Journal Of Proteomics[JOURNAL]
Sun
200 papers
On-filter fractionation by empFASP improves identification of membrane peptides in proteomic experiments.
Březinová J, Pravdová A, Korecký M … +4 more , Khoroshyy P, Škerle J, Hubálek M, Stříšovský K
J Proteomics · 2026 Jul · PMID 42401291 · Publisher ↗
Membrane proteins remain among the most analytically challenging targets in bottom-up proteomics due to their limited solubility and low abundance of protease-accessible sites within transmembrane domains. In addition, h...
Membrane proteins remain among the most analytically challenging targets in bottom-up proteomics due to their limited solubility and low abundance of protease-accessible sites within transmembrane domains. In addition, hydrophobic peptides are frequently lost during detergent removal and the on-filter processing steps. Here, we present empFASP, a straightforward on-filter-fractionation-based modification of the enhanced filter-aided sample preparation (eFASP) workflow that enhances recovery of membrane-embedded peptides otherwise lost during digestion and cleanup. The method combines controlled on-filter inversion with sequential ethyl acetate extraction at defined pH values, enabling recovery of peptide material retained on the filter and redistributed into detergent micelles. Compared with SP3 and SP4 in HEK293T lysates, empFASP increased unique hydrophobic peptide identifications by up to 48% and increased the proportion of detected transmembrane peptides. Application to mouse mitochondrial membranes and phosphatidylethanolamine-deficient and PE-containing Escherichia coli membranes showed that the additional fractions of empFASP contribute complementary recovery of hydrophobic and membrane-associated peptides, with the strongest gains observed at the peptide level. Because empFASP requires no specialized reagents or instrumentation, it can be readily implemented in standard proteomics workflows to improve coverage of membrane-embedded regions. SIGNIFICANCE: The empFASP (enhanced membrane peptide) workflow offers a practical solution to one of the persistent limitations in membrane proteomics-the underrepresentation of hydrophobic and transmembrane peptides in standard digests. By integrating simple pH-controlled extractions into an on-filter format, empFASP recovers peptides otherwise lost through adsorption or detergent micelle retention, substantially improving coverage of the membrane proteome. This method expands the analytical reach of bottom-up proteomics without requiring specialized instrumentation, making it immediately applicable for studies of membrane topology, protein-lipid interactions, and the structural consequences of altered membrane composition.
Transpulmonary proteomic gradient analysis in women with pulmonary arterial hypertension associated with systemic sclerosis.
Teixeira M, Couto DS, Oliveira MI … +4 more , Aires I, Domingues P, Ribeiro F, Santos M
J Proteomics · 2026 Jun · PMID 42379418 · Publisher ↗
This study investigated proteomic alterations in the pulmonary circulation of patients with pulmonary arterial hypertension associated with systemic sclerosis (PAH-SSc) by analyzing the transpulmonary protein gradient an...
This study investigated proteomic alterations in the pulmonary circulation of patients with pulmonary arterial hypertension associated with systemic sclerosis (PAH-SSc) by analyzing the transpulmonary protein gradient and comparing the proteomic profiles with systemic sclerosis (SSc) without PAH. Twenty women were included (10 PAH-SSc, 64.6 ± 10.8 years; 10 SSc, 62.8 ± 11.5 years). The transpulmonary gradient was defined as the difference in biomarker concentrations between wedge-position and pulmonary artery blood samples. Peptides were analysed using liquid chromatography-mass spectrometry, and differentially abundant proteins were identified with Proteome Discoverer. Protein-protein interaction networks were generated with STRING and visualized in Cytoscape. A total of 270 proteins were detected, with no significant transpulmonary gradient alterations. However, patients with PAH-SSc showed distinct proteomic profiles compared to SSc. Multivariate analysis identified 48 differentially abundant proteins in pulmonary artery plasma, with 15 overrepresented and 33 downregulated in PAH-SSc. Among these, the downregulation of transforming growth factor-beta-induced protein ig-h3 (TGFβI/ig-h3) points to a potential involvement of the TGF-β-related extracellular matrix remodelling pathway in PAH-SSc. However, further validation in larger and independent cohorts is required before its relevance as a biomarker or therapeutic target can be established. In conclusion, while no transpulmonary proteomic gradient was observed, the proteomic profiles of PAH-SSc and SSc were different. The profile in PAH-SSc was characterized by differences in immune response, lipid metabolism, and hemostatic proteins. SIGNIFICANCE: This study offers the first proteomic characterization of the transpulmonary gradient in PAH-SSc and SSc. Although no differences in the gradient were found, the pulmonary artery plasma proteome of PAH-SSc patients showed a distinct pattern compared to SSc. Several proteins associated with immune function, haemostasis, and cellular processes were altered, which may indicate specific pathophysiological features of PAH-SSc or suggest how lung dysfunction develops in SSc. Targeting dysregulated proteins like TGFβI/ig-h3 or addressing immune-coagulation imbalances may support future research studies. Overall, these findings refine the molecular profile of PAH-SSc and provide a basis for future large-scale studies aimed at clarifying disease mechanisms and identifying clinically relevant molecular signatures.
Multiomic insights into fungal polylactic acid degradation: Metabolic adaptation and hydrolytic mechanisms of Sporobolomyces pararoseus.
Feng J, Zhou W, Luo C … +4 more , Lin X, Mo X, Wang Y, Li J
J Proteomics · 2026 Jun · PMID 42365927 · Publisher ↗
Polylactic acid (PLA), a biodegradable polyester from renewable resources, is a sustainable alternative to petrochemical plastics. However, its environmental degradation is inefficient naturally, requiring specific micro...
Polylactic acid (PLA), a biodegradable polyester from renewable resources, is a sustainable alternative to petrochemical plastics. However, its environmental degradation is inefficient naturally, requiring specific microbial activities. While bacterial PLA-degrading mechanisms are well documented, fungal degrading systems-particularly their molecular mechanisms-are underexplored.We isolated Sporobolomyces pararoseus ZRQ01 from the gut microbiota of PLA-fed mealworms. This fungal strain noticeably degraded PLA in PLA-containing medium supplemented with 2% glucose. Biodegradation assays revealed 22.8% loss of the PLA film weight after 35 days of incubation, and scanning electron microscopy confirmed extensive surface erosion and pore formation. Integrated transcriptomic and proteomic analyses, together with the reference genome of S. pararoseus ZRQ01, revealed that S. pararoseus ZRQ01 upregulates hydrolytic enzymes at both transcript and protein levels to cleave PLA into lactic acid. After lactic acid is transferred into S. pararoseus ZRQ01 cells by monocarboxylate transporters with increased abundance, it is assimilated by pathways of pyruvate metabolism and the TCA cycle with increased protein abundance. Intriguingly, upregulation of genes in autophagy-related and MAPK signaling pathways underscores an adaptive stress response potentially supporting cellular homeostasis and degradation-related gene expression. Our results highlight S. pararoseus ZRQ01's metabolic potential for bioremediation and offer insights into fungal bioplastic degradation pathways.
Temporal proteomic analysis reveals a three-phase adaptation strategy in Phytophthora cinnamomi during salinity stress.
Vinson LS, Loo T, Kulshrestha S … +2 more , Dobson RCJ, Meisrimler CN
J Proteomics · 2026 Jun · PMID 42342110 · Publisher ↗
Phytophthora cinnamomi, a highly invasive hemibiotrophic oomycete, threatens global agriculture, forestry, and native ecosystems. Although drought and temperature effects on P. cinnamomi-host interactions are well studie...
Phytophthora cinnamomi, a highly invasive hemibiotrophic oomycete, threatens global agriculture, forestry, and native ecosystems. Although drought and temperature effects on P. cinnamomi-host interactions are well studied, current knowledge of abiotic stress responses in P. cinnamomi remains largely centered on infection and phytopathology, with limited molecular insight into the pathogen's direct response to salinity independent of its host. To address this gap, we combined growth assays, time-resolved proteomics, and network analysis to define how P. cinnamomi responds and adapts to salinity exposure. Growth assays showed that NaCl-modified agar enhanced mycelial expansion in a concentration-dependent manner, with 100 mM NaCl significantly increasing growth at 48, 72, and 96 h compared with controls, while 50 mM NaCl remained comparable to control conditions. Temporal proteomic analysis of 100 mM NaCl treatment at 0, 1, 6, 12, and 24 h post treatment revealed dynamic shifts in protein abundance. Early induction of ROS (Reactive Oxygen Species)-detoxifying enzymes, including glutathione S-transferases and peroxidases, was consistent with ROS-specific staining assays. Network analysis identified modules enriched for redox regulation, ATP generation, ion transport, and translational control, highlighting multi-layered adaptation to elevated NaCl levels. Notably, clusters of conserved hypothetical proteins were strongly upregulated, indicating unexplored stress tolerance components in Phytophthora species. Here, we propose that P. cinnamomi rapidly activates a three-phase strategy involving metabolism readjustments, redox defenses, and cellular structure alterations under salinity conditions. With increasing soil salinization due to climate change, our study provides first mechanistic insights into P. cinnamomi's adaptive plasticity and ecological resilience to abiotic stress. SIGNIFICANCE: This study represents the first temporal proteomic analysis of salinity stress adaptation in Phytophthora cinnamomi, revealing a sophisticated three-phase adaptation strategy. This research fundamentally advances our understanding of how this globally destructive plant pathogen, P. cinnamomi, maintains environmental resilience. Our findings reveal proteome remodelling as a mechanistic framework for understanding stress tolerance in oomycetes, a group of microorganisms responsible for some of the world's most destructive agricultural and forest diseases. Our results show proteins involved in emergency damage control through metabolic recalibration to sustained adaptation. These findings have relevance for predicting pathogen behavior under climate change scenarios, where increasing soil salinity threatens agricultural productivity while simultaneously enhancing pathogen survival and virulence. Understanding how P. cinnamomi responds to prolonged salinity exposure may inform targeted biocontrol strategies and improve predictive models of disease pressure in salt-affected agricultural regions. The temporal analysis framework we present offers a broadly applicable approach for understanding microbial stress adaptation, with implications extending beyond plant pathology to environmental microbiology and biotechnology applications where stress tolerance is paramount.
Proteomic and phosphoproteomic profiles of time-dependent dynamic changes in LPS-induced macrophage polarization.
Wu X, Li W, Zhang J … +3 more , Wang R, Li X, Wang M
J Proteomics · 2026 Jun · PMID 42336198 · Publisher ↗
The temporal proteomic and phosphoproteomic reprogramming during early M1 macrophage polarization (0-6 h) remains poorly understood. We performed time-resolved proteomic and phosphoproteomic analyses of LPS-stimulated RA...
The temporal proteomic and phosphoproteomic reprogramming during early M1 macrophage polarization (0-6 h) remains poorly understood. We performed time-resolved proteomic and phosphoproteomic analyses of LPS-stimulated RAW264.7 macrophages at seven time points within 6 h. Time-clustering of differentially expressed molecules revealed two patterns: initial change with partial recovery, and sustained dysregulation. Upregulated proteins and phosphorylation sites were enriched in the Rho GTPase signaling pathway, T-cell receptor signaling pathway, NF-κB cascade, osteoclast differentiation pathway, and antiviral immune pathway. Downregulated pathways were associated with cell cycle regulation, chromatin remodeling, RNA metabolism, and mRNA processing, indicating resource reallocation to prioritize acute inflammatory responses. Kinase-substrate network analysis confirmed the mitogen-activated protein kinase (MAPK), cyclin-dependent kinase (CDK), protein kinase B (AKT), and ribosomal S6 kinase (RSK) families as core upstream phosphorylation regulators. Integrated analysis revealed synergistic and antagonistic relationships between proteomic and phosphoproteomic changes. This study provides a temporal molecular atlas of M1 polarization, delineating inflammatory signaling dynamics and offering a basis for therapeutic target discovery in inflammatory diseases. SIGNIFICANCE: Macrophage M1 polarization is a central event in innate immune defense against pathogenic invasion, yet its dysregulation is a pivotal driver of the onset and progression of a broad spectrum of inflammation-associated disorders, spanning autoimmune diseases, infectious conditions and inflammatory bone diseases, making the dissection of its molecular regulatory mechanisms an urgent research priority in immunology and translational medicine. Dynamic molecular events within 0-6 h after LPS stimulation are critical for initiating and shaping M1 inflammatory activation, yet systematic time-resolved proteomic and phosphoproteomic profiling remains insufficient.In this study, we comprehensively characterized temporal proteome and phosphoproteome changes at seven consecutive time points during macrophage polarization, clarified two distinct dynamic molecular patterns, identified core signaling pathways and key kinase regulators involved in inflammatory reprogramming, and uncovered the leading role of post-translational phosphorylation modifications in initiating polarization. This work delineates the time-series molecular atlas of early macrophage activation, provides novel insights into the temporal regulatory mechanism of inflammatory signaling networks, and lays a solid experimental foundation for exploring new intervention targets and regulatory nodes in clinical translational research.
From prediction to mechanism: Explainable AI uncovers plasma and CSF proteomic signatures of Alzheimer's disease.
Donmez TB, Mansour M
J Proteomics · 2026 Jun · PMID 42297098 · Publisher ↗
Alzheimer's disease (AD) plasma and cerebrospinal fluid (CSF) proteomics can distinguish AD from cognitively normal controls, but the generalizability of machine learning performance and the recurrence of biological sign...
Alzheimer's disease (AD) plasma and cerebrospinal fluid (CSF) proteomics can distinguish AD from cognitively normal controls, but the generalizability of machine learning performance and the recurrence of biological signals across datasets require cautious interpretation. We developed an explainable artificial intelligence framework spanning two fluids and four ADNI proteomic datasets, covering 2082 modality specific samples, all analysed internally within ADNI. Phase 1 analysed plasma using a 119 analyte NULISA and targeted UPENN panel (n = 727; 216 CE, 511 controls). Phase 2 extended the analysis to CSF using SOMAscan7k, TMT-MS and targeted SET2, with Elecsys Aβ42, Aβ40, total tau and p-tau181 as anchor biomarkers. Only SOMAscan was subject-independent relative to Phase 1 plasma; TMT-MS and SET2 overlapped with Phase 1 for 96.0% and 97.7% of subjects and therefore are not independent replication cohorts. Under subject-level splits with fold internal preprocessing, we compared Elastic Net, Explainable Boosting Machines and gradient boosted trees with SHAP-based explanations. Among the candidate pipelines, we selected the pipeline with the highest held-out test ROC AUC for each platform; the selected values were 0.927 in plasma and 0.954-0.973 across the three CSF datasets. Because the same held out test performance was used for pipeline selection and headline reporting, these are optimistically selected single-holdout estimates, not unbiased estimates of generalizable or clinical performance. Explanations identified five recurring biological axes within ADNI: cholinergic (ACHE), tau/14-3-3 (YWHAG, YWHAZ, YWHAB, YWHAE), neuro-axonal (NEFL, NEFH), microglial/complement (CHIT1, SMOC1, CHI3L1, C7, CFH) and synaptic (NPTXR, NPTX2, DLG4, SYT5, VSNL1, ELAVL2). CSF analyses showed synaptic vesicle-cycle enrichment (q = 2 × 10), and CSF YWHAG correlated strongly with total tau (ρ = 0.87). Cross-fluid directional concordance was modest overall (54-57%) but increased to 73-80% among mapped analyte/protein rows reaching q < 0.05 in CSF. These findings provide hypothesis-generating, internally supported evidence within ADNI. Independent external cohorts with locked pipelines are required to evaluate generalizable performance and biological reproducibility; the overlapping TMT-MS and SET2 analyses should not be interpreted as independent replication.
Twenty years of the Mexican Proteomics Society.
Encarnación-Guevara S, Teran LM, Huerta-Ocampo JÁ
J Proteomics · 2026 Jun · PMID 42288149 · Publisher ↗
The Mexican Proteomics Society (MPS), founded in 2005, is the earliest proteomics society in Latin America. It is a non-profit organization comprising academics and professionals committed to advancing research in proteo...
The Mexican Proteomics Society (MPS), founded in 2005, is the earliest proteomics society in Latin America. It is a non-profit organization comprising academics and professionals committed to advancing research in proteomics, metabolomics, and mass spectrometry. To fulfill its mission, MPS organizes symposia and academic events that foster collaboration and knowledge exchange among researchers and professionals interested in these fields. MPS actively promotes human resource training and scientific outreach. Mexican researchers are engaged in international initiatives such as HUPO and consortia, including pi-HuB and the Chromosome-Centric Human Proteome Project, underscoring the country's growing role in global proteomics. The biennial MPS symposium has become a solid academic forum in proteomics and metabolomics, where international experts share their latest findings, and technology developers present advances in analytical instrumentation and software. The topics covered at the symposium held in Oaxaca, Mexico, on November 9-13, 2024, were as diverse as our country's biodiversity and as broadly applicable as mass spectrometry. These include human health (e.g., cancer, chronic degenerative diseases, allergies), plants, foodomics, lipidomics, venomics, microbial proteomics, computational omics, and analytical methods development. This Special Issue, which features research presented at the symposium, reflects the diversity of our community and highlights the value of scientific collaboration. SIGNIFICANCE: For the past 20 years, the Mexican Proteomics Society (MPS) has advanced proteomics and metabolomics in México. The society hosts a trusted biennial event where global experts and vendors share the latest breakthroughs in mass spectrometry, metabolomics, and proteomics. Through hands-on workshops, the MPS trains students and professionals in essential protein and metabolite analysis and the use of open-access bioinformatics tools. The society has also hosted prestigious global events, including the 2022 HUPO World Congress. The topics represented in the articles of this special issue reflect the diversity of our community and highlight the value of scientific collaboration.
Multi-omics reveals that burdock seed aglycone alleviates renal fibrosis by restoring mitochondrial oxidative phosphorylation function.
Luo Y, Wu G, Zhao L … +9 more , Bo Y, Yang D, Guo J, Zhao D, Lv Y, Tian Y, Wang M, Yang X, An M
J Proteomics · 2026 Jun · PMID 42276167 · Publisher ↗
Renal fibrosis (RF), a common pathological process driving chronic kidney disease (CKD) progression to end-stage renal failure, is closely associated with oxidative phosphorylation (OXPHOS). Arctigenin (ATG), the main ac...
Renal fibrosis (RF), a common pathological process driving chronic kidney disease (CKD) progression to end-stage renal failure, is closely associated with oxidative phosphorylation (OXPHOS). Arctigenin (ATG), the main active component of burdock seed, exhibits anti-inflammatory and anti-fibrotic activities, but its mechanisms in RF treatment remain unclear. Here, we performed integrated transcriptomic and proteomic analyses to identify key targets and pathways of ATG in a unilateral ureteral obstruction-induced rat RF model. Multi-omics enrichment analysis revealed that NDUFS8 and NDUFS2 were the core targets of ATG, with the OXPHOS pathway as the central intersecting pathway. Our results suggest that ATG exerts anti-renal fibrosis effects by targeting the OXPHOS pathway to inhibit excessive reactive oxygen species production and oxidative stress. SIGNIFICANCE: Chronic kidney disease (CKD) continues to impose an escalating global health and socioeconomic burden, while renal fibrosis (RF), as the convergent pathological endpoint of virtually all progressive nephropathies, remains the principal determinant of irreversible renal failure and adverse clinical outcomes. Despite extensive efforts to develop antifibrotic therapies, effective clinical interventions remain elusive, largely due to the complex and multifactorial nature of RF pathogenesis. In this study, we employed an integrated multi-omics framework encompassing transcriptomics, proteomics, and metabolomics to systematically decipher the antifibrotic mechanism of arctigenin (ATG), a bioactive natural compound derived from traditional Chinese medicine. Our findings identify mitochondrial oxidative phosphorylation as the pivotal regulatory axis underlying the renoprotective effects of ATG and further establish key catalytic subunits of mitochondrial complex I as its direct molecular targets. Mechanistically, ATG not only restores complex I activity and reprograms mitochondrial energy metabolism but also preserves the intracellular stability and localization of these subunits, thereby preventing their aberrant release-mediated inflammatory activation and disrupting the self-perpetuating cycle linking metabolic dysfunction, inflammation, and fibrosis progression. Beyond revealing a previously unrecognized dual mechanism integrating metabolic and inflammatory regulation, this study provides compelling evidence that mitochondrial dysfunction is not merely a secondary consequence of tissue injury but a fundamental driver of fibrotic remodeling. Importantly, our work highlights the translational potential of natural product-based mitochondrial interventions for CKD treatment and supports a broader conceptual shift toward metabolism-centered therapeutic strategies for chronic fibrotic diseases. Given the central role of mitochondrial dysfunction across multiple organs, these findings may also have far-reaching implications for the treatment of systemic fibrosis-related disorders beyond the kidney.
Proteomics in environmental pollution research: Advances, challenges, and future directions.
Wei C, Zeng B, Zhou X … +9 more , Qing B, Deng L, Wu Y, Huang W, Zhang Z, Jin Y, Peng S, Zhang C, Qiu S
J Proteomics · 2026 Jun · PMID 42276166 · Publisher ↗
Environmental proteomics has emerged as a powerful approach for elucidating the molecular mechanisms underlying pollutant-induced biological effects. Although this field has developed rapidly, the systematic review of re...
Environmental proteomics has emerged as a powerful approach for elucidating the molecular mechanisms underlying pollutant-induced biological effects. Although this field has developed rapidly, the systematic review of recent proteomics applications in environmental pollution research remains limited. This review explored the emerging roles of toxicoproteomics in biomarker discovery and mechanistic elucidation, as well as ecotoxicoproteomics in ecological risk assessment and bioremediation strategies. Here, we review the field, highlighting recent trends such as the integration of proteomics with genomics, transcriptomics, and metabolomics to provide a comprehensive view of biological responses to environmental stressors. We further discuss the growing application of artificial intelligence in improving proteomics data interpretation and accelerating biomarker discovery. In addition, recent technological advances in environmental proteomics are highlighted, including next-generation tissue microarray proteomics, nanoscale proteomics, single-cell proteomics, and spatial proteomics. Despite its potential, proteomics faces challenges, such as high operational costs, computational complexity in analysis, and technical limitations in low-abundance protein detection. We propose that the convergence of proteomics with artificial intelligence and multi-omics approaches offers promising solutions to these challenges, enhancing the practical application of proteomics in environmental monitoring and risk assessment.
Violacein as a multitarget agent in bladder cancer cells.
Idiarte JF, Canclini L, Alem D … +2 more , García-Laviña CX, Castro-Sowinski S
J Proteomics · 2026 Jun · PMID 42276165 · Publisher ↗
Violacein is a bacterial purple pigment with several biological activities, including anticancer. We previously showed its antiproliferative effect in cervical and bladder cancer cells. Here, we report quantitative diffe...
Violacein is a bacterial purple pigment with several biological activities, including anticancer. We previously showed its antiproliferative effect in cervical and bladder cancer cells. Here, we report quantitative differential proteomics in T24 bladder cancer cells, complemented with qRT-PCR of selected genes. Violacein treatment induced overproduction of proteins associated with tumor microenvironment remodeling, cell adhesion, immune response, apoptosis, autophagy, and cell cycle arrest. ICAM-1 emerged as a potential key driver, showing 24-fold gene overexpression and 6-fold protein overproduction, suggesting a protective role of violacein in enhancing immune cell infiltration into tumors. Violacein also reduced Annexin levels, which may limit their tumor-promoting and metastatic functions. Additionally, we identified proteins associated with better prognosis in cancer patients. Together, these findings highlight ICAM-1 as a central mediator of violacein's anticancer effects, and suggest that violacein is a multitarget agent that may modulate tumor microenvironment remodeling, tumor suppression, and immune responses. SIGNIFICANCE: Quantitative differential proteomics and qPCR analyses demonstrate that the bacterial pigment violacein functions as a multitarget agent capable of modulating multiple cancer-related pathways in the T24 bladder cancer cell line. Among these, violacein exerts tumor-suppressive effects by altering the tumor microenvironment and regulating immune-response pathways in bladder cancer cells, potentially contributing to improved patient prognosis.
ALG13 deficiency impairs cortical development via suppression of the PI3K/AKT/mTOR pathway.
Guo B, Li X, Yang Z … +15 more , Sun Y, Liu J, Gao P, Li Z, Liang L, Cheng G, Lv W, Zhang Z, Xie S, Zhang H, Wang Y, Xu A, Su S, Sun T, Zhang J
J Proteomics · 2026 Jun · PMID 42264299 · Publisher ↗
ALG13 mutations cause congenital disorders of glycosylation and neurodevelopmental deficits, but how asparagine-linked glycosylation 13 (ALG13) deficiency impairs brain development remains unclear. This study aimed to el...
ALG13 mutations cause congenital disorders of glycosylation and neurodevelopmental deficits, but how asparagine-linked glycosylation 13 (ALG13) deficiency impairs brain development remains unclear. This study aimed to elucidate the underlying mechanisms in Alg13 knockout (ALG13KO) mice. We first confirmed neurodevelopmental delays and abnormal cortical neuron distribution in ALG13KO mice. Quantitative proteomic analysis of the postnatal day 7 cerebral cortex revealed widespread protein abundance changes. Subsequent bioinformatic and protein-protein interaction net-work analyses pinpointed the phosphatidylinositol-3-kinase (PI3K)/protein kinase B (AKT)/ mammalian target of rapamycin (mTOR) pathway. Pathway as a central hub. Parallel reaction monitoring validated the downregulation of key upstream regulators Laminin γ-1 (LAMC1), Focal Adhesion Kinase (FAK), and Integrin α6 (ITGA6). Western blot confirmed the inhibition of PI3K/AKT/mTOR phosphorylation. Our findings demonstrate that ALG13 deficiency disrupts cortical development, likely via suppression of the PI3K/AKT/mTOR pathway through the LAMC1-ITGA6-FAK axis. This study reveals a critical, early-developmental suppression of mTOR signaling, contrasting with its reported hyperactivation in adult epileptic ALG13KO mice, highlighting a stage-dependent role. SIGNIFICANCE: This study provides the first proteomic evidence of early postnatal suppression of the PI3K/AKT/mTOR pathway in a mouse model of ALG13-congenital disorder of glycosylation (ALG13-CDG). By integrating unbiased quantitative proteomics, targeted validation, and phenotyping, we identify the LAMC1-ITGA6-FAK axis as a novel upstream regulator mediating this suppression, linking a glycosylation defect directly to a key neurodevelopmental signaling hub. Importantly, our finding contrasts with reported mTOR hyperactivation in adult epileptic mice, revealing a critical, previously unrecognized stage-dependent duality of mTOR signaling in ALG13-CDG pathophysiology. This work not only advances the mechanistic understanding of neurodevelopmental deficits in CDG but also showcases the power of a focused, early time-point proteomic strategy to disentangle primary developmental pathophysiology from secondary disease states.
Growth mode-dependent proteomic responses of Bacillus subtilis to cerium oxide nanoparticles: Pellicle biofilm versus swarming.
Darrouzet E, Luche S, Diemer H … +4 more , Cianférani S, Lafond-Fenonjoie D, Rabilloud T, Lelong C
J Proteomics · 2026 Jun · PMID 42264144 · Publisher ↗
Proteomic analysis revealed that Bacillus subtilis exhibits markedly different physiological adaptations under pellicle biofilm and swarming growth conditions, and that these lifestyles strongly influence the bacterial r...
Proteomic analysis revealed that Bacillus subtilis exhibits markedly different physiological adaptations under pellicle biofilm and swarming growth conditions, and that these lifestyles strongly influence the bacterial response to CeO₂ nanoparticles. In pellicle biofilms, proteins involved in respiration, amino acid acquisition, Mn/Fe uptake, and SUF-mediated iron‑sulfur cluster synthesis were upregulated, together with oxidative stress defense systems, indicating adaptation to microaerobic and heterogeneous biofilm conditions. In contrast, swarming cells displayed increased sporulation-associated processes and a stronger stringent response. Exposure to CeO₂ nanoparticles induced a pronounced response, particularly under swarming conditions, where central carbon metabolism enzymes were strongly repressed and stringent response pathways were reinforced. In biofilms, CeO₂ effects were more moderate, with limited metabolic perturbation and a slight stimulation of biofilm formation. The contrasting responses between lifestyles appear primarily linked to differences in metabolic state, oxidative stress physiology, and nanoparticle accessibility within the biofilm matrix rather than to direct nanoparticle toxicity alone. Overall, these findings demonstrate that nanoceria impacts B. subtilis physiology in a growth mode-dependent manner and highlight the importance of considering bacterial lifestyle when evaluating nanoparticle toxicity. SIGNIFICANCE: This research provides a biologically understanding of how Bacillus subtilis, an important bacterium for soil, plant, and animal health, adapts to environmental stress under more physiologically realistic growth conditions. Using shotgun proteomics, we demonstrated that pellicle biofilm and swarming lifestyles are associated with profoundly distinct physiological states, notably in metabolism, oxidative stress management, metal homeostasis, and developmental regulation. Extending this approach to exposure to cerium oxide nanoparticles (CeO₂ NPs), a widely distributed environmental nanomaterial, we showed that bacterial responses are strongly dependent on growth mode. Swarming cells exhibited pronounced metabolic repression and activation of stringent response pathways, whereas biofilms displayed more limited perturbations together with slight stimulation of biofilm formation. These contrasting responses appear to result primarily from lifestyle-dependent differences in metabolic activity, oxidative stress physiology, and nanoparticle accessibility within the biofilm matrix rather than from direct nanoparticle toxicity alone. Since regulatory toxicology frameworks such as REACH often overlook subtle physiological adaptations, this study highlights the importance of considering microbial lifestyle and physiological context when assessing the ecological risks of emerging chemicals and nanomaterials.
Protein-protein interactions in Escherichia coli: Using cross-linking/mass spectrometry (XLMS) to reveal our current knowledge gaps in interactomes.
de Araújo GL, Reis-de-Oliveira G, Gozzo F
J Proteomics · 2026 Jun · PMID 42248543 · Publisher ↗
Protein-protein interactions (PPIs) are fundamental to cellular processes and often define phenotypes more accurately than protein abundance alone. Despite their importance, confidently identifying direct physical intera...
Protein-protein interactions (PPIs) are fundamental to cellular processes and often define phenotypes more accurately than protein abundance alone. Despite their importance, confidently identifying direct physical interactions remains challenging. Even in the benchmark organism Escherichia coli, our survey of the IntAct database reveals that only 8% of reported interactions are annotated as direct physical associations. Of these, 44% rely on gold-standard structural methods, while XLMS accounts for only 11%, highlighting a lack of high-confidence, scalable data for primary interactors. In this study, we employed an XLMS workflow using the MS-cleavable cross-linker DSSO and SCX-based enrichment to investigate the E. coli interactome. This targeted approach yielded 21,599 cross-linked spectrum matches (CSMs), corresponding to 2334 residue pairs. These data mapped 663 intra-protein cross-linking and 137 PPIs, 47 of which were previously unreported. Notably, XLMS identified interactions with confidence scores below 0.7 in the STRING database, demonstrating its capability to detect low-confidence or uncharacterized associations. We further illustrate the power of this technique by analyzing the ElaB-YqjD complex, where our experimental distance constraints revealed a mismatch with AlphaFold 3 predictions. These results demonstrate how XLMS can effectively bridge the gap in current PPI datasets, providing high-confidence, mechanistically informative data even in well-studied biological systems. SIGNIFICANCE: Protein-protein interactions (PPIs) are essential to cellular organization and function, and even the extensively studied Escherichia coli, the majority of interactions remain either uncharacterized or poorly supported by high-confidence experimental data. As part of this study, we conducted a systematic analysis of the IntAct database, which showed that only 8% of annotated interactions correspond to direct physical associations, with 44% supported by gold-standard structural methods and only 11% derived from XL-MS. This analysis highlights a clear gap between interaction annotations and experimentally validated physical interactions, providing the rationale for the experimental strategy adopted here. To address this gap, we applied a state-of-the-art cross-linking mass spectrometry (XL-MS) approach using the cleavable cross-linker DSSO, coupled with SCX enrichment and advanced data analysis tools, to generate a high-confidence, experimentally derived E. coli interactome. This effort uncovered 47 novel PPIs and revealed substantial discrepancies between database annotations and physical interaction evidence. Our integrative workflow not only provides direct evidence of protein interactions within native cellular environments but also yields spatial constraints that challenge and refine current structural models, as illustrated by the elaB-yqjD complex. By bridging the gap between proteomic data and structural validation, this work demonstrates how XL-MS can meaningfully expand and validate biological interaction networks.
Proteomics at scale: Bottlenecks and opportunities for early-career researchers in a fast developing field.
Chion M, Costanzo M, Gebelin M … +13 more , van Gelder CAGH, Grunauer SV, Lechner M, Leytens A, Nasery MM, Ingola M, Peinado-Izaguerri J, Provasi C, Puchalski M, Schebesta AS, Schmidt LM, Sugár S, Young Proteomics Investigators Club. Electronic address: ypic@eupa.org
J Proteomics · 2026 May · PMID 42184951 · Publisher ↗
The field of proteomics has rapidly evolved over the last five years enabled by rapid advances in instrumentation and computation. At the same time, the proteomics community is also growing. This is reflected by the incr...
The field of proteomics has rapidly evolved over the last five years enabled by rapid advances in instrumentation and computation. At the same time, the proteomics community is also growing. This is reflected by the increasing participation in international conferences such as those organized by the European Proteomics Association and the Human Proteome Organization. These events provide early-career researchers with unique opportunities to exchange ideas, develop collaborations, and build networks that support professional development. One such network is the Young Proteomics Investigators Club, a European initiative supported by European Proteomics Association and led by early-career researchers. In this Community-Driven project, we investigate recent trends in proteomics by screening conference abstracts and evaluating the session attendance at Human Proteome Organization Congresses and European Proteomics Association conferences. Based on these analyses, we identified five areas that, from our perspective, are shaping the current trends in proteomics: clinical proteomics, proteomics of post-translational modifications, single-cell proteomics, systems biology and multi-omics, and computational proteomics. For each area, we highlight both unique challenges and identify a common theme: a shift from exploratory studies with manageable sample numbers towards large screenings and cohorts and the generation of big data, which often comes with the lack of computational support, organizational networks, and infrastructure. In this light, we describe the unique challenges and opportunities faced by early-career researchers. We point to actionable directions for enabling reproducible and transparent proteomics as well as community-driven projects and initiatives, which are often providing training and support. SIGNIFICANCE: In this perspective, the Young Proteomics Investigators Club (YPIC) discusses advances in analytical developments and computational approaches in proteomics research. Based on empirical analysis of recent European Proteomics Association conference and Human Proteome Organization congresses contributions, we identify clinical, single-cell, post-translational and systems-level proteomics as the research areas that have gained most momentum in the last three to five years. What makes this work distinctive is that it is written by and for early-career researchers, thereby uniquely identifying where momentum, challenges, and unmet needs converge for the newest generation of proteomics researchers. Rather than cataloguing advances, we examine the widening gap between what modern proteomics can generate and what individual researchers can realistically process, validate, and interpret. We describe specific structural barriers including access to high performance computing, limited formal training in scalable data analysis, the need for unified benchmarking standards and navigating clinical collaboration frameworks. We then highlight opportunities for the field, such as community-curated benchmarks, interdisciplinary mentorship models, and shared computational infrastructure. By making these challenges explicit from an early-career researchers standpoint, we aim to inform how training, funding, and community initiatives can be shaped to support the next generation of proteomics researchers.
Guard cell-enriched phosphoproteome reveals phosphorylation of endomembrane proteins in closed stomata.
Pullen AM, Lyons SP, Mordant AL … +3 more , Herring LE, Akpa BS, Rojas-Pierce M
J Proteomics · 2026 May · PMID 42173481 · Publisher ↗
Control of the stomatal aperture is multifaceted, involving a complex interplay of environmental cues and intracellular signaling pathways. It is well established that changes in ion gradients drive water movement into a...
Control of the stomatal aperture is multifaceted, involving a complex interplay of environmental cues and intracellular signaling pathways. It is well established that changes in ion gradients drive water movement into and out of the guard cell, thereby altering cell volume and modulating the opening or closing of the stomatal pore. These rapid responses are often regulated by phosphorylation cascades to efficiently transmit environmental status and either reduce water loss or enhance carbon assimilation. The role of endomembrane trafficking networks in stomatal dynamics is not well characterized. Here, we investigated the regulation of stomatal opening and closing by generating a proteome and phosphoproteome of guard cell-enriched tissue. This deep proteome captured a protein profile that was similar to previously characterized guard cell proteomes. The guard cell-enriched tissue with closed stomata showed greater levels of phosphorylation of proteins related to endomembrane trafficking and vacuoles when compared to both whole leaf tissue with closed stomata and guard cell-enriched tissue with open stomata. These results support the hypothesis that phosphorylation of endomembrane proteins may contribute to the regulation of stomatal movements. SIGNIFICANCE: Stomatal movements are tightly regulated and are critical for gas exchange and water retention in plants. Stomatal movements are regulated by light, temperature, CO, humidity and hormones, and are driven by changes in cellular turgor and metabolism. Stomatal opening is the result of a complex signaling pathway involving the activity of blue light photoreceptors, plasma membrane H ATPases, and inward-rectifying K channels. Stomatal closing is induced by the stress hormone ABA, and involves the activation of specific anion channels that lead to K efflux. Phosphorylation cascades are key signaling cues for this pathway, and many kinases and phosphatases have been implicated in regulating stomatal movements. This work describes the first phosphoproteome of guard cell-enriched tissue. Isolation of intact guard cells, followed by treatment with opening or closing conditions, allowed the isolation of proteins in their open or closed-responsive state. Quantitative phosphoproteomics enabled quantitative detection of changes in phosphorylated peptide abundance between open and closed states. GO enrichment analysis supports the hypothesis that phosphorylation cascades induced by stomatal closing may target endomembrane proteins, which could be important for the endomembrane remodeling that follows decreases in cellular volume. Overall, this dataset serves as a key resource for hypothesis generation regarding plant stomatal function.
JAM-A as a potential surface marker of human pluripotent stem cells.
Konze SA, Beimdiek J, Oberbeck A … +1 more , Buettner FFR
J Proteomics · 2026 May · PMID 42162608 · Publisher ↗
Human pluripotent stem cells can be differentiated into a variety of different cell types, for instance cardiomyocytes. Especially in the context of future application in regenerative medicine, it is crucial to understan...
Human pluripotent stem cells can be differentiated into a variety of different cell types, for instance cardiomyocytes. Especially in the context of future application in regenerative medicine, it is crucial to understand the developmental processes taking place upon differentiation. Moreover, the identification of a panel of cell surface markers suitable for characterization and purification is necessary to ensure quality of human pluripotent stem-cell derived products. In this study, we used quantitative mass spectrometry to characterize proteomic changes in early mesendodermal differentiation. Two human pluripotent stem cell lines, one embryonic (H3) and one induced pluripotent stem cell line (I2), were analyzed under pluripotent conditions and after two days of embryoid body-based differentiation. Functional clustering and enrichment analysis showed down-regulation of proteins associated with pluripotency and the tricarboxylic acid cycle at day two. In contrast, proteins related to the proteasome and annexin family were up-regulated upon differentiation. Among the proteins that were down-regulated upon differentiation in both, H3 and I2, the membrane protein junctional adhesion molecule A (JAM-A) emerged as potentially associated with pluripotency. Flow cytometry and immunocytochemistry further confirmed down-regulation of JAM-A on the cell surface of human induced pluripotent stem cells that were differentiated toward mesendoderm for just two days. STATEMENT OF SIGNIFICANCE: Understanding early molecular changes during human pluripotent stem cell differentiation is essential for stem cell biology and regenerative medicine. This study provides a comparative proteomic analysis of two cell lines during early differentiation and identifies coordinated metabolic and pluripotency-associated changes. The understanding of changes that occur in the early phase of cardiomyocyte differentiation might be helpful to more precisely monitor the differentiation process. Importantly, we identify the membrane protein JAM-A as a robustly down-regulated cell surface protein, highlighting its potential as marker for human pluripotent stem cells. In the future, JAM-A might be used in a panel of cell surface markers for pluripotent stem cells in order to remove pluripotent stem cells from stem cell-derived therapeutic products.
Standardizing tear proteomics preanalytics: Capillary vs Schirmer sampling and denaturing vs mild elution buffers shape proteome depth and abundance profiles.
Cerro-Pardo I, Mendizabal A, Azkargorta M … +3 more , Elortza F, Rodríguez-Agirretxe I, Acera A
J Proteomics · 2026 Jun · PMID 42119778 · Publisher ↗
Tear fluid is a promising minimally invasive source of biomarkers for ocular surface diseases (OSDs). However, variability in sampling and pre-analytical processing remains a major limitation for reproducibility and cros...
Tear fluid is a promising minimally invasive source of biomarkers for ocular surface diseases (OSDs). However, variability in sampling and pre-analytical processing remains a major limitation for reproducibility and cross-study comparability. Here, we quantitatively evaluated two commonly used tear collection methods, microcapillary tubes (CT) and Schirmer strips (SCH), and assessed the effect of elution buffer composition on protein recovery from SCH. In Study I, tears were collected from the same healthy donors using CT and SCH. In Study II, SCH from additional donors were longitudinally split and eluted with phosphate-buffered saline (PBS) or a denaturing cell lysis buffer (CLB; 7 M urea, 2 M thiourea, 4% CHAPS), enabling paired within-strip comparisons. Samples were analyzed by Evosep-timsTOF Pro DIA mass spectrometry and quantified using library-free DIA-NN. Overall, 3749 proteins were identified. SCH markedly increased proteome coverage compared with CT, reflecting recovery of both soluble tear proteins and ocular surface-derived cellular material. Functional annotation showed enrichment of intracellular compartments in SCH samples, particularly cytoplasmic, nuclear, and cytoskeleton-related proteins. For SCH extraction, CLB modestly increased unique protein identifications compared with PBS while preserving high quantitative concordance. These findings show that pre-analytical choices strongly influence tear proteome depth and abundance profiles. SIGNIFICANCE: Tear proteomics is increasingly recognized as a valuable platform for biomarker discovery in ocular, neurological, and systemic diseases. However, substantial methodological heterogeneity in tear collection and pre-analytical processing remains a major source of variability, limiting reproducibility and cross-study comparability. By directly comparing microcapillary tube and Schirmer strip sampling within the same donors, and by evaluating mild versus denaturing elution conditions from Schirmer strips using a within-strip paired design, this study provides quantitative evidence that pre-analytical choices systematically shape both proteome depth and quantitative abundance profiles. Schirmer strip sampling markedly expands detectable proteome coverage, partly through co-recovery of ocular surface-derived cellular material, whereas denaturing extraction enhances the recovery of protein subsets insufficiently solubilized under mild conditions while preserving high quantitative concordance. Collectively, these findings demonstrate that sampling and extraction strategies are not neutral technical variables but key determinants of the biological space interrogated by tear proteomics. The data presented here inform rational study design, improve inter-laboratory comparability, and support the development of harmonized standard operating procedures for robust tear-based proteomic biomarker discovery and translational applications.
Integrated analysis of transcriptomes and proteomes reveals the molecular mechanisms underlying the development of Dorper sheep hair follicles.
Wang S, Zhang N, Wang C … +3 more , Jing B, Yang F, Li X
J Proteomics · 2026 May · PMID 42107703 · Publisher ↗
Understanding the molecular mechanisms underlying normal hair follicle development is important for improving wool traits in sheep and skin traits in mammals. This study aims to investigate the genetic determinants influ...
Understanding the molecular mechanisms underlying normal hair follicle development is important for improving wool traits in sheep and skin traits in mammals. This study aims to investigate the genetic determinants influencing hair follicle (HF) development by conducting an integrated analysis of transcriptomic and proteomic datasets from skin tissues of adult Dorper ewes at different groups of shedding and non-shedding. We employed DIA quantitative proteomics technology to identify 2176 differentially abundant proteins (DAPs) across three stages in both the shedding and non-shedding groups. Six DAPs were validated using parallel reaction monitoring (PRM) to confirm the reliability of the discovery proteomics data. Functional enrichment analysis revealed that a series of biological processes and signaling pathways associated with HF development, such as glutathione metabolism, ferroptosis, Wnt, JAK-STAT, and PI3K-Akt pathways, were strongly enriched by these DAPs. Association analysis and protein interaction network analysis further indicated that ACTG1, ANPEP, CTNNB1, GCLC, GCLM, CSNK2A2, COL1A1, GLUL, VTN, CDK6, IKBKG, STAM2, ITGA3, and members of the keratin (KRT) family may be key factors contributing to the developmental differences in the hair follicle cycle. Our study contributes to the understanding of the genetic and proteomic mechanisms underlying the normal growth and development of hair follicles and mammalian skin-related traits. SIGNIFICANCE: The morphology of secondary hair follicles in Dorper sheep plays a crucial role in determining the hair follicle cycle. The hair follicle cycle, as well as hair follicle growth and morphogenesis, are coordinated and complex processes. This study constructed a protein regulatory network within the signaling pathways associated with the cyclic growth and development of Dorper sheep hair follicles, and investigated key genes whose expression levels were positively correlated between mRNA and protein. Understanding the genetic mechanisms underlying the hair-shedding ability of Dorper sheep is crucial for enhancing the economic value of meat sheep and advancing the breeding of automatically hair-shedding sheep.
Comparative peptidomics of four wasp venoms reveals extensive peptide diversity, proteolytic patterns, and predicted bioactivities.
Wang K, Qiao J, Quinton L … +5 more , Eppe G, Meng X, Huang G, Haubruge E, Zhang H
J Proteomics · 2026 Jun · PMID 42097502 · Publisher ↗
Wasp venoms possess complex compositions and diverse bioactivities, making them potential pharmacological sources. In this study, venoms from four wasp species (Vespa mandarinia, V. velutina, V. basalis, and Provespa bar...
Wasp venoms possess complex compositions and diverse bioactivities, making them potential pharmacological sources. In this study, venoms from four wasp species (Vespa mandarinia, V. velutina, V. basalis, and Provespa barthelemyi) were collected by electrical stimulation and analyzed using liquid chromatography-tandem mass spectrometry. A total of 681 peptides were identified, nearly 90% of which had not been previously reported. Comparative analyses revealed pronounced species-specific signatures at both peptide and peptide family levels. Sequence-based analyses indicated that peptide release is consistent with targeted proteolytic cleavage patterns, exhibiting features resembling known substrate preferences of metalloproteases and serine proteases, rather than stochastic degradation. Bioinformatic predictions identified 291 peptides with potential bioactive properties spanning multiple functional categories, with angiotensin-converting enzyme (ACE) and dipeptidyl peptidase IV (DPP4) inhibitory activities being the most prominently represented. Among these, eight ACE inhibitory peptides and seventeen DPP4 inhibitory peptides were prioritized as candidates based on predicted safety profiles, and sequence-based analysis further identified ten putative cryptides. Overall, this study establishes the first comparative peptidomic dataset across four wasp venoms, providing insights into peptide diversity, inferred generation patterns, and predicted activities. SIGNIFICANCE: Venoms are rich sources of biologically active molecules and have historically provided templates for clinically used therapeutics. Although major protein toxins have been extensively characterized, the endogenous low-molecular-weight peptide fraction remains comparatively underexplored, particularly in social wasps, and systematic comparative resources remain limited. Venom peptidomic datasets inherently contain multiple layers of biological information, including diversification patterns, peptide origin, and potential bioactivity, yet these aspects are often interpreted independently. By integrating these dimensions, this study establishes a multi-level analytical framework for extracting biological insights and function-related information from venom peptidomes. The identification of consistent cleavage patterns suggests a degree of regulation in peptide generation, shifting the interpretation of venom peptides from degradation by-products toward biologically organized repertoires. Moreover, candidate prioritization illustrates how peptidomic datasets can generate experimentally testable functional hypotheses rather than serving solely as descriptive catalogs. The resulting dataset serves as a reference resource for cumulative comparative analyses. The analytical framework presented here also provides a transferable strategy for functional peptide discovery in other complex secretions.
Cosine similarity analysis of venom proteomes of Indian cobras, Naja naja and Naja kaouthia reveals significant interspecies and geographic variations.
Bansode S, Modi K, Ziya S … +3 more , Goel A, Kulkarni M, Naik N
J Proteomics · 2026 May · PMID 42097501 · Publisher ↗
The Indian cobra (genus Naja) is one of the 'Big Fours' responsible for dreaded snakebite incidents in India. Immediate anti-snake venom (ASV) treatment is the only solution for cobra envenomation. Currently available AS...
The Indian cobra (genus Naja) is one of the 'Big Fours' responsible for dreaded snakebite incidents in India. Immediate anti-snake venom (ASV) treatment is the only solution for cobra envenomation. Currently available ASVs are not efficacious nationwide, probably due to geographical variations in venom. The lack of precise information on venom variation is the foremost hurdle to ASV improvement. Hence, mapping of geographical variation in snake venom proteome is of utmost importance. Here, we report mass spectrometry-based proteomic analysis of the venom of Naja naja and Naja kaouthia, collected in the wild from seven regions in India. For the first time, the proteomes of N. kaouthia venom from two Northeastern States of India, Assam and Mizoram, have been characterized. More than 65 proteins from the 12 major protein families were detected in venom samples from all locations. The identification of unique proteins enabled us to understand the variation in venom. In all the venom samples, most of the unique proteins belonged to two families: 3FTX and PLA2. N. kaouthia venom from Assam and Mizoram contained unique proteins in the SVMP and SVSP families. In N. naja only one unique SVMP is seen in the venom from Chandigarh. Cosine similarity analysis revealed an interesting and distinctive similarity between samples from western and northeastern regions. Similarity analysis of proteomic profiles demonstrated the use of machine learning to solve the snakebite problem. SIGNIFICANCE: This study highlights the importance of understanding the geographic variation in the venom of Indian cobras (Naja naja and Naja kaouthia) to improve anti-snake venom (ASV) treatments. The current ASVs are not effective across all regions in India due to differences in venom composition. By mapping the venom proteome from different regions, a unique set of proteins was identified. This knowledge is crucial for developing more effective ASVs that can save lives by providing targeted treatment for cobra envenomation.
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