Proteomes

20 pages, 1900 KB

Open AccessArticle

Proteomic Insights into the Immune and Sex-Specific Proteins in the Skin Mucus of Barramundi (Lates calcarifer)

by Varsha V. Balu, Dean R. Jerry and Andreas L. Lopata

Proteomes 2026, 14(1), 15; https://doi.org/10.3390/proteomes14010015 - 20 Mar 2026

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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 chromatography-tandem mass spectrometry (LC-MS/MS) following protein extraction and S-Trap digestion. [...] Read more.

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 chromatography-tandem mass spectrometry (LC-MS/MS) following protein extraction and S-Trap digestion. Results and Discussion: A total of 1801 protein groups were matched to the L. calcarifer reference proteome and functionally annotated using Gene Ontology (GO) terms via UniProt ID mapping, with representation across Biological Process, Cellular Component, and Molecular Function categories. Functional classification using eggNOG-mapper further associated leading protein group sequences with Clusters of Orthologous Groups (COGs) and Kyoto Encyclopaedia of Genes and Genomes (KEGG) pathways. GO-based screening prioritised 352 putatively immune-relevant protein groups and 24 protein groups associated with sex- and reproduction-related processes, highlighting the functional complexity of the skin mucus proteome. Comparative analysis revealed sex-associated patterns in protein group detection and relative abundance, with differential abundance analysis identifying 244 protein groups exhibiting statistically significant differences between male and female samples. Conclusions: This study provides the first comprehensive discovery-based characterisation of the barramundi skin mucus proteome and establishes a baseline reference dataset for this aquaculture-relevant species. The findings support the utility of skin mucus proteomics for exploring immune and sex-associated molecular patterns and provide a baseline dataset for future validation studies investigating non-invasive health and reproductive monitoring. Full article

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14 pages, 8721 KB

Open AccessReview

Emergence of Catalytic Activity in VRK3: Phosphoproteomic Insights into the Regulatory Network of a Former Pseudokinase

by Ayadathil Sujina, Amal Fahma, Suhail Subair, Rajesh Raju and Poornima Ramesh

Proteomes 2026, 14(1), 14; https://doi.org/10.3390/proteomes14010014 - 18 Mar 2026

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Abstract

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 phosphorylate Barrier to Autointegration Factor (BAF) proteins through [...] Read more.

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 phosphorylate Barrier to Autointegration Factor (BAF) proteins through its extracatalytic domain. VRK3 regulates diverse cellular pathways through scaffold interactions and context-dependent phosphorylation. This review is centered around the phosphoregulatory network that modulates VRK3 phosphorylation with implications in its abundance and function. A large-scale phosphoproteomic data integration was performed by combining phosphoproteomics profiling and differential phosphorylation from 115 mass spectrometry studies, identifying 32 high-confidence phosphorylation sites on VRK3. Notably, VRK3 (S59), (S82), and (S83) were predominantly observed highlighting plausible functional significance. These phosphorylation sites share 33 potential upstream kinases, and multiple interactor proteins, which in combination are known to regulate ERK, Hippo, and GPCR pathways. These insights advance the understanding of phosphorylation control by kinases and highlight opportunities to target VRK3-associated networks for therapeutic intervention in diseases such as glioma and liver cancer. Full article

(This article belongs to the Section Proteome Bioinformatics)

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15 pages, 1617 KB

Open AccessArticle

Dimethyl Sulfoxide Enhances HLA Peptide Identification

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

Proteomes 2026, 14(1), 13; https://doi.org/10.3390/proteomes14010013 - 13 Mar 2026

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Abstract

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 ionisation and fragmentation efficiency. Methods: To address these limitations, we [...] Read more.

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 ionisation and fragmentation efficiency. Methods: To address these limitations, we investigated the impact of incorporating 5% dimethyl sulfoxide (DMSO) into LC-MS/MS mobile-phase buffers on immunopeptidomic workflows. Using B-lymphoblastoid cell lines expressing HLA class I and II alleles and elastase-digested HeLa lysates as a surrogate for non-tryptic peptides, we assessed peptide identification, ionisation efficiency, charge state distribution, and fragmentation quality. Results: DMSO significantly increased peptide identifications across all sample types, with gains of ~1.33 folds for HLA class I, ~1.55 folds for HLA class II, and ~1.24 folds for elastase digests. Improvements were systematic and reproducible, driven by enhanced electrospray ionisation, higher charge states, and superior MS2 spectral quality, evidenced by ~2-fold increase in b- and y-ion intensities. Importantly, DMSO did not introduce major sequence bias, preserving motif integrity and predicted binding characteristics. Conclusions: Overall, these findings establish DMSO as a robust additive for improving sensitivity and reliability in immunopeptidomics, particularly for low-input or clinically derived samples. Full article

(This article belongs to the Section Proteomics Technology and Methodology Development)

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15 pages, 510 KB

Open AccessReview

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

by Anastasia Boura-Theodorou, Konstantina Psatha, Stefania Maniatsi, Areti Kourti, Georgia Kaiafa, Michalis Aivaliotis and Kali Makedou

Proteomes 2026, 14(1), 12; https://doi.org/10.3390/proteomes14010012 - 12 Mar 2026

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Abstract

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 immune system. The severity [...] Read more.

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 immune system. The severity of ITP is linked to diminished production of platelets due to the blockage of production in the bone marrow niche and increased destruction of platelets, which confirms the diagnosis of the disorder. The investigation of the pathogenesis of ITP is of critical importance as it can give an important indication of the state of the patient, guiding us through risk assessment and treatment. Proteomics can provide tools to explore the protein profile of ITP. In this review, we aimed to uncover different biomarkers, both diagnostic and prognostic, that have been investigated with proteomic methodologies and that might help in understanding the pathogenesis of ITP and providing personalized treatment to patients. Several differentially abundant proteins were identified, including haptoglobin isoforms, heat shock proteins (HSPA6, HSPA8), integrin β3 (ITGB3), 14-3-3 protein eta (YWHAH), vitamin D-binding protein, fibrinogen chains, MYH9, and FETUB, which are involved in key signaling pathways, such as PI3K/akt, TNF-a, and mTOR, and they demonstrate potential as diagnostic and prognostic biomarkers. Collectively, current data support the value of proteomics for uncovering the molecular landscape of ITP and guiding the development of precision diagnostics and personalized therapeutic strategies. Full article

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34 pages, 14889 KB

Open AccessArticle

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

by Sabine Lüthje, Ayse Gül Yilmaz, Kalaivani Ramanathan, Waldemar Gräfenstein, Jenny M. Tabbert, Stefanie Wienkoop, Katrin Heino, François Clement Perrineau and Sönke Harder

Proteomes 2026, 14(1), 11; https://doi.org/10.3390/proteomes14010011 - 25 Feb 2026

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Abstract

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, plasma membrane, and tonoplast sub-proteomes were [...] Read more.

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, plasma membrane, and tonoplast sub-proteomes were studied. Methods: Control and Cd²⁺-treated maize (Zea mays L.) were grown in hydroponics for 18 days. Soluble peroxidases were partially purified by chromatofocusing and characterized by substrate specificity. Membrane-bound peroxidases were analyzed spectrophotometrically and by non-reducing SDS-PAGE. Soluble and plasma membrane-bound peroxidases were identified by mass spectrometry. Shotgun proteomics was used to identify membrane proteins of differential abundance. Results: Guaiacol peroxidase activities increased in soluble fractions of Cd²⁺ samples. A Cd²⁺-specific soluble peroxidase (ZmPrx101) was identified, and ZmPrx85 abundance increased significantly in the plasma membrane. Substrate specificity of peroxidases revealed a preference for ferulic acid and esculetin, which was confirmed by docking analyses. Primary active transporters increased auxin efflux (brachytic2, ABCB9, and ABCB21), Cd²⁺ exclusion (ABCG34), and sequestration into the vacuole (HMA2, ABCB27). Evaluation of sub-proteome fractions demonstrated significant changes for proteins involved in disease resistance responses and cell wall modification. Conclusions: Molecular adjustments of maize root proteome to long-term Cd²⁺ exposure revealed relevance of low-abundant proteins for Cd²⁺ tolerance and putative stress markers. Full article

(This article belongs to the Special Issue Plant Genomics and Proteomics)

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14 pages, 986 KB

Open AccessArticle

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

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

Proteomes 2026, 14(1), 10; https://doi.org/10.3390/proteomes14010010 - 18 Feb 2026

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Abstract

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 analytical column by removing salts and contaminants. Recently, monolithic trap columns with micropillar architecture have [...] Read more.

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 analytical column by removing salts and contaminants. Recently, monolithic trap columns with micropillar architecture have emerged as alternatives to conventionally packed traps. This study compares the performance of a packed and a micropillar monolithic trap column for the analysis of tryptic peptides. Methods: A tryptic digest of HeLa cell lysate was analyzed under identical LC–MS conditions using both trap types. Peptides were detected at 214 nm and analyzed by nano-ESI on a Q Exactive Plus Orbitrap. Data were searched against the human UniProt database (February 2023) using FragPipe v20.0, and statistical evaluation of MaxLFQ intensities was performed in Perseus using Welch’s t-test and clustering analysis. Results: Over 2500 proteins were identified with both setups. The packed trap column yielded more total peptides, particularly those with post-translational modifications and higher hydrophilicity, whereas the monolithic column favored peptides of intermediate hydrophobicity. Chromatographic profiles confirmed a slight reduction in the trapping efficiency of hydrophilic peptides by the monolithic trap. Conclusions: Trap column design significantly influences peptide recovery and proteome coverage. Full article

(This article belongs to the Section Proteomics Technology and Methodology Development)

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20 pages, 2949 KB

Open AccessArticle

Scout-Triggered Multiple Reaction Monitoring Enables Robust Quantification of Host Cell Proteins Across Bioprocess Matrices

by Julie Flecheux, Chloé Bardet, Laura Herment, Tanguy Fortin and Jérôme Lemoine

Proteomes 2026, 14(1), 9; https://doi.org/10.3390/proteomes14010009 - 17 Feb 2026

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Abstract

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 reaction monitoring (MRM) enable protein-specific HCP quantification but are difficult to [...] Read more.

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 reaction monitoring (MRM) enable protein-specific HCP quantification but are difficult to apply in highly multiplexed assays because of retention time (RT) variability across complex bioprocess matrices. Methods: Here, we show that conventional RT-scheduled MRM workflows lack transferability when applied to heterogeneous drug substances and process intermediates. Using a targeted assay comprising 240 peptides corresponding to 97 CHO-derived HCPs, RT shifts of several minutes resulted in truncated chromatographic peaks and peptide signal loss, even when wide scheduling windows were used. To overcome this limitation, a scout-triggered MRM (st-MRM) acquisition strategy based on event-driven monitoring was implemented. Results: This approach enabled robust peptide detection across diverse matrices within a single injection, without method re-optimization. Absolute quantification using stable isotope-labeled peptides spanned six orders of magnitude, with HCPs quantified down to 2.9 ppm in purified drug substances. Conclusion: Overall, st-MRM improves the robustness and transferability of highly multiplexed targeted proteomics workflows for HCP analysis. Full article

(This article belongs to the Section Proteomics Technology and Methodology Development)

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26 pages, 2509 KB

Open AccessArticle

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

by Akhina Palollathil, Althaf Mahin, Athira Perunelly Gopalakrishnan, Tejaswini R Poojari, Alimath Sambreena, Prathik Basthikoppa Shivamurthy and Rajesh Raju

Proteomes 2026, 14(1), 8; https://doi.org/10.3390/proteomes14010008 - 13 Feb 2026

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Abstract

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 developmental disorders and carcinogenesis. As membrane-bound receptors, they represent promising targets for therapeutic [...] Read more.

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 developmental disorders and carcinogenesis. As membrane-bound receptors, they represent promising targets for therapeutic intervention and drug development. Methods: This study employed a systematic in silico analysis of publicly available phosphoproteomics datasets to provide a comprehensive overview of the phosphorylation regulatory network of the FGFR family. Results: We identified predominant phosphosites in FGFR1-4 that exhibited differential abundance across diverse experimental conditions, specifically, Y653 in FGFR1; S453, Y586, Y656, and Y657 in FGFR2; S444 and S445 in FGFR3; and S573 in FGFR4. Our analysis identified 32 and 89 significantly co-modulated phosphosites on other proteins with FGFR3 and FGFR4, respectively. Beyond the upstream kinases from the FGFR family, we also identified MAPK1 as a potential upstream kinase of FGFR4. Furthermore, disease enrichment analysis revealed that proteins co-modulated with FGFR3 were primarily involved in skeletal developmental disorders, such as brachydactyly, short toe, and syndactyly of fingers, whereas those associated with FGFR4 were linked to various cancers. Conclusions: Our findings highlight key disease-associated phosphosites within the FGFRs and offer a foundation for advancing phosphosite-focused therapeutic research. Full article

(This article belongs to the Section Proteome Bioinformatics)

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19 pages, 2370 KB

Open AccessArticle

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

by Yury Yu. Strogov, Sergey A. Spirin, Mark V. Ivanov, Maria A. Kulebyakina, Anastasia Yu. Efimenko and Oleg I. Klychnikov

Proteomes 2026, 14(1), 7; https://doi.org/10.3390/proteomes14010007 - 2 Feb 2026

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Abstract

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-shifts in one run. In contrast, closed search [...] Read more.

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-shifts in one run. In contrast, closed search algorithms are more sensitive but limited in the number of PTMs that can be specified in one search. Methods: In this manuscript, we propose an optimized Python algorithm based on the IdentiPy search engine that performs an automated sequential search for each PTM based on previous annotations from public databases and customized protein lists. We also determined the sufficient size of the search space to increase the significance of false discovery rate (FDR) estimation. We modified the FDR calculation algorithm by implementing a spline approximation of the ratio of the modified decoys, and by calculating error propagation to filter out unstable data and determine the cutoff value. Results: The results of this pipeline for a test dataset were comparable to previously published data in terms of the number of unmodified peptides and proteins. Additionally, we identified 13 different types of peptide PTMs and achieved an increase in relative protein coverage. Our filtration method based on spline transferred FDR showed a superior number of identified peptides compared to separate FDR. Conclusions: Our developed pipeline can be used as a standalone application or as a module of multiple PTM search in data analysis platforms. Full article

(This article belongs to the Section Proteome Bioinformatics)

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31 pages, 3822 KB

Open AccessArticle

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

by Mohadeseh Montazeri Shatouri, Igor Pirozzi, Pinar Demir Soker, Zeshan Ali, Ardeshir Amirkhani and Paul A. Haynes

Proteomes 2026, 14(1), 6; https://doi.org/10.3390/proteomes14010006 - 29 Jan 2026

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Abstract

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 the effects of two commercial diets, diet A (higher land animal protein) and [...] Read more.

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 the effects of two commercial diets, diet A (higher land animal protein) and diet B (higher fish meal content), on the protein profile in the brain, liver, and intestine of barramundi (Lates calcarifer). A 12-week feeding trial was conducted with controlled water quality, and proteomic profiling was performed using data-independent acquisition. Results: Differential analysis revealed consistent changes between diets across all tissues, with a higher percentage of differentially abundant proteins observed in between-diet comparisons (12.99% in brain, 12.73% in liver, and 16.59% in intestine) than within-diet controls (<8%), confirming a measurable dietary effect size. In total, 3901 proteins in the brain, 3660 in the liver, and 5025 in the intestine were quantified. Functional enrichment highlighted upregulation of ferroptosis pathways, downregulation of apelin signaling in the brain, and increased digestive proteases in the liver. ICP-MS confirmed elevated iron concentrations in the brain, liver, and intestine of fish fed on diet B. Conclusions: These findings demonstrate that molecular pathways linked to iron metabolism, digestion, and growth regulation are very sensitive to dietary composition, highlighting how proteomics can help identify subtle impacts of compositional differences in aquaculture feeding. Although physiological parameters did not differ significantly, the proteomic alterations observed across tissues likely indicate organ-specific metabolic adaptations to the differing nutrient availability between diets. Full article

(This article belongs to the Section Animal Proteomics)

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23 pages, 8773 KB

Open AccessArticle

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

by Xia Peng, Jing Chen, Xiaoyu Zheng, Xige Zhao, Yijia Wang, Xiaotong Wang and Juan Du

Proteomes 2026, 14(1), 5; https://doi.org/10.3390/proteomes14010005 - 23 Jan 2026

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Abstract

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 TGFβ-activated phosphorylation cascades remains largely unknown. Here, we investigated the [...] Read more.

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 TGFβ-activated phosphorylation cascades remains largely unknown. Here, we investigated the interplay between these pathways during palatogenesis. Methods: H&E and IHC analyses revealed increased expression of Beclin 1 and LC3 during the critical period of palatal shelf elevation and fusion (E13.5–E15.5). Bulk RNA sequencing (Bulk RNA-seq) further revealed enrichment of autophagy-related pathways and their interaction with TGFβ signaling. TMT-based phosphoproteomics was performed on TGFβ2-treated MEPM cells. Results: We identified 23,471 peptides and 3952 proteins, including 6339 phosphopeptides corresponding to 2195 phosphoproteins. Differential analysis found 477 phosphopeptides with increased abundance and 53 with decreased abundance, revealing the enrichment of seven serine (p-Ser) motifs (RxxS, SDxD, SDxE, SP, SxDE, SxEE, SxxxxD) and one threonine (p-Thr) motif (TP). Notably, kinase-substrate enrichment analysis identified CSNK2A as a previously unrecognized phosphorylation regulator, together with MAPKs and CDKs. Functional enrichment showed significant involvement of mTOR, MAPK, and autophagy/mitophagy pathways. Conclusions: Our findings revealed that TGFβ2 reshapes the MEPM phosphoproteome through Smad-independent pathway, expanding the palate-specific phospho-signaling atlas beyond the canonical Smad cascade. Full article

(This article belongs to the Section Animal Proteomics)

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21 pages, 56584 KB

Open AccessArticle

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

by Hinano Takase, Sotaro Katagiri, Takuma Ide, Aina Nagano, Haruki Sakurai, Hana Kokubo, Taiki Yanagisawa, Masanori Okamoto and Taishi Umezawa

Proteomes 2026, 14(1), 4; https://doi.org/10.3390/proteomes14010004 - 20 Jan 2026

Cited by 1 | Viewed by 1232

Abstract

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 divergence across plant species remain unclear. Methods: Here, we performed phosphoproteomic [...] Read more.

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 divergence across plant species remain unclear. Methods: Here, we performed phosphoproteomic analysis using LC-MS/MS in Arabidopsis, rice (Oryza sativa), and soybean (Glycine max) to compare ABA-responsive phosphorylation profiles among monocots, dicots, and legumes. Results: ABA treatments on Arabidopsis, rice, and soybean seedlings yielded approximately 24,604, 18,865, and 24,930 phosphopeptides, respectively. Comparative analyses revealed both conserved and species-specific ABA-responsive phosphoproteins. Conclusions: This work provides insights into the evolutionary diversification of ABA signaling and its potential applications in improving crop stress tolerance. Full article

(This article belongs to the Special Issue Plant Genomics and Proteomics)

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28 pages, 8605 KB

Open AccessArticle

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

by Sarena Banu, P. V. Anusha, Pedro Beltran-Alvarez, Mohammed M. Idris, Katharina C. Wollenberg Valero and Francisco Rivero

Proteomes 2026, 14(1), 3; https://doi.org/10.3390/proteomes14010003 - 8 Jan 2026

Cited by 1 | Viewed by 1534 | Correction

Abstract

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 cycle is widely available, only early-stage data exist [...] Read more.

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 cycle is widely available, only early-stage data exist at the proteome level. This study characterizes and compares the proteomes of D. discoideum cells at the vegetative, aggregation, mound, culmination and fruiting body stages. Methods: Samples were collected from cells developing synchronously on nitrocellulose filters. Proteins were extracted and digested with trypsin, and peptides were analyzed by liquid chromatography–tandem mass spectrometry. Data were processed using Proteome Discoverer™ for protein identification and label-free quantification. Results: A total of 4502 proteins were identified, of which 1848 (41%) were present across all stages. Pairwise comparisons between adjacent stages revealed clear transitions, the largest ones occurring between the culmination and fruiting body and between the fruiting body and vegetative stage, involving 29% and 52% of proteins, respectively. Hierarchical clustering assigned proteins to one of nine clusters, each displaying a distinct pattern of abundances across the life cycle. Conclusions: This study presents the first complete developmental proteomic time series for D. discoideum, revealing changes that contribute to multicellularity, cellular differentiation and morphogenesis. Full article

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16 pages, 3734 KB

Open AccessArticle

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

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

Proteomes 2026, 14(1), 2; https://doi.org/10.3390/proteomes14010002 - 4 Jan 2026

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Abstract

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 fundamental bioprocesses in healthy and injured states. Methods: [...] Read more.

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 fundamental bioprocesses in healthy and injured states. Methods: Using mass spectrometry-based shotgun proteomics, we characterized the cellular fraction (CF) and conditioned medium (CM) proteomes of mesothelial cell line MeT-5A. The datasets were analyzed for Gene Ontology (GO) terms and canonical pathway enrichments to identify biological themes. Results: Our analysis identified 5087 protein groups, including 1532 shared proteins, 3122 unique to the CF and 433 exclusive to the CM. GO annotation revealed distinct functional enrichment profiles, reflecting the differing roles of intracellular and secreted proteins. While intracellular proteins were linked to core cellular functions, the extracellular proteome was enriched for signaling and cell-to-cell interaction pathways. The proteins shared by both compartments provided an integrated view of the molecular coordination between the cellular and extracellular environments. Conclusions: This study provides the first comprehensive baseline proteome for mesothelial cells and their secreted medium, offering a vital resource for future investigations into the mesothelium, particularly in the context of disease or injury. Full article

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20 pages, 1892 KB

Open AccessArticle

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

by Brett Sather, James Larson, Kian Hutt Vater, Jade Westrum, Timothy R. McDermott and Brian Bothner

Proteomes 2026, 14(1), 1; https://doi.org/10.3390/proteomes14010001 - 4 Jan 2026

Cited by 2 | Viewed by 764

Abstract

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 investigated the proteomic landscape of Escherichia coli strains [...] Read more.

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 investigated the proteomic landscape of Escherichia coli strains with and without ArsR to elucidate ArsR as an activator in both non-stressing and arsenic-stressing conditions. Methods: Using mass-spectrometry-based shotgun proteomics and statistical analyses, we characterized the differential abundance of proteins across AW3110 (ΔarsRBC), AW3110 complemented with arsR, and wild-type K-12 strains under control and arsenite-stressed conditions. Results: Our study shows that ArsR influences proteomic networks beyond the ars operon, integrating metabolic and redox responses crucial for cellular adaptation and survival. This suggests that ArsR has a significant role in gut microbiome metabolomic profiles in response to arsenite. Proteins involved in alanine, lactaldehyde, arginine, thioredoxin, and proline pathways were significantly elevated in strains where ArsR was detected, both with and without arsenite. We identified proteins exhibiting an “ArsR-dependent” activation pattern, highlighting ArsR’s potential role in redox balance and energy metabolism. Conclusions: These findings challenge the classical view of ArsR as a repressor and position it as a pleiotropic regulator, including broad activation. Full article

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