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Proteomes, Volume 14, Issue 1

2026 March - 15 articles

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Articles (15)

  • Article
  • Open Access
3,106 Views
20 Pages

Background: Fish skin mucus contains proteins involved in diverse biological pathways, representing a valuable non-invasive diagnostic of fish health. Methods: Skin mucus from three male and three female barramundi was analysed using liquid chromatog...

  • Review
  • Open Access
2,408 Views
14 Pages

Vaccinia-Related Kinase 3 (VRK3) is increasingly recognized as a crucial signaling modulator in both normal and pathological processes. This kinase was long thought of as a catalytically inactive pseudokinase, until recently it was established to pho...

(This article belongs to the Section Proteome Bioinformatics)
  • Article
  • Open Access
3,144 Views
15 Pages

Dimethyl Sulfoxide Enhances HLA Peptide Identification

  • Terry C. C. Lim Kam Sian,
  • Yue Ding,
  • Scott A. Blundell,
  • Ralf B. Schittenhelm and
  • Pouya Faridi

Background: Mass spectrometry (MS)-based immunopeptidomics has emerged as the gold standard for profiling HLA-bound peptides, yet detection remains challenging due to their non-tryptic nature, variable lengths, and lack of basic residues, which limit...

(This article belongs to the Section Proteomics Technology and Methodology Development)
  • Review
  • Open Access
1 Citations
2,897 Views
15 Pages

Proteomic Analysis in Search of New Biomarkers of Immune Thrombocytopenia (ITP)—A Review of Current Data

  • Anastasia Boura-Theodorou,
  • Konstantina Psatha,
  • Stefania Maniatsi,
  • Areti Kourti and ,
  • Georgia Kaiafa,
  • Michalis Aivaliotis and
  • Kali Makedou
  • + 2 authors+ 0 author

Immune thrombocytopenia (ITP) is a hematological disorder commonly found in individuals of any gender, race, or age. Patients with ITP will present with thrombocytopenia either in a primary form or because of an infection or a dysfunction in the immu...

  • Article
  • Open Access
2 Citations
3,275 Views
34 Pages

Cellular Responses of Maize Roots to Long-Term Cadmium Exposure: Adjustments of Class III Peroxidases, Plasma Membrane and Tonoplast Sub-Proteomes

  • Sabine Lüthje,
  • Ayse Gül Yilmaz,
  • Kalaivani Ramanathan,
  • Waldemar Gräfenstein and ,
  • Jenny M. Tabbert,
  • Stefanie Wienkoop,
  • Katrin Heino,
  • François Clement Perrineau and
  • Sönke Harder
  • + 4 authors+ 0 author

25 February 2026

Background: Crop plants have to deal with long-term cadmium exposure to farmlands contaminated by intensive use of fertilizers and pesticides. For uptake and sequestration, Cd2+ has to pass the plasma membrane and tonoplast. Class III peroxidases, pl...

(This article belongs to the Special Issue Plant Genomics and Proteomics)
  • Article
  • Open Access
1 Citations
1,905 Views
14 Pages

Comparison of the Trapping Efficiency for Tryptic Peptides on Particle-Packed and Micro-Pillar Trap Columns for Proteomics Analyses

  • Jadranka Miletić Vukajlović,
  • Bojana Ilić,
  • Bella Bruszel,
  • Tanja Panić-Janković and
  • Goran Mitulović

18 February 2026

Background: Low-volume trapping columns are essential for sample enrichment, desalting, and injection profile focusing on nano-LC–MS-based proteomics. They enable higher sample loading, improve chromatographic performance, and protect the analy...

(This article belongs to the Section Proteomics Technology and Methodology Development)
  • Article
  • Open Access
2,024 Views
20 Pages

17 February 2026

Background: Host cell proteins (HCPs) are process-related impurities that must be monitored in biopharmaceutical products due to their potential impact on product quality and patient safety. Targeted LC–MS/MS approaches such as multiple reactio...

(This article belongs to the Section Proteomics Technology and Methodology Development)
  • Article
  • Open Access
5 Citations
1,708 Views
26 Pages

Proteome-Wide Analysis of Functional Phosphosites in the FGFR Family of Proteins: Insights from Large-Scale Phosphoproteomic Analysis

  • Akhina Palollathil,
  • Althaf Mahin,
  • Athira Perunelly Gopalakrishnan,
  • Tejaswini R Poojari and ,
  • Alimath Sambreena,
  • Prathik Basthikoppa Shivamurthy and
  • Rajesh Raju
  • + 2 authors+ 0 author

13 February 2026

Background: Fibroblast growth factor receptors (FGFRs) play a crucial role in tissue homeostasis and organ development by regulating cellular processes, including proliferation, differentiation, and survival. Dysregulation of FGFRs contributes to dev...

(This article belongs to the Section Proteome Bioinformatics)
  • Article
  • Open Access
1,769 Views
19 Pages

PTMs_Closed_Search: Multiple Post-Translational Modification Closed Search Using Reduced Search Space and Transferred FDR

  • Yury Yu. Strogov,
  • Sergey A. Spirin,
  • Mark V. Ivanov,
  • Maria A. Kulebyakina and ,
  • Anastasia Yu. Efimenko and
  • Oleg I. Klychnikov
  • + 1 author+ 0 author

Background: Currently, post-translational modification (PTM) search in MS/MS data is performed using either open modification search (OMS) or closed search (CS) algorithms. The OMS method allows for the determination of many PTMs and unknown mass-shi...

(This article belongs to the Section Proteome Bioinformatics)
  • Article
  • Open Access
3 Citations
2,680 Views
31 Pages

Evaluating the Impact of Two Different Diets on the Protein Profile of the Brain, Liver, and Intestine of the Barramundi

  • Mohadeseh Montazeri Shatouri,
  • Igor Pirozzi,
  • Pinar Demir Soker,
  • Zeshan Ali and ,
  • Ardeshir Amirkhani and
  • Paul A. Haynes
  • + 1 author+ 0 author

Background: Commercial feed formulations are increasingly being evaluated for their nutritional impacts on aquaculture species, yet the molecular consequences of commonly used commercial diets remain underexplored. Methods: This study investigated th...

(This article belongs to the Section Animal Proteomics)
  • Article
  • Open Access
1,982 Views
23 Pages

Integrated Phosphoproteomics Identifies TGFβ-Dependent Phosphorylation Events Linking Kinase Signaling to Autophagy in Palatogenesis

  • Xia Peng,
  • Jing Chen,
  • Xiaoyu Zheng,
  • Xige Zhao and ,
  • Yijia Wang,
  • Xiaotong Wang and
  • Juan Du
  • + 2 authors+ 0 author

Background: Cleft palate (CP) is a prevalent craniofacial malformation, with the TGFβ pathway playing a critical role. Recent evidence links autophagy to regulating mouse embryonic palatal mesenchyme (MEPM) cells, but its interaction with TGF&be...

(This article belongs to the Section Animal Proteomics)
  • Article
  • Open Access
2 Citations
2,323 Views
21 Pages

Cross-Species Analysis of ABA-Induced Phosphosignaling Landscapes in Rice, Soybean, and Arabidopsis

  • Hinano Takase,
  • Sotaro Katagiri,
  • Takuma Ide,
  • Aina Nagano and ,
  • Haruki Sakurai,
  • Hana Kokubo,
  • Taiki Yanagisawa,
  • Masanori Okamoto and
  • Taishi Umezawa
  • + 4 authors+ 0 author

Background: Abscisic acid (ABA) is a key phytohormone that regulates plant growth and stress responses through protein phosphorylation. While ABA-induced phosphosignaling has been extensively studied in Arabidopsis thaliana, its conservation and dive...

(This article belongs to the Special Issue Plant Genomics and Proteomics)
  • Article
  • Open Access
3 Citations
2,799 Views
28 Pages

The Proteome of Dictyostelium discoideum Across Its Entire Life Cycle Reveals Sharp Transitions Between Developmental Stages

  • Sarena Banu,
  • P. V. Anusha,
  • Pedro Beltran-Alvarez,
  • Mohammed M. Idris and ,
  • Katharina C. Wollenberg Valero and
  • Francisco Rivero
  • + 1 author+ 0 author

Background: Dictyostelium discoideum is widely used in developmental and evolutionary biology due to its ability to transition from a single cell to a multicellular organism in response to starvation. While transcriptome information across its life c...

  • Article
  • Open Access
1,577 Views
16 Pages

Proteomics and Bioinformatics Profiles of Human Mesothelial Cell Line MeT-5A

  • Rachel L. Watkin,
  • Avedis A. Kazanjian,
  • Jennifer R. Damicis and
  • Elizabeth Yohannes

Background: Despite existing proteomics studies of other cell types, a comprehensive proteome of mesothelial cells has not been characterized. This study establishes a crucial baseline proteome for mesothelial cells to better understand their fundame...

  • Article
  • Open Access
2 Citations
1,731 Views
20 Pages

Beyond Repression: ArsR Functions as a Global Activator of Metabolic and Redox Responses in Escherichia coli

  • Brett Sather,
  • James Larson,
  • Kian Hutt Vater,
  • Jade Westrum and ,
  • Timothy R. McDermott and
  • Brian Bothner
  • + 1 author+ 0 author

Background: The arsenic-responsive repressor, ArsR, has long been understood as a canonical regulator of the arsRBC operon, which confers resistance to arsenic stress. However, recent studies suggest a broader regulatory scope for ArsR. Here, we inve...

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Proteomes - ISSN 2227-7382