages

Proteomic Profiling Reveals Novel Molecular Insights into Dysregulated Proteins in Established Cases of Rheumatoid Arthritis

  • Afshan Masood,
  • Hicham Benabdelkamel,
  • Assim A. Alfadda,
  • Abdurhman S. Alarfaj,
  • Amina Fallata,
  • Salini Scaria Joy,
  • Maha Al Mogren,
  • Anas M. Abdel Rahman and
  • Mohamed Siaj

Background: Rheumatoid arthritis (RA) is a chronic autoimmune disorder that predominantly affects synovial joints, leading to inflammation, pain, and progressive joint damage. Despite therapeutic advancements, the molecular basis of established RA re...

  • Article
  • Open Access
1 Citations
2,408 Views
21 Pages

Comparative Label-Based Proteomics of Venoms from Echis ocellatus, Naja nigricollis, and Bitis arietans

  • Abdulbaki Alfa-Ibrahim Adio,
  • Samuel Odo Uko,
  • Jiddah Muhammad Lawal,
  • Ibrahim Malami,
  • Nafiu Lawal,
  • Amina Jega Yusuf Jega,
  • Bilyaminu Abubakar,
  • Muhammad Bashir Bello,
  • Kasimu Ghandi Ibrahim and
  • Mustapha Umar Imam
  • + 3 authors

Background: Snake envenomation is a major public health issue in Nigeria, primarily due to bites from Echis ocellatus, Naja nigricollis, and Bitis arietans. Understanding their venom composition is essential for effective antivenom development. This...

  • Article
  • Open Access
2,146 Views
21 Pages

SDS Depletion from Intact Membrane Proteins by KCl Precipitation Ahead of Mass Spectrometry Analysis

  • Tania Iranpour,
  • Mapenzi Mirimba,
  • Chloe Shenouda,
  • Adam Lynch and
  • Alan A. Doucette

Background: Membrane proteins are preferentially solubilized with sodium dodecyl sulfate (SDS), which necessitates a purification protocol to deplete the surfactant prior to mass spectrometry analysis. However, maintaining solubility of intact membra...

  • Article
  • Open Access
1 Citations
1,527 Views
16 Pages

Alterations in Tear Proteomes of Adults with Pre-Diabetes and Type 2 Diabetes Mellitus but Without Diabetic Retinopathy

  • Guoting Qin,
  • Cecilia Chao,
  • Shara Duong,
  • Jennyffer Smith,
  • Hong Lin,
  • Wendy W. Harrison and
  • Chengzhi Cai

Background: Type 2 diabetes mellitus (T2DM) is an epidemic chronic disease that affects millions of people worldwide. This study aims to explore the impact of T2DM on the tear proteome, specifically investigating whether alterations occur before the...

  • Article
  • Open Access
1 Citations
1,428 Views
15 Pages

Background: Alterations in protein abundance profiles in yeast deletion strains are frequently utilized to gain insights into cellular functions and regulatory networks, most of which are conserved in higher eukaryotes. Methods: This study investigat...

  • Article
  • Open Access
1 Citations
1,196 Views
16 Pages

Proteoform Patterns in Hepatocellular Carcinoma Tissues: Aspects of Oncomarkers

  • Elena Zorina,
  • Natalia Ronzhina,
  • Olga Legina,
  • Nikolai Klopov,
  • Victor Zgoda and
  • Stanislav Naryzhny

Background: Human proteins exist in numerous modifications—proteoforms—which are promising targets for biomarker studies. In this study, we aimed to generate comparative proteomics data, including proteoform patterns, from hepatocellular...

  • Review
  • Open Access
3,670 Views
27 Pages

Next-Generation Protein–Ligand Interaction Networks: APEX as a Powerful Technology

  • José Miguel Quintero-Ferrer,
  • Lucas Silva de Oliveira,
  • Paula Marian Vieira Goulart,
  • Thiago Albuquerque Souza Campos,
  • Coralie Martin,
  • Philippe Grellier,
  • Izabela Marques Dourado Bastos and
  • Sébastien Charneau

Peroxidases are essential enzymes that catalyze redox reactions, with wide-ranging biological implications. Among these, an enhanced ascorbate peroxidase (APEX) has emerged as a valuable tool for studying intricate intracellular events with spatiotem...

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Proteomes - ISSN 2227-7382