Proteomes

28 pages, 19515 KB

Open AccessArticle

Integrative Proteomic Analysis Implicates Inhibition of Intracellular Protein Trafficking in Therapy-Induced Migrastasis in Prostate Cancer

by Weining Chen, Saadyeh Rashidi, Henry C.-H. Law, Fangfang Qiao, Johnny W. Zigmond, Katelyn L. O’Neill, Nicholas T. Woods, Chittibabu Guda and Raymond C. Bergan

Proteomes 2026, 14(3), 45; https://doi.org/10.3390/proteomes14030045 - 28 Aug 2026

Abstract

Background: Dysregulated cell migration leading to metastasis remains the primary cause of cancer-related mortality. It has been challenging to understand how cells regulate migration. We have previously created the first selective inhibitor of cell migration, KBU2046. Here, we use it as a probe [...] Read more.

Background: Dysregulated cell migration leading to metastasis remains the primary cause of cancer-related mortality. It has been challenging to understand how cells regulate migration. We have previously created the first selective inhibitor of cell migration, KBU2046. Here, we use it as a probe to identify regulatory processes. Methods: Metastatic and primary human prostate cancer cells were treated for different times and at different concentrations with KBU2046. Immunofluorescent microscopy examined protein localization in cells. Label-free mass spectrometry (MS) was performed on total cell proteins, Tandem Mass Tag (TMT) labeling MS was used on membrane fractions, and temporal phosphoproteomic profiling was performed. Results were analyzed with a suite of bioinformatic tools. Results: KBU2046-induced migrastasis is associated with the accumulation of activated integrin β1 into focal adhesions. Whole-cell proteomics demonstrated suppression of processes that mediate intracellular protein trafficking and increases in mitochondrial energy-generation signatures. Evaluation of the membrane fraction identified increases in membrane repair and maintenance processes and decreases in those that drive motility. Temporal- and concentration-dependent phosphoproteomic profiling revealed that KBU2046 initiates a dynamic, cascading sequence of transient signaling waves rather than a static block. Conclusions: KBU2046-induced migrastasis appears to operate through spatial decoupling rather than structural degradation. By restricting the intracellular trafficking machinery required for receptor recycling, KBU2046 limits focal adhesion turnover, providing, in PC3 prostate cancer cells, a correlative framework to inhibit metastatic dissemination independent of direct cytotoxicity. Full article

(This article belongs to the Section Proteomics of Human Diseases and Their Treatments)

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42 pages, 1321 KB

Open AccessReview

Beyond Protein Abundance: Proteoform Diversity and Phosphoproteome Remodeling in Maize (Zea mays L.) Responding to Drought and Heat Stresses

by Jan Bocianowski

Proteomes 2026, 14(3), 44; https://doi.org/10.3390/proteomes14030044 - 27 Aug 2026

Abstract

Drought and heat stresses are among the most important environmental constraints limiting maize (Zea mays L.) productivity worldwide. Over the past two decades, advances in mass spectrometry-based proteomics have generated extensive datasets describing proteins with altered abundance in maize tissues exposed to [...] Read more.

Drought and heat stresses are among the most important environmental constraints limiting maize (Zea mays L.) productivity worldwide. Over the past two decades, advances in mass spectrometry-based proteomics have generated extensive datasets describing proteins with altered abundance in maize tissues exposed to water deficit and elevated temperatures. These studies have identified numerous stress-responsive proteins involved in photosynthesis, energy metabolism, antioxidant defense, proteostasis, signaling pathways, and cellular homeostasis. In parallel, phosphoproteomic investigations have revealed extensive remodeling of phosphorylation networks that regulate stress perception, signal transduction, and adaptive responses. However, most available studies remain focused on protein-level observations and provide limited insight into the molecular diversity underlying stress adaptation. This review synthesizes current knowledge on the proteomic and phosphoproteomic responding of maize to drought and heat stresses through the emerging perspective of proteoform biology. We discuss how phosphorylation, oxidative modifications, proteolytic processing, alternative splicing, and genetic variation contribute to proteoform generation and expand the functional complexity of the maize stress proteome. Particular emphasis is placed on the integration of quantitative proteomics, phosphoproteomics, and proteogenomics as complementary approaches for characterizing stress-responsive molecular networks. We further evaluate current methodological limitations, including the predominance of bottom-up workflows, the underrepresentation of combined-stress studies and reproductive tissues, and the limited application of proteoform-resolved analytical strategies. We propose that future advances in maize stress biology will require a transition from protein-centered analyses toward proteoform-centered investigations capable of resolving functionally distinct molecular species. The integration of top-down proteomics, phosphoproteomics, proteogenomics, and systems-level approaches is expected to provide a more comprehensive understanding of stress adaptation mechanisms and facilitate the identification of molecular determinants of climate resilience. Such efforts may ultimately support the development of maize cultivars better adapted to increasingly challenging environmental conditions. Full article

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

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20 pages, 1984 KB

Open AccessArticle

Urinary Proteome Profiling by Several Methods Identifies Titin as the Most-Differentiating Noninvasive Urinary Biomarker of Disease Severity in Becker Muscular Dystrophy

by Kimchi K. Le, Emily H. Canessa, Corrine M. Stahura, Jenna Mayers, Katie A. Edwards, Marissa Barbieri, Eric P. Hoffman and Yetrib Hathout

Proteomes 2026, 14(3), 43; https://doi.org/10.3390/proteomes14030043 - 25 Aug 2026

Abstract

Background: Beckers muscular dystrophy (BMD) is a clinically heterogeneous dystrophinopathy caused by in-frame mutations in the dystrophin gene, resulting in variable disease severity. This variability limits the effectiveness of standardized functional measures for tracking progression. Circulating biomarkers, including urinary titin fragments generated during [...] Read more.

Background: Beckers muscular dystrophy (BMD) is a clinically heterogeneous dystrophinopathy caused by in-frame mutations in the dystrophin gene, resulting in variable disease severity. This variability limits the effectiveness of standardized functional measures for tracking progression. Circulating biomarkers, including urinary titin fragments generated during muscle injury, offer a promising non-invasive approach for assessing disease status. Methods: Mass spectrometry-based urinary proteomic profiling identified titin fragments as candidate biomarkers of muscle injury in BMD. These titin fragments were validated by two independent methods, targeted mass spectrometry and ELISA, using subsets of ambulatory BMD, non-ambulatory BMD and age matched healthy volunteers. Results: Urinary titin levels were significantly elevated by 4.56-fold and 2.32-fold in ambulatory and non-ambulatory BMD patients, respectively, compared with healthy controls. Titin levels also distinguished ambulatory from non-ambulatory BMD patients, demonstrating potential utility for monitoring disease progression and therapeutic response. Conclusions: Urinary titin fragments represent a promising non-invasive biomarker for BMD, with potential applicability to related neuromuscular disorders and clinical trials evaluating disease progression and treatment efficacy. Full article

(This article belongs to the Special Issue Clinical Proteomics: Unravelling Drug and Disease Mechanisms (Fifth Edition))

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31 pages, 12452 KB

Open AccessArticle

DOG1-Mediated Priming Followed by Environmentally Tunable Plasticity: A Two-Phase Model for Dormancy Establishment in Xanthium strumarium

by Iman Nemati, Somayeh Gholizadeh, Dinakaran Elango, Sara Hamzelou, Karthik Shantharam Kamath, Mohammad Sedghi, Reza Tavakkol Afshari and Paul A. Haynes

Proteomes 2026, 14(3), 42; https://doi.org/10.3390/proteomes14030042 - 21 Aug 2026

Abstract

Background: Seed dormancy is crucial for plant survival and agricultural productivity, yet its molecular mechanisms, particularly the role of maternal effects, remain poorly understood. Methods: In this study, we applied a SWATH-based, label-free, quantitative shotgun proteomic mass spectrometry approach to investigate the temporal [...] Read more.

Background: Seed dormancy is crucial for plant survival and agricultural productivity, yet its molecular mechanisms, particularly the role of maternal effects, remain poorly understood. Methods: In this study, we applied a SWATH-based, label-free, quantitative shotgun proteomic mass spectrometry approach to investigate the temporal dynamics of dormancy establishment in Xanthium strumarium, a wild plant with two seeds in one burr that, despite sharing the same genetic and environmental conditions, exhibit distinct dormancy states. Results: Our data show that dormant seeds undergo coordinated metabolic suppression, marked by a decrease in energy metabolism, cell cycle arrest, and auxin signaling, explaining their smaller size. Simultaneously, dormant seeds exhibit metabolic re-prioritization towards fatty acid desaturation, cell wall modification, and an active epigenetic program stabilized by dormancy-promoting factors alongside a transcriptionally quiescent state in early–mid development. However, in the late developmental stage, molecular signaling pathways showed a recalibration distinguished by changes in seed metabolism (such as carbon–nitrogen reallocation, sulfur assimilation, and GABA production), hormonal fluctuations, and epigenetic regulation. Notably, previously reported high DOG1 transcript abundance, together with the absence of detectable DOG1 protein in the proteomic dataset, suggests that post-transcriptional mechanisms may contribute to DOG1 regulation. Conclusions: Based on these findings and the available literature, we propose a framework whereby dormancy establishment occurs in two phases: an early DOG1-mediated priming phase followed by a temperature-sensitive plasticity phase during seed maturation. Full article

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

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42 pages, 11117 KB

Open AccessArticle

A Propeller with a Flexible Twist: A Computational Analysis of Intrinsically Disordered Regions in PIEZO Gating and PIEZO-Associated Channelopathies

by Shivam Shukla, Mason Elzy, Abiral Shrestha and Vladimir N. Uversky

Proteomes 2026, 14(3), 41; https://doi.org/10.3390/proteomes14030041 - 11 Aug 2026

Abstract

Background: Mechanosensitive ion channels PIEZO1 and PIEZO2 are key mediators of mechanotransduction, which converts physical forces into cellular signals involved in proprioception, touch, vascular function, and other physiological processes. Mutations in human PIEZO proteins are linked to various diseases, such as hereditary xerocytosis, [...] Read more.

Background: Mechanosensitive ion channels PIEZO1 and PIEZO2 are key mediators of mechanotransduction, which converts physical forces into cellular signals involved in proprioception, touch, vascular function, and other physiological processes. Mutations in human PIEZO proteins are linked to various diseases, such as hereditary xerocytosis, lymphatic dysplasia, and proprioceptive dysfunction. However, the role of intrinsic disorder in the regulation of these proteins and their susceptibility for disease-associated mutations remains unclear. Methods: We analyzed canonical human PIEZO1 and PIEZO2 protein sequences using machine learning, neural network, and energy-based disorder predictors, together with the prediction of disorder-mediated binding regions, phase separation propensity, interaction networks, evolutionary conservation, clinically annotated human variants, and peptide structural modeling. Results: Both proteins showed moderate intrinsic disorder, with PIEZO2 having slightly greater disorder propensity and higher predicted phase separation potential. Intrinsically disordered regions frequently overlapped binding-prone segments and post-translational modification sites, supporting regulatory functions. Evolutionary comparisons showed strong conservation of PIEZO proteins, while selected disordered regions retained disorder propensity despite greater sequence variability. Disease-causing variants mainly affected the ordered regions of both proteins, whereas disordered regions contained proportionally more benign variants and relatively few pathogenic mutations. The modeling of mutations within disordered hotspots showed altered local conformational tendencies, indicating that some disease variants may disrupt dynamic interaction interfaces rather than global structure. Interaction network analysis linked both proteins to enriched mechanotransduction, ion transport, and cytoskeletal pathways. Conclusions: Overall, our findings identify intrinsic disorder as an underappreciated feature of PIEZO channel biology and provide a framework for interpreting PIEZO-associated channelopathies. PIEZO proteins also perfectly illustrate the proteoform concept, where one gene yields a highly diverse kit of mechanosensitive molecular tools. While humans only have two primary PIEZO genes (PIEZO1 and PIEZO2), the body generates a vast array of functional variations. Full article

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19 pages, 931 KB

Open AccessArticle

Comparative Analysis of Progesterone Secretion and Plasma Proteome Across the Pregnant and Non-Pregnant Luteal Phase of the Koala (Phascolarctos cinereus)

by Brooke E. Hartley, Stephen D. Johnston, Yolande Campbell, Kerry Fanson, Vere Nicolson, Ashleigh Neal and Taylor Pini

Proteomes 2026, 14(3), 40; https://doi.org/10.3390/proteomes14030040 - 6 Aug 2026

Abstract

Background: Koalas are a vulnerable marsupial species with unique reproductive traits. Efforts to develop assisted breeding technologies have been hindered by a limited understanding of maternal recognition of pregnancy and physiological changes induced by the foeto-placental unit. Differences in the reproductive physiology of [...] Read more.

Background: Koalas are a vulnerable marsupial species with unique reproductive traits. Efforts to develop assisted breeding technologies have been hindered by a limited understanding of maternal recognition of pregnancy and physiological changes induced by the foeto-placental unit. Differences in the reproductive physiology of pregnant and non-pregnant koalas were examined to investigate the possibility of maternal recognition and identify potential pregnancy and/or embryonic loss biomarkers. Methods: Koalas were separated into three groups: pregnant (n = 4 cycles from three females), mated but non-parturient (n = 4 cycles from three females), and gonadotropin-releasing hormone (GnRH) agonist-treated females (n = 7). Plasma was collected on day of mating/GnRH injection (D0) and on multiple subsequent days. Progesterone concentrations were measured by enzyme immunoassay, and plasma proteomes were analysed using filter-aided sample preparation followed by liquid chromatography-tandem mass spectrometry (LC-MS/MS), employing sequential window acquisition of all theoretical fragment ion spectra. Results: Ovulation induction mechanisms influenced peri-ovulatory progesterone secretion (pregnant 40.7 ± 3.3 ng/mL vs. GnRH-treated 15.7 ± 1.8 ng/mL), with no significant differences in progesterone that occurred later in the luteal phase. LC-MS/MS identified 158 proteins, representing the first koala plasma proteome. Leucine-rich alpha-2-glycoprotein (LRG1) was significantly elevated at D2 in pregnant females compared to GnRH-treated females, and pregnant D9 and D19. In pregnant females, fibronectin (FN1) was significantly more abundant at D19 compared to D9 but not significantly different between treatments. Conclusions: These preliminary findings provide foundational data for further investigation into maternal recognition and pregnancy/embryonic loss in koalas. Full article

(This article belongs to the Section Animal Proteomics)

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22 pages, 6583 KB

Open AccessArticle

Proteomic Analysis of Paraffin-Embedded Intestines from Schistosoma mansoni Infection in Mice: Highlighting Molecular Players During Acute Schistosomiasis

by Lara Geralda Magela dos Santos Vieira, Ana Flávia Pinho Souza, Camilo Elber Vital, Dávila Regina Pacheco Silva, Flávia de Souza Marques, Gustavo Gonçalves Silva, Paula Melo de Abreu Vieira, R Alan Wilson and William Castro-Borges

Proteomes 2026, 14(3), 39; https://doi.org/10.3390/proteomes14030039 - 29 Jul 2026

Abstract

Background: Adult Schistosoma mansoni parasites inhabit the hepatic portal system of the vertebrate host, their deposited eggs causing granulomatous pathology in both the intestines and liver. In the intestines, egg secretions drive inflammatory processes involved in extravasation to the gut lumen. Methods: Here, [...] Read more.

Background: Adult Schistosoma mansoni parasites inhabit the hepatic portal system of the vertebrate host, their deposited eggs causing granulomatous pathology in both the intestines and liver. In the intestines, egg secretions drive inflammatory processes involved in extravasation to the gut lumen. Methods: Here, we investigate parasite-host interactions in a mouse model during the acute phase of a patent infection at 5 and 7 weeks, using parallel histological and proteomic analysis of paraffin-embedded ileal tissues. Results: Histology at week 7 showed infected animals had more inflammation and longer villi than at week 5, as well as more Goblet cells reflecting enhanced mucus production. LC-MS/MS analysis of deparaffinized ileal sections, subjected to in-solution tryptic digestion, revealed a total of 1615 protein groups. Differentially abundant proteins were found early at week 5, coinciding with the onset of egg deposition. A contrasting scenario, dominated by upregulation of protein components from the innate and adaptive immune systems, was seen at week 7; at this point, egg migration and excretion are underway. Among the proteins were mast cell proteases, fibrinogens, arginase-1, and molecules associated with extracellular matrix remodeling. Conclusions: Our findings reflect intestinal proteome changes likely participating in S. mansoni egg passage from the vascular bed to the intestinal lumen. Full article

(This article belongs to the Section Animal Proteomics)

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27 pages, 1926 KB

Open AccessArticle

Proteomic Mediators Linking Autoimmune Diseases to Major Adverse Cardiovascular Events: Insights from the UK Biobank

by Jingwen Huang, Chang Liu, Laurence S. Sperling, Arshed A. Quyyumi and Yan V. Sun

Proteomes 2026, 14(3), 38; https://doi.org/10.3390/proteomes14030038 - 24 Jul 2026

Abstract

Background: Autoimmune diseases (AIDs) are associated with increased cardiovascular risk. However, specific protein mediators linking AIDs to major adverse cardiovascular events (MACE) and cardiovascular death (CV death) remain unexplored. This study identifies proteomic mediators linking AIDs to MACE via high-dimensional mediation analysis in [...] Read more.

Background: Autoimmune diseases (AIDs) are associated with increased cardiovascular risk. However, specific protein mediators linking AIDs to major adverse cardiovascular events (MACE) and cardiovascular death (CV death) remain unexplored. This study identifies proteomic mediators linking AIDs to MACE via high-dimensional mediation analysis in the UK Biobank. Methods: We used UK Biobank data with proteomic profiling by Olink platform. Participants with prevalent myocardial infarction (MI), stroke, and heart failure at baseline were excluded. AIDs were categorized into musculoskeletal (MSK), vasculitis, gastrointestinal (GI), neurologic, and rheumatic fever subsets. Fine–Gray models assessed associations between AIDs and MACE and CV death. Proteome-wide association studies identified proteins associated with both AIDs and cardiovascular outcomes. High-dimensional mediation analysis (HIMA) explored protein-mediated pathways. All models adjusted for age, sex, lipids, BMI, smoking, hypertension, diabetes, chronic kidney disease, atrial fibrillation, and coronary artery disease. Results: Among 400,633 participants (median follow-up 14.5 years, 44.8% male), AIDs were present in 28,754 (7.2%). All AID categories were associated with increased MACE (sHR: MSK 1.34, vasculitis 1.67, GI 1.20, neurologic 1.33, rheumatic fever 1.38; all p < 0.001). For CV death, MSK, vasculitis, and rheumatic fever showed increased risk (sHR 1.34, 1.78, 1.51; all p ≤ 0.004), but not GI or neurologic AIDs. In 43,599 participants with proteomic data, HIMA identified 66 and 32 unique potential mediators linking AIDs to MACE and CV death, respectively. Four proteins (Growth Differentiation Factor 15, Interleukin-15, urokinase plasminogen activator receptor, and Tenascin C) mediated the AID-MACE relationship across multiple AID categories. Growth Differentiation Factor 15 and Interleukin-15 were shared mediators for CV death. Conclusions: This proteomic analysis identifies specific proteins that may mediate the association between AIDs and adverse cardiovascular outcomes, offering mechanistic insights into immune-related cardiovascular risk. These findings are hypothesis-generating and require replication and validation before the identified proteins can be considered causal mediators or adopted for clinical risk stratification. Full article

(This article belongs to the Section Proteomics of Human Diseases and Their Treatments)

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27 pages, 10788 KB

Open AccessArticle

Proteomic Profiling Reveals Region-Specific Brain Responses During Acclimation to Elevated Water Temperature in Atlantic Salmon (Salmo salar L.)

by Manojkumar Chandraprakasham, Gianluca Amoroso, Chris G. Carter, Chloe J. English, Lambertus Koster, Richard Wilson, Richard S. Taylor and Omar Mendoza-Porras

Proteomes 2026, 14(3), 37; https://doi.org/10.3390/proteomes14030037 - 23 Jul 2026

Cited by 1

Abstract

Background: Increasing summer seawater temperatures pose challenges for Atlantic salmon aquaculture, while brain region-specific responses to elevated temperature remain poorly understood. Methods: Atlantic salmon in the warm treatment (WT) underwent thermal ramping from 15 °C to 19 °C, with mortality observed at the [...] Read more.

Background: Increasing summer seawater temperatures pose challenges for Atlantic salmon aquaculture, while brain region-specific responses to elevated temperature remain poorly understood. Methods: Atlantic salmon in the warm treatment (WT) underwent thermal ramping from 15 °C to 19 °C, with mortality observed at the end of week 4 (15.78%). The WT temperature was subsequently reduced to 18 °C in week 5, while the control treatment (CT) was adjusted from 15 °C to 14 °C, and the WT (18 °C) and CT (14 °C) conditions were maintained thereafter. At the end of the trial (week 10), six brain regions, including the cerebellum (CBE), hypothalamus (HYP), medulla oblongata (MED), optic tectum (OPT), pituitary gland (PIT), and telencephalon (TEL), were analysed using data-independent acquisition mass spectrometry-based proteomics. Results: Over 9000 protein groups were identified per brain region, and exploratory differential abundance analysis revealed predominantly region-specific protein abundance changes. Increased SERPINH1 (HSP47) abundance was observed in HYP, PIT, and TEL, suggesting roles in protein-folding and stress regulation. Functional enrichment analyses indicated differential regulation of translation, transcription, energy metabolism, and metabolic pathways across brain regions in the WT group. Conclusions: This study provides a brain region-specific proteomic resource for Atlantic salmon and advances understanding of molecular responses associated with recovery from a temperature reduction (19 °C to 18 °C) and subsequent thermal adjustment at 18 °C. Full article

(This article belongs to the Section Animal Proteomics)

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18 pages, 7604 KB

Open AccessArticle

Protein Language Model Embeddings Reveal Proteome-Scale Ortholog Divergence Relevant to Cross-Species Pharmacology

by Taichi Endoh, Gerry Amor Camer, Kotetsu Kayama, Daiji Endoh and Hiroki Teraoka

Proteomes 2026, 14(3), 36; https://doi.org/10.3390/proteomes14030036 - 23 Jul 2026

Abstract

Background: Comparative proteome analysis can reveal functional conservation and divergence among orthologous proteins, with important implications for pharmacology and toxicology. Protein language models (PLMs) may capture sequence-derived functional relationships beyond what conventional alignment metrics capture. Methods: Orthologous proteins from Danio rerio and Danio [...] Read more.

Background: Comparative proteome analysis can reveal functional conservation and divergence among orthologous proteins, with important implications for pharmacology and toxicology. Protein language models (PLMs) may capture sequence-derived functional relationships beyond what conventional alignment metrics capture. Methods: Orthologous proteins from Danio rerio and Danio aesculapii were compared using embeddings generated by the Evolutionary Scale Modeling 2 (ESM-2) protein language model. Reciprocal best-hit inference identified 68,971 high-confidence ortholog pairs, of which 51,086 were available for embedding-based analysis. PLM divergence was quantified using cosine distance and evaluated using length-matched and bitscore-matched random controls, Gene Ontology graph-distance analysis, and localized domain-level comparisons. Results: Ortholog pairs showed strong global conservation, with a median PLM distance of 0.000487, whereas randomized controls exhibited substantially greater divergence. Increasing Gene Ontology graph distance broadened PLM-distance distributions, and leaf–parent comparisons demonstrated significant functional ordering (Wilcoxon p = 2.44 × 10⁻⁴). Local analyses revealed increased divergence in pathophysiologically relevant regions of aryl hydrocarbon receptor (AHR) and potassium channel proteins. Conclusions: PLM embeddings provide a scalable framework for comparative proteome characterization, complement conventional sequence-based analyses, and prioritize orthologs or protein regions with elevated functional divergence for experimental validation in cross-species pharmacology, toxicology, and systems biology. Full article

(This article belongs to the Section Proteome Bioinformatics)

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18 pages, 1943 KB

Open AccessArticle

Lyophilization Prior to Homogenisation and Extraction Increases Membrane Protein Detection in Gram-Negative Bacterial Proteomic Analyses

by Breyer Woodland, Luke A. Farrell, Matthew B. O’Rourke and Matthew P. Padula

Proteomes 2026, 14(3), 35; https://doi.org/10.3390/proteomes14030035 - 15 Jul 2026

Abstract

Background: Multi-drug resistant Gram-negative bacteria (GNB) are major contributors to the antimicrobial resistance (AMR) burden. AMR mechanisms are primarily mediated by proteoforms; therefore, proteomic analyses of GNB offers a significant advantage in understanding the mechanisms of AMR. A large portion of these mechanisms [...] Read more.

Background: Multi-drug resistant Gram-negative bacteria (GNB) are major contributors to the antimicrobial resistance (AMR) burden. AMR mechanisms are primarily mediated by proteoforms; therefore, proteomic analyses of GNB offers a significant advantage in understanding the mechanisms of AMR. A large portion of these mechanisms are mediated by membrane proteins; however, they are often difficult to extract due to their hydrophobic nature and complex interactions with other components of the cell membrane. To extract the greatest number of proteoforms, an efficient homogenisation protocol is required to effectively disrupt the rigid cell wall and membrane. Methods: Using Escherichia coli, Klebsiella pneumoniae, Acinetobacter baumannii and Pseudomonas aeruginosa, we systematically compared the extraction efficiency of bead-beating with flash frozen and lyophilized cell pellets. Results: We demonstrate that lyophilization improves bead-beating extraction methods by increasing the detection of membrane proteins. We detected numerous unique membrane proteins in each bacterial isolate, including ABC transporters and proteins involved in lipopolysaccharide synthesis, when lyophilizing prior to bead-beating, compared to only flash-freezing. Conclusions: As membrane proteins play a central role in AMR mechanisms, this improvement in their isolation and identification will aid in understanding the resistance and molecular mechanisms associated with multi-drug resistant GNB. Full article

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

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8 pages, 520 KB

Open AccessTechnical Note

An Ultrafast GPU-Enabled MGVB

by Metodi V. Metodiev

Proteomes 2026, 14(3), 34; https://doi.org/10.3390/proteomes14030034 - 7 Jul 2026

Abstract

Background: cMGVB is a graphical processing unit (GPU)-enabled implementation of the computational proteomics data analysis toolset MGVB. MGVB was released in 2025 as a Linux program designed to run on multi-node servers. It utilizes a novel algorithm for finding combinations of post-translational [...] Read more.

Background: cMGVB is a graphical processing unit (GPU)-enabled implementation of the computational proteomics data analysis toolset MGVB. MGVB was released in 2025 as a Linux program designed to run on multi-node servers. It utilizes a novel algorithm for finding combinations of post-translational modification in peptide MS/MS data. The original combinatorial algorithm required a significant amount of resources to be practical. Hence, the aim of the research reported here was to port the algorithm to GPU and thus increase its speed and efficiency. Methods: To accomplish this it was recoded in CUDA C; recursive functions and data structures were re-implemented as non-recursive, and the algorithm was incorporated in a new version of MGVB, now termed cMGVB. Results: The re-implemented algorithm is much faster and, unlike the original program, can run on single CPU workstations equipped with inexpensive GPUs and still be much faster than the original algorithm running on HPC clusters. A typical focused search is completed in about a minute by cMGVB compared to 10–15 min by the original implementation. Illustrative case studies are presented and discussed in this report. Conclusions: cMGVB enables workflows that were not practical or even possible with the original MGVB. Full article

(This article belongs to the Section Proteome Bioinformatics)

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13 pages, 3418 KB

Open AccessArticle

A Dual-Background Statistical Framework for Phosphoproteomics Highlights Intrinsic, High-Confidence Phosphorylation Signature by Mitigating Orthogonal Sources of Bias

by Bin Deng

Proteomes 2026, 14(3), 33; https://doi.org/10.3390/proteomes14030033 - 7 Jul 2026

Abstract

Background: Distinguishing genuine kinase–substrate motifs from background noise is a growing challenge, as mass spectrometry (MS)-based global phosphoproteomics identifies a rapidly expanding set of phosphorylation sites. One of the major limitations is selecting an appropriate background model that systematically controls both technical and [...] Read more.

Background: Distinguishing genuine kinase–substrate motifs from background noise is a growing challenge, as mass spectrometry (MS)-based global phosphoproteomics identifies a rapidly expanding set of phosphorylation sites. One of the major limitations is selecting an appropriate background model that systematically controls both technical and biological sources of bias. Although using the entire proteome as a background in a FASTA format considers the overall amino acid composition, it is still prone to biases from protein abundance and the uneven distribution of sequence space (particularly around low-abundance proteins). By contrast, internal background methods can control experiment-specific detection biases, but they may not fully capture residue-specific compositions or general trends in phosphorylation. Methods: I develop a Dual-Background Enrichment (DBE) framework with a position-specific enrichment (PSE) strategy, which involves analyzing motif enrichment against two distinct background models: (1) A residue-heterogeneous internal background composed of phospho-motifs centered on the residue; e.g., phosphoserine (pS) motifs are tested relative to the pool of all detected phosphothreonine (pT) and phosphotyrosine (pY) motifs from the same experiment. (2) A FASTA background that includes all S, T, and Y residues in the UniProtKB proteome sequences. Results: Motifs are classified as high confidence if they meet statistical significance (q ≤ 0.05, fold enrichment > 1.5) against both background models. Conclusion: By applying the DBE strategy to a large-scale phosphoproteomics dataset, we distinguish motifs driven by amino acid composition (enriched in FASTA background only) from those reflecting kinase substrate specificity (enriched in both backgrounds). This dual-reference approach reduces false positives arising from sequence composition bias and enriches high-confidence candidate kinase recognition motifs. Full article

(This article belongs to the Section Proteome Bioinformatics)

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24 pages, 1650 KB

Open AccessReview

A One Health Framework for Proteomics Across the Tree of Life to Advance Food Security, Animal Health, and Ecosystem Resilience

by Tarun Mishra, Ritudhwaj Tiwari, Tuyelee Das and Maneesh Lingwan

Proteomes 2026, 14(3), 32; https://doi.org/10.3390/proteomes14030032 - 24 Jun 2026

Abstract

As global ecosystems and food systems face unprecedented anthropogenic and climatic challenges, there is a demand for an integrated understanding of biological systems. Proteomics has emerged as a definitive approach offering a direct view of the molecular phenotype, yet it is traditionally separated [...] Read more.

As global ecosystems and food systems face unprecedented anthropogenic and climatic challenges, there is a demand for an integrated understanding of biological systems. Proteomics has emerged as a definitive approach offering a direct view of the molecular phenotype, yet it is traditionally separated into plant and animal disciplines. With recent advances in mass spectrometry (MS) and bioinformatics tools, this prospective review proposes that combining a One Health proteomics approach with deep-learning data analysis can revolutionize global food security, animal productivity, and ecosystem health by uncovering proteoform signatures that drive resilience across life. The potential of a unified One Health proteomic framework, highlighting major developments, including 4D proteomics, Data-Independent Acquisition (DIA), and single-cell resolution, and emphasizes their capacity to resolve the complex proteoform landscape across kingdoms. Review emphasizes the applications of proteogenomics as a cross-disciplinary tool to improve genome annotations, explain evolutionary differences, discover biomarkers in animals and resolve complex signaling networks in plants under stress. Nevertheless, contemporary proteogenomics methods still show limitations in their ability to comprehensively resolve proteoforms due to the fact that the use of peptide-based approaches makes it difficult to fully appreciate the post-translational modifications specific to each protein isoform. We show that One Health proteomics will provide a transformative roadmap for deciphering the functional proteoform signatures that underpin resilience across the tree of life. Full article

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

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17 pages, 1902 KB

Open AccessArticle

Nuclear Proteomics to Understand the Promotive Effect of Plant-Derived Smoke Solution on Wheat Under Salt Stress

by Sheikh Shohag, Hisateru Yamaguchi, Keisuke Hitachi, Kunihiro Tsuchida, Shafiq Ur Rehman and Setsuko Komatsu

Proteomes 2026, 14(2), 31; https://doi.org/10.3390/proteomes14020031 - 15 Jun 2026

Cited by 1

Abstract

Background: Salinity, which hampers wheat growth and development, is one of the major abiotic stresses. Plant-derived smoke (PDS) solution alleviates salt stress and promotes wheat growth and development; however, the underlying molecular mechanisms have not been completely clarified. Methods: In this study, nuclear [...] Read more.

Background: Salinity, which hampers wheat growth and development, is one of the major abiotic stresses. Plant-derived smoke (PDS) solution alleviates salt stress and promotes wheat growth and development; however, the underlying molecular mechanisms have not been completely clarified. Methods: In this study, nuclear proteomics was employed to reveal the promotive effect of PDS solution on salt-stressed wheat. Nuclear fractions were isolated from wheat roots, and their purity was confirmed via enrichment of histone H3 and reduction of cytosolic ascorbate peroxidase. Using this nuclear purification technique, label-free nano LC–MS/MS-based nuclear proteomics was performed to identify differentially abundant nuclear proteins in salt-stressed wheat with or without PDS solution treatment. Results: Salt stress decreased histone H2A and DNA polymerase levels, whereas PDS solution treatment of salt-stressed wheat increased levels of histone variants (H2A, H2B, H3, and H4), DNA polymerase, and DNA topoisomerase II. In addition, the PDS solution increased the levels of pre-mRNA cleavage factor Im 25 kDa subunit and RNA helicase in salt-stressed wheat. Immunoblot analysis further validated the increase in histone deacetylase levels triggered by the PDS solution treatment in the salt-stressed wheat. Conclusions: These results suggest that PDS solution alters nuclear proteins in a way that contributes to chromatin remodeling and transcription during salt stress. Full article

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

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20 pages, 3043 KB

Open AccessArticle

Development of a Xylene-Free Sample Preparation Protocol for Quantitative Proteomics of Clinically Relevant Formaldehyde-Fixed Paraffin-Embedded Needle Biopsy Samples

by Gontse Mabuse Moagi, Lívia Beke, Gábor Méhes, Gábor Kecskeméti, Zoltán Szabó, Lilla Turiák and Éva Csősz

Proteomes 2026, 14(2), 30; https://doi.org/10.3390/proteomes14020030 - 14 Jun 2026

Abstract

Background: Fresh frozen tissues are considered the gold standard for proteomic analyses due to their superior preservation of protein integrity; however, their use is limited by the logistical and financial requirements of long-term cold storage. Formaldehyde-fixed paraffin-embedded (FFPE) tissues provide a practical alternative, [...] Read more.

Background: Fresh frozen tissues are considered the gold standard for proteomic analyses due to their superior preservation of protein integrity; however, their use is limited by the logistical and financial requirements of long-term cold storage. Formaldehyde-fixed paraffin-embedded (FFPE) tissues provide a practical alternative, owing to their stability and widespread availability in clinical settings. A critical step in FFPE proteomics is deparaffinization, which traditionally relies on organic solvents such as xylene, along with the efficient reversal of formaldehyde-induced crosslinks. Methods: In this study, we evaluated multiple FFPE protein extraction and digestion workflows including chaotropic, surfactant-based, and detergent-free approaches in combination with xylene-free deparaffinization strategies, using label-free data-independent acquisition (DIA) LC-MS/MS. Results: Among the tested methods, a chaotropic, reductant, and surfactant-free in-solution digestion workflow demonstrated robust protein and peptide recovery. A modified version of this protocol further improved peptide coverage while maintaining comparable protein depth. The applicability of the optimized workflow was assessed using FFPE needle biopsy samples from control, hepatic steatosis, and liver fibrosis groups. Exploratory proteomic patterns were observed across conditions, with hepatic steatosis associated with early activation of stress-response pathways, while fibrosis showed evidence suggesting altered lipid metabolism. Conclusions: Overall, this study presents a simple, xylene-free, and MS-compatible workflow for FFPE proteomics that is suitable for low-input clinical samples and may support broader application of archival tissues in proteomic research. Full article

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

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19 pages, 1412 KB

Open AccessSystematic Review

Systematic Review of Protein Signatures for Clinical Monitoring of Osteonecrosis of the Jaw: Meta-Analysis and Insights from Bioinformatics-Driven Proteomics

by Helena Oliveira Deróbio, Isabela dos Reis Souza, François Isnaldo Dias Caldeira, Fernanda Gonçalves Basso and Taisa Nogueira Pansani

Proteomes 2026, 14(2), 29; https://doi.org/10.3390/proteomes14020029 - 10 Jun 2026

Abstract

Background: Several studies have investigated the clinical and immunological aspects of medication-related osteonecrosis of the jaw (MRONJ). However, the underlying immunological mechanisms and signaling pathways involved in its pathophysiology remain incompletely understood. This systematic review and meta-analysis, complemented by bioinformatics analyses, aimed to [...] Read more.

Background: Several studies have investigated the clinical and immunological aspects of medication-related osteonecrosis of the jaw (MRONJ). However, the underlying immunological mechanisms and signaling pathways involved in its pathophysiology remain incompletely understood. This systematic review and meta-analysis, complemented by bioinformatics analyses, aimed to identify proteomic biomarkers associated with MRONJ. Methods: Six databases (PubMed, Embase, Scopus, Web of Science, Cochrane Library, and VHL) were searched, along with gray literature and manual searches. Observational studies in English comparing proteomic profiles of individuals with and without MRONJ were included. Study selection and data management were conducted using EndNote™ X8 and Rayyan.ai, and risk of bias was assessed using the QUADOMICS tool. Functional enrichment analysis was performed using g:Profiler and Reactome, and interaction networks were constructed using GeneMANIA, STRING, and MetaboAnalyst (Cytoscape program; version 3.10.1). Meta-analysis was performed in RStudio (R-4.5, Rstudio extension 2025.05.1+513) (α = 0.05). Results: Three studies were included in the review, and two in the meta-analysis. The meta-analysis showed higher salivary levels of Apolipoprotein B-100 (APOB), Apolipoprotein A-II (APOA2), and Heparin Cofactor 2 (SERPIND1) in MRONJ patients, while the protein Keratin (KRT16) showed reduced levels without statistical significance. Bioinformatics analyses indicated involvement in lipid metabolism, impaired tissue repair, and inflammatory and immune responses. Conclusions: These findings suggest altered salivary proteomic signatures in MRONJ for APOB, APOA2, SERPIND1, and KRT16 proteins. Full article

(This article belongs to the Section Identification of Potential Biomarkers and Potential Therapeutic Targets)

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34 pages, 12216 KB

Open AccessReview

Diverse Forms of Autophagy and Their Roles in Liver Disease and Aging: A Comprehensive Review

by Seoyoon Heo, Min Young Lee, Che Yeon Jeong, Dong Ha Kim and Ji Hye Jun

Proteomes 2026, 14(2), 28; https://doi.org/10.3390/proteomes14020028 - 27 May 2026

Abstract

The liver is a central metabolic organ that integrates nutrient sensing, lipid handling, and detoxification to maintain systemic homeostasis. In metabolic dysfunction–associated steatotic liver disease (MASLD), chronic metabolic overload accelerates hepatocyte senescence, impairing regenerative capacity and promoting progression toward fibrosis and hepatocellular carcinoma. [...] Read more.

The liver is a central metabolic organ that integrates nutrient sensing, lipid handling, and detoxification to maintain systemic homeostasis. In metabolic dysfunction–associated steatotic liver disease (MASLD), chronic metabolic overload accelerates hepatocyte senescence, impairing regenerative capacity and promoting progression toward fibrosis and hepatocellular carcinoma. While transcriptomic studies have provided important insights into stress-responsive pathways, they incompletely capture the proteome remodeling and proteoform-level alterations that govern hepatocyte function during aging and disease. Recent mass spectrometry–based proteomics studies have revealed that disruption of autophagy-dependent proteome homeostasis is a defining feature of senescent hepatocytes. Quantitative analyses demonstrate coordinated alterations in selective autophagy pathways—including lipophagy, mitophagy, ferritinophagy, ER-phagy, and pexophagy—accompanied by organelle-specific protein abundance signatures and remodeling of autophagy-related proteoforms. These findings position proteomics as an essential tool for resolving the spatial and functional reorganization of hepatocyte proteomes that cannot be inferred from transcript abundance alone. In this review, we synthesize proteomics-driven evidence defining selective autophagy dysfunction in aging and MASLD livers, critically evaluate methodological limitations, and propose a conceptual framework in which impaired selective autophagy acts as a proteome-level driver of hepatocyte senescence. We further outline future directions for proteoform-resolved and spatial proteomics approaches aimed at identifying actionable targets for therapeutic intervention in liver disease. Full article

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25 pages, 9441 KB

Open AccessArticle

Quantitative Metaproteomic Characterization of Acetic Acid Bacteria Reveals Functional Dynamics During Verdejo Wine Acetification

by Cristina Campos-Vázquez, Juan C. García-García, Juan Carbonero-Pacheco, Juan J. Román-Camacho, Roger Consuegra-Rivera, Teresa García-Martínez, Isidoro García-García, Inés M. Santos-Dueñas and Juan Carlos Mauricio

Proteomes 2026, 14(2), 27; https://doi.org/10.3390/proteomes14020027 - 20 May 2026

Abstract

Background: Acetification is a complex process driven by acetic acid bacteria (AAB), in which high ethanol and acidity levels require strong microbial metabolic adaptation. Although the microbiota involved in vinegar production has been described, the functional mechanisms that enable these bacteria to maintain [...] Read more.

Background: Acetification is a complex process driven by acetic acid bacteria (AAB), in which high ethanol and acidity levels require strong microbial metabolic adaptation. Although the microbiota involved in vinegar production has been described, the functional mechanisms that enable these bacteria to maintain metabolic activity remain poorly understood. In this study, the functional dynamics of AAB during Verdejo vinegar acetification were analyzed using a quantitative metaproteomic approach. Methods: Acetification was performed in submerged culture under semi-continuous conditions, and samples were collected at four stages of the cycle (S1–S4). Results: LC-MS/MS analysis led to the identification of 1626 proteins, of which 1409 were assigned to the Acetobacteraceae family. Komagataeibacter europaeus was the dominant species (73.7%). Hierarchical clustering revealed four protein abundance patterns, and differential analysis identified 350 proteins with increased abundance and 169 with decreased abundance, with the greatest changes observed between S1 and S4. Functional annotation and protein–protein interaction analyses indicated that the main metabolic adaptations involve pathways related to energy metabolism, amino acid biosynthesis, membrane-associated functions, cellular homeostasis, and acid stress response. Conclusions: Overall, the results show that K. europaeus concentrates most of the metabolic activity during acetification and that proteome reorganization reflects key molecular strategies for adaptation and survival under high-acidity conditions. Full article

(This article belongs to the Section Microbial Proteomics)

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