Journal Of Proteomics[JOURNAL]
Sun
200 papers
Machine learning-enhanced plasma proteomics discriminates pancreatic cancer-associated diabetes from type 2 diabetes mellitus.
Lazari LC, Donnarumma CDC, Matheus LHG … +10 more , D'Alpino Peixoto R, de Matos MR, Valerio HP, Rosa-Fernandes L, Oba-Shinjo SM, Machado MCC, Machado MAC, Marie SKN, Correa-Giannella ML, Palmisano G
J Proteomics · 2026 Jun · PMID 42069247 · Publisher ↗
Pancreatic ductal adenocarcinoma (PDAC) is frequently preceded by new-onset diabetes mellitus (NODM), yet differentiating PDAC-associated DM from type 2 diabetes (T2D) remains clinically challenging. We investigated whet...
Pancreatic ductal adenocarcinoma (PDAC) is frequently preceded by new-onset diabetes mellitus (NODM), yet differentiating PDAC-associated DM from type 2 diabetes (T2D) remains clinically challenging. We investigated whether plasma proteomic profiling combined with machine learning could discriminate these conditions. Plasma samples from individuals with PDAC (with and without DM), long-standing T2D, and controls were analyzed by MALDI-TOF mass spectrometry. Spectral features were processed through a nested cross-validation framework to prevent data leakage, and model interpretability was explored using SHAP values. In parallel, low-molecular-weight proteins were characterized by GeLC-MS followed by LC-MS/MS and differential abundance analysis. Machine learning models distinguished PDAC-associated DM from T2D with a balanced accuracy of 85%. Proteomic analyses identified distinct signatures in PDAC- associated DM, including downregulation of erythrocyte-related proteins and PPBP, and upregulation of acute-phase reactants such as FGA, CP, and SERPINA3. Treatment-naïve cases displayed increased circulating epithelial and keratin-associated proteins, which were attenuated after therapy, suggesting dynamic tumor-related remodeling. These findings demonstrate that integrating MALDI-TOF profiling with machine learning can capture plasma signatures associated with PDAC-associated DM. Although exploratory, this approach supports further validation in prospective cohorts aimed at improving PDAC risk stratification among individuals with NODM. SIGNIFICANCE: Pancreatic ductal adenocarcinoma (PDAC) is a highly lethal malignancy with a dismal 5-year survival rate, primarily due to late-stage diagnosis. The frequent occurrence of new-onset diabetes mellitus (NODM) as a paraneoplastic syndrome offers a critical window for early detection. However, the clinical challenge of distinguishing PDAC-associated diabetes (PDAC-DM) from type 2 diabetes mellitus (T2D) has hindered the implementation of effective screening strategies. This study addresses this significant clinical problem by leveraging a multi-faceted proteomics approach. We demonstrate that the integration of MALDI-TOF mass spectrometry peptide profiling with machine learning algorithms can accurately discriminate PDAC-DM from T2D with 85% accuracy. Furthermore, we used LC-MS/MS to identify specific low molecular weight proteins that are differentially regulated between these conditions, providing a molecular basis for the observed discrimination. Our work is significant as it presents a novel, high-throughput pipeline for biomarker discovery that combines the scalability of MALDI-TOF with the analytical power of LC-MS/MS and machine learning. The identified plasma signatures hold strong translational potential to improve risk stratification in patients with NODM, ultimately enabling earlier diagnosis of PDAC and improving patient survival prospects. This research directly contributes to the field of clinical proteomics by providing a robust methodological framework and candidate biomarkers for the early detection of one of oncology's most challenging diseases.
Functional and protein interaction analysis of Nop7 in trypanosomatid parasites.
Nepomuceno-Mejía T, Espinosa-Renteria L, Miranda-Muñoz AY … +4 more , Torres-Morales E, Osorio-Méndez JF, Florencio-Martínez LE, Martínez-Calvillo S
J Proteomics · 2026 Jun · PMID 42061506 · Publisher ↗
Nucleolar protein 7 (Nop7), also known as Pescadillo or PES1, is a conserved factor required for ribosome biogenesis, cell proliferation, and nucleolar organization in opisthokonts; however, its function in early-branchi...
Nucleolar protein 7 (Nop7), also known as Pescadillo or PES1, is a conserved factor required for ribosome biogenesis, cell proliferation, and nucleolar organization in opisthokonts; however, its function in early-branching eukaryotes remains poorly understood. Here, we characterize Nop7 in the kinetoplastid parasites Trypanosoma brucei and Leishmania major, organisms that possess atypical ribosomes containing extensively fragmented 28S-type ribosomal RNA. Structural in silico analyses revealed lineage-specific features in trypanosomatid Nop7 proteins that may support specialized protein-protein interactions. Using tandem affinity purification coupled with mass spectrometry, we defined the Nop7-associated interactome, identifying numerous conserved trans-acting ribosome assembly factors, including Erb1 and Ytm1, consistent with the presence of a PeBoW-like complex involved in 60S ribosome subunit maturation. Comparative proteomic analyses also uncovered several previously uncharacterized nucleolar proteins, suggesting the existence of parasite-specific components within the ribosome biogenesis machinery. Functional assays showed that RNAi-mediated depletion of TbNop7 causes severe growth defects, morphological abnormalities, and significant alterations in 5.8S and 28S pre-rRNA maturation. Collectively, these findings provide the first proteomic map of the Nop7 interaction network in trypanosomatids and offer new insights into ribosome biogenesis in evolutionarily divergent eukaryotes. SIGNIFICANCE: Trypanosoma brucei and Leishmania major are two medically relevant kinetoplastid parasites that possess an atypical cytosolic ribosome, whose large subunit is composed of eight ribosomal RNA species of distinct lengths and origins, suggesting specialized biogenesis mechanisms. Here, we characterize the nucleolar protein 7 (Nop7) from T. brucei and L. major and demonstrate that Nop7 is necessary for parasite proliferation, cell cycle progression, and ribosome biogenesis. Bioinformatics analyses reveal conserved functional domains, predicted SUMOylation sites, and trypanosomatid-specific structural features that may facilitate processing of their unique 28S-like rRNA. Proteomic interaction networks indicate that Nop7 associates with canonical ribosome biogenesis factors as well as parasite-specific partners, highlighting an evolutionarily adapted molecular machinery. Collectively, our findings provide new insights into ribosome biogenesis in early-diverging eukaryotes and suggest some potential molecular targets for antiparasitic therapy.
Integrated physiological characteristics and proteomes of Bacillus licheniformis response to 6-month spaceflight.
Li C, Shen S, Zhang H … +4 more , Liu T, Miao R, Liu H, Li Y
J Proteomics · 2026 Jun · PMID 42035870 · Publisher ↗
Bacillus licheniformis (BL) is used for clinical treatment of acute and chronic enteritis and diarrhea. The present study explored the physiological characteristics and proteomes of BL response to 6-month spaceflight abo...
Bacillus licheniformis (BL) is used for clinical treatment of acute and chronic enteritis and diarrhea. The present study explored the physiological characteristics and proteomes of BL response to 6-month spaceflight aboard the China Space Station. 6-month spaceflight delayed BL lag phase, reduced cell wall thickness, and impaired BL biofilm formation and adhesion capacity to Caco-2 cells. After 6-month spaceflight, activity of β-amylase, alkaline protease and lipase in BL was increased by 21.6%,67.3% and 42.5%. The alkaline resistance of BL at pH 11.0 was increased by 29.6%. Proteomics identified 6051 proteins in the BL. Of these, 62 of differentially abundant proteins (DAPs) groups were screened based on fold change (FC) > 1.5 and < 0.667 (P < 0.05). Thirty-six DAP groups exhibited an up-regulation trend with the maximum FC reaching 9.53. Twenty-six DAP groups were down-regulated. The molecular functions of DAPs were mainly classified into the transport of nutrients and ions, cell wall biosynthesis, mRNA metabolism and protein translation. These results revealed that 6-month spaceflight led to notably changes of physiological characteristics and proteins in BL. The novel findings may supply new insights into BL response to long-term complex space environment. SIGNIFICANCE OF STUDY: Complex space environment could lead to gastrointestinal system disorders of astronauts and enhance the risk of intestinal infections. BL, a Gram-positive probiotic bacterium, has potential to protect intestinal health of astronauts. To date, space microbiology studies on probiotic Gram-positive bacteria is rather limited. Physiological properties of BL onboard spaceflight missions are still lacking. The effect of long-term spaceflight on proteomes of BL has not been reported. The functional changes of DAPs in BL exposed to complex space environment remains unelucidated. Thus, it is urgent to carry out comprehensive study on spaceflight-BL. The purpose of present study was to explore the physiological characteristics and proteomic changes in BL abord the Shenzhou-15 spaceship into the China Space Station for 6 months. The novel findings are helpful to understand the response patterns of BL to spaceflight and provide a scientific support for the intestinal health protection of astronauts and the in-orbit application of this probiotic.
Proteomic insights into the effects of shipping noise on blue mussel early development.
Beauclercq S, Veillard D, Bernay B … +6 more , Tanguy A, Marcotte I, Tremblay R, Olivier F, Auffret M, Madec S
J Proteomics · 2026 Jun · PMID 42035869 · Publisher ↗
Anthropogenic underwater noise is a growing environmental stressor in coastal ecosystems, yet its molecular effects on invertebrate early life stages remain poorly understood. Using a data-independent acquisition proteom...
Anthropogenic underwater noise is a growing environmental stressor in coastal ecosystems, yet its molecular effects on invertebrate early life stages remain poorly understood. Using a data-independent acquisition proteomic workflow, we characterized the proteome of blue mussel (Mytilus edulis) post-larvae and examined changes in protein abundance following exposure to realistic cargo-shipping noise. A total of 7249 proteins were identified, of which 902 showed significant abundance differences across low, medium, and high sound pressure levels (i.e., 121, 127, and 151 dB re 1 μPa, respectively). Functional enrichment and interaction analyses revealed coordinated, intensity-dependent changes in proteins involved in metabolic, cytoskeletal, and regulatory processes. Forty-nine proteins were consistently regulated across treatments, including candidates associated with developmental regulation, morphogenesis, and shell-related pathways, indicating a conserved molecular response to acoustic exposure. Those results provide a reference proteomic dataset for M. edulis post-larvae and highlight proteome-level plasticity associated with shipping-related acoustic disturbance during metamorphosis.
The proteomics analysis of mitochondria-enriched fractions reveals alteration of key mitochondrial pathways in breast cancer cell lines.
Vázquez-Narváez HD, Labra-Barrios ML, Ríos-Castro E … +8 more , Castañón-Sánchez CA, Uribe-Carvajal S, Hernández-Martínez E, Hernández-Hernández JM, León-Ávila G, Pérez-Rangel A, Ángeles-Morales EB, Luna-Arias JP
J Proteomics · 2026 Jun · PMID 42025918 · Publisher ↗
Breast cancer, the leading cause of death in women worldwide, shows significant heterogeneity that makes this disease extremely difficult to treat. Many reports point to metabolic shifts, mainly those carried out into mi...
Breast cancer, the leading cause of death in women worldwide, shows significant heterogeneity that makes this disease extremely difficult to treat. Many reports point to metabolic shifts, mainly those carried out into mitochondria, as key processes governing the behavior and heterogeneity of several types of breast cancer. In this study, we performed label-free proteomics analysis on mitochondria-enriched fractions from T47D and MDA-MB-231 breast cancer cell lines, which have distinct molecular classifications, using bioinformatics analyses to identify differentially expressed proteins compared to MCF-12F healthy breast cells. Cancer cells exhibited down-regulated protein levels of subunits from the respiratory chain's Complex I. However, both showed differentially abundant proteins involved in ligase and oxidoreductase activities, including enzymes of glycolysis, pyruvate metabolism, the Krebs cycle, and gluconeogenesis. Many of these enzymes also participate in other metabolic processes, such as mitochondrial localization, mitochondrial gene expression, and the metabolism of amino acids, fatty acids, purines, and pyrimidines. Gene Set Enrichment Analysis revealed that OXPHOS subunits are integrated as signatures of neurodegenerative disease pathways. A protein set with little or no evidence in breast cancer was identified, which could lead to future research in breast cancer mitochondrial metabolism. Data are available via ProteomeXchange with identifier PXD069883. SIGNIFICANCE: This manuscript determined the protein expression profiles of mitochondria-enriched fractions from T47D (Luminal A, stage IV) and MDA-MB-231 (triple negative, Stage IV) breast cancer cell lines compared to the MCF-12F healthy breast cell line. We found that breast cancer cell lines exhibited low expression levels of Complex I subunits from the respiratory chain. However, both breast cancer cell lines presented high expression levels of some proteins related to ligase and oxidoreductase activities, the latter on CH-OH groups in cellular respiration processes, such as some enzymes from glycolysis, pyruvate metabolism, Krebs cycle and gluconeogenesis. Moreover, many of these enzymes also participate in other metabolic processes, such as localization to the mitochondrion, mitochondrial gene expression, amino acid, fatty acid, purine, and pyrimidine metabolism. We also observed through Gene Set Enrichment Analysis that OXPHOS enzymes have a key role in many neurodegenerative disease pathways as well. Finally, we found a protein set with little or no evidence in breast cancer that could lead to future pivotal research in the mitochondrial metabolism of breast cancer.
Proteomic characterization of primary pancreatic fibroblasts derived from neoadjuvant chemotherapy treated versus treatment-naïve PDAC.
Amrutkar M, Finstadsveen AV, Labori KJ … +2 more , Verbeke CS, Gladhaug IP
J Proteomics · 2026 Jun · PMID 42025917 · Publisher ↗
Neoadjuvant chemotherapy (NAT) is increasingly used in the treatment of pancreatic ductal adenocarcinoma (PDAC). However, the actual molecular impact of NAT on the tumor remains unknown, particularly on the cancer-associ...
Neoadjuvant chemotherapy (NAT) is increasingly used in the treatment of pancreatic ductal adenocarcinoma (PDAC). However, the actual molecular impact of NAT on the tumor remains unknown, particularly on the cancer-associated fibroblasts (CAFs) remains largely unknown. Here, mass-spectrometry (MS)-based proteomic profiling of primary CAFs derived from treatment-naïve (TN) and NAT-treated resected PDAC (n = 10 in each group) was conducted to explore potential NAT-associated changes. Differentially abundant proteins (DAPs; p < 0.05) in NAT versus TN CAFs accounted for 10.6% of all 5438 proteins mapped by MS. According to gene ontology analysis, DAPs with higher abundance (273) in NAT versus TN were involved in protein transport and carbohydrate metabolism, while DAPs with lower abundance (305) were mainly related to RNA processing. Protein-protein interactions identified several cluster networks of closely linked DAPs. Exploring the correlation between DAPs abundance and survival identified a negative correlation for 30 of 42 DAPs in NAT group. In addition, several proteins were found to be differentially abundant among different NAT regimens. In conclusion, this exploratory study reveals significant NAT-associated changes in CAF proteome profiles, which are related to the fundamental biological processes of RNA processing and protein transport. Further validation of these preliminary findings using a large independent cohort is needed.
Falcon plasma proteomics to improve avian aspergillosis diagnosis.
Vieu S, Lozano C, Azmanis P … +3 more , Beaudeau F, Guillot J, Armengaud J
J Proteomics · 2026 Jun · PMID 41990917 · Publisher ↗
Aspergillosis is a respiratory disease in birds, particularly falcons, often diagnosed late due to nonspecific signs and limited performance of current diagnostic tools. This study aimed to identify novel plasma biomarke...
Aspergillosis is a respiratory disease in birds, particularly falcons, often diagnosed late due to nonspecific signs and limited performance of current diagnostic tools. This study aimed to identify novel plasma biomarkers for aspergillosis comparing plasma samples from 15 healthy falcons and 15 affected falcons (9 with early and 6 with advanced aspergillosis). First, the presence of the causative agent, Aspergillus fumigatus, was ruled out through a proteotyping strategy. Proteomic profiling using data-independent acquisition mass spectrometry further identified 861 avian proteins. In advanced infection, 50 host proteins were significantly modulated in terms of abundance, including acute-phase proteins such as the haptoglobin isoform X2, alpha-1-acid glycoprotein, and serum amyloid A-like protein. Several immunoglobulin isoforms and functionally uncharacterized proteins were also differentially abundant. In contrast, no significant changes were observed between healthy and early affected birds. Comparison between early and advanced cases revealed nine proteins with significant abundance shifts, suggesting that they could be interesting disease progression markers. These findings highlight specific host protein responses in advanced aspergillosis animals and support the potential of targeted monitoring of plasma biomarkers for earlier, non-invasive diagnosis in falcons. Further validation on a larger cohort is warranted to assess clinical relevance and diagnostic performance in veterinary medicine. SIGNIFICANCE: Aspergillosis remains one of the most significant infectious diseases affecting birds, where delayed diagnosis frequently results in fatal outcomes. Current noninvasive diagnostic is still challenging due to non-specific clinical signs and limited sensitivity and specificity of current diagnostic tests. This study presents a comprehensive proteomic characterization of falcon plasma during aspergillosis, taking advantage of recent advances in high-resolution data-independent acquisition mass spectrometry and the availability of annotated falcon genomes. Comparison of healthy, early, and advanced clinical stages revealed 50 significantly dysregulated proteins, including key acute-phase proteins such as haptoglobin, serum amyloid A, alpha-1-acid glycoprotein, ceruloplasmin, and immunoglobulin light chains. These alterations reflect systemic inflammatory and immune responses to infection and highlight promising biomarkers for early, noninvasive diagnosis. This work contributes to the development of protein-based diagnostic assays, thereby improving clinical management and welfare of captive and wild birds, while also expanding proteomic resources for non-model avian species.
Proteomics of the extremotolerant yeast Meyerozyma guilliermondii 4LYP0 isolated from the Yanamate tailings Cerro de Pasco (Peru) upon exposure to Cu, Cd, and Cr ions.
Macedo-Prada D, Iwai LK, Espinoza-Culupú A … +4 more , Montoni F, Huamantalla-Huamán M, Jara-Peña E, Sánchez-Rojas T
J Proteomics · 2026 Jun · PMID 41956203 · Publisher ↗
Meyerozyma guilliermondii 4LYP0, a yeast isolated from the Yanamate mine tailings in Cerro de Pasco - Peru, was investigated to characterize its proteomic response to heavy metal exposure. This work provides the first co...
Meyerozyma guilliermondii 4LYP0, a yeast isolated from the Yanamate mine tailings in Cerro de Pasco - Peru, was investigated to characterize its proteomic response to heavy metal exposure. This work provides the first comprehensive proteomic profile of a native M. guilliermondii strain exposed to Cu, Cd, and Cr. Metal concentrations were selected based on measurable growth effects, and microscopy confirmed visible stress-related changes in cell morphology. Using label-free quantitative mass spectrometry, we identified 496 differentially abundant proteins (DAPs) in response to the metals. Network analyses of DAPs revealed that commonly proteins showing increased DAPs were mainly involved in oxidoreductase activity and aminoacyl-tRNA synthetases, and ATP-binding proteins indicated the activation of redox balancing, translational reprogramming, and energy-dependent detoxification pathways. Metal-specific responses included the upregulation of proteins involved in amino acid biosynthesis in Cu treated cells (A5DCG0, A5DP23, A5DEL5, A5DLT8), longevity regulation under Cd stress (AD5QN0, A5DE29), and acetate metabolism upon Cr exposure (A5DN62, A5D1A7). This study represents the first proteomic characterization of M. guilliermondii from Peru under heavy metal stress and provides new insights into the molecular basis of oxidative stress tolerance and its potential application in metal-rich or contaminated environments. Significance of the study: This study provides the first proteomic characterization of Meyerozyma guilliermondii 4LYP0, an extremotolerant yeast isolated from mining-contaminated environments in the Peruvian Andes. The analysis of its proteomic adaptation under heavy metal stress reveals valuable insights into the molecular strategies employed by extremotolerant yeasts to survive in metal-rich environments. A total of 496 differential abundance proteins were identified, including those involved in oxidoreductase activity, such as amino acid biosynthesis, longevity regulation, and acetate metabolism. These results highlight of this yeast to maintain redox homeostasis and metabolic flexibility under toxic metal conditions. Moreover, these findings expand the current understanding of eukaryotic microbial responses to oxidative stress and contribute to the broader field of environmental proteomics. From an applied perspective, elucidating these adaptive mechanisms enhances the potential use of M. guilliermondii as a biotechnological model for metal tolerance, detoxification, and bioremediation. The proteomic insights obtained her e open perspectives for engineering or selecting yeast strains optimized for industrial wastewater treatment, biosorption, or metal recovery. Furthermore, this work underscores the importance of expanding proteomic investigations in native extremotolerant microorganisms from underexplored ecosystems, such as the high Andes of Peru, to enhance our global understanding of microbial resilience in metal-impacted environments.
Mining foreign proteins in honey by shotgun label-free proteomics: Implications for quality and authenticity.
Erban T, Shcherbachenko E, Pavlovova A … +3 more , Markovic M, Harant K, Talacko P
J Proteomics · 2026 Jun · PMID 41946431 · Publisher ↗
Honey may contain various foreign proteins, most notably from protein and carbohydrate supplements or from artificial additions to mask enzyme activity. Here, we analyzed 29 honey samples and one royal jelly sample, whic...
Honey may contain various foreign proteins, most notably from protein and carbohydrate supplements or from artificial additions to mask enzyme activity. Here, we analyzed 29 honey samples and one royal jelly sample, which served as a control alongside "our" own production-verified honeys. We also reanalyzed a previous dataset of 45 honey samples. We found that the honey samples in both datasets contained different "foreign" enzymes used for syrup production and/or as bee fondant. The accuracy of their identification is supported by the large number of unique peptides obtained for each protein. These include Aspergillus glucoamylase (γ-amylase), Saccharomyces invertase, and α-amylase. The results also suggest that Aspergillus catalase, used as a highly efficient antioxidant, is a foreign enzyme. Furthermore, we identified the presence of soy seed storage proteins such as glycinin and conglycinin. The presence of these proteins alongside foreign enzymes indicates either poor beekeeping practices regarding supplemental feeding or the intentional use of supplemental feeding. We also report the presence of plant- and human-derived proteins in honey. In summary, our study broadens the usefulness of shotgun proteomics in identifying the various proteins in honey that can be used to determine its composition, quality, and authenticity. SIGNIFICANCE: Despite the use of sophisticated methods such as NMR, HRMS, and IRMS, honey is one of the most adulterated foods, and fraud is widespread. One of the useful methods for solving the problem of honey fraud is proteomics. This study demonstrates the ability of proteomics to identify proteins that should not be present in honey. These "foreign proteins" can indicate honey fraud and/or bad beekeeping practices, resulting in low honey quality. The results suggest that a group of these proteins are enzymes used in the industrial production of syrup. These enzymes include α-amylase, glucoamylase (γ-amylase), and invertase (β-fructofuranosidase). Additionally, proteomics can be used to detect proteins such as glycinin/conglycinin and lipoxygenase from soybean seeds in honey. Their identification suggests that the bees were fed protein supplements, the residues of which are found in honey. All these proteins should not be present in high-quality honey. This study also identified other proteins that were not previously reported in honey. In particular, these is an array of human-derived proteins whose identification is consistent with the fact that beekeeping, honey harvesting, and processing are not sterile activities. Identifying human proteins is scientifically interesting because it helps us understand honey properties and can be used in database searches. Overall, analysis using discovery/untargeted proteomics can identify proteins of interest in honey, including those associated with fraud, quality issues, or botanical origin. One specific group of interest is plant-derived proteins.
Curcumin mitigates gas explosion-induced traumatic brain injury in male rats by regulating key molecular signatures: A multiomics analysis.
Dong X, Su Y, Li C … +11 more , Ma X, Zhu Z, Yang J, Luo Z, Gao J, Ma Y, Yao S, Wu W, Bai Y, Zhang C, Ren W
J Proteomics · 2026 Jun · PMID 41935781 · Publisher ↗
Treatment with curcumin following gas explosion-induced traumatic brain injury (TBI) can mitigate inflammatory brain damage; however, the underlying mechanisms remain unclear. This study performed transcriptomic and prot...
Treatment with curcumin following gas explosion-induced traumatic brain injury (TBI) can mitigate inflammatory brain damage; however, the underlying mechanisms remain unclear. This study performed transcriptomic and proteomic analyses of brain tissue from a rat GE-induced TBI model to identify related dysregulated molecules and signaling pathways. Additionally, an integrated transcriptomic and proteomic analysis was performed, and key molecular signatures were validated in blood serum and brain tissue. Treatment with curcumin significantly reduced histological abnormalities and microscopic structural changes induced by the gas explosion trauma in the brain. Further, it markedly reduced gas explosion-induced the levels of neuroinflammatory signaling molecules, including interleukin-1β and TNF-α. Notably, curcumin modulated 547 differentially expressed genes, which were primarily associated with the cAMP signaling pathway. This study identified candidate molecules and their perturbed biological pathways in gas explosion-induced TBI and explored the effects of curcumin using multi-omics approaches. SIGNIFICANCE: There remains insufficient understanding of gas explosion-induced TBI, and no relevant studies have been performed using multiple omics analysis to clarify the mechanisms of gas exposure-induced TBI in male rats. This important aspect of the unknown need to be further studied and explored. This study provides a biologically grounded, multi-omics characterization of gas explosion-induced traumatic brain injury by integrating quantitative proteomics with transcriptomic profiling in a controlled animal model. By identifying convergent dysregulation of inflammatory and cAMP-related signaling pathways and validating key molecular signatures at both the tissue and circulating levels, this study moves beyond descriptive proteomics toward pathway-level interpretation linked to structural and functional brain injury. The findings demonstrate how integrated proteomic analyses can be used to uncover mechanistic targets of neuroinflammation and therapeutic modulation, thereby contributing to the development of predictive biological models for blast-related brain injury and advancing the application of hypothesis-driven proteomics in neurotrauma research. This study focuses on curcumin treatment on the brain injury effects induced by gas explosion and stays in close touch with progress at the forefront of methods in modelling and simulation to aid mechanistic insights into neuroinflammation, immunoregulatory response, novel findings of therapeutic relevance to the central nervous system, and address modes of action including multiomics, systems biology, quantitative measurements biomarkers, histopathology, etc. So, we think it is appropriate for this journal.
Proteomic analysis of ammonia-induced stress in Chinese hamster ovary (CHO) cell cultures.
Ryan D, Henry M, Sideri CK … +2 more , Efeoglu E, Meleady P
J Proteomics · 2026 Jun · PMID 41932361 · Publisher ↗
Ammonia (NH₃) and its ionic form ammonium (NH₄) are both metabolic waste products and essential nitrogen sources within Chinese hamster ovary (CHO) cell cultures. Although necessary for amino acid synthesis, excessive ac...
Ammonia (NH₃) and its ionic form ammonium (NH₄) are both metabolic waste products and essential nitrogen sources within Chinese hamster ovary (CHO) cell cultures. Although necessary for amino acid synthesis, excessive accumulation in the extracellular environment can exert stress, reducing cell proliferation and impairing the efficiency of recombinant protein production. Proper endoplasmic reticulum (ER) function is critical for CHO cells as biotherapeutic producers. Previous work has linked elevated ammonia concentrations to reduced productivity via altered N-glycosylation pathways, but its broader effects on ER biology remain unclear. In this study, we applied high-resolution mass spectrometry to perform a comprehensive analysis of changes in the ER proteome in CHO cells exposed to two ammonia concentrations, 10 mM and 30 mM, 48 and 120 h after supplementation. Both conditions suppressed cell growth and reduced product titre; however, the 10 mM supplementation resulted in a minor increase in specific cell productivity. Gene Ontology analysis revealed that ammonia strongly affected the tricarboxylic acid cycle, as well as key metabolic, catabolic and biogenetic processes. Several ER membrane proteins, including HMGCR and PREB, were consistently downregulated. In extended cultures, transmembrane proteins linked to Golgi-transport were upregulated, while vesicle transport associated proteins were downregulated, indicating altered intracellular trafficking. SIGNIFICANCE: This study provides a novel perspective on CHO cell biology under environmental stress by investigating the impact of ammonia accumulation in culture. Despite its presence in CHO culture, ammonia has been relatively under-investigated, compared to other culture conditions. Using high-throughput mass spectrometry for comprehensive proteomic profiling, we characterise the cellular response to ammonia build-up with a level of depth not previously applied to the study of this biological stressor. By specifically analysing proteins localised to the ER, we identify candidate pathways and molecular mechanisms that contribute to reduced CHO cell growth and productivity, offering insights directly relevant to industrial bioprocessing conditions. The link between ammonia concentration and a decrease in productivity has previously been linked to genes involved in N-glycosylation of the recombinant biotherapeutic, but the full extent of ammonia stress on ER function has not yet been investigated. These methods were applied to two IgG producing CHO cell lines to allow for comparison of cell line specific stress adaptations, as well as comparing the short- and long-term effects of excess ammonia.
Proteomics in biopharmaceutical industries.
Padrón G
J Proteomics · 2026 Jun · PMID 41881249 · Publisher ↗
Proteomic tools have been integral to the biopharmaceutical industry since its inception, supporting both the discovery of new drugs and the production of recombinant therapeutic proteins. Mass spectrometry combined with...
Proteomic tools have been integral to the biopharmaceutical industry since its inception, supporting both the discovery of new drugs and the production of recombinant therapeutic proteins. Mass spectrometry combined with liquid chromatography has proven to be an indispensable analytical approach for the characterization and analysis of therapeutic proteins. The relatively recent emergence of the Multi-Attribute Method, an advanced mass spectrometry-based analytical approach, is being increasingly incorporated in the biopharmaceutical industry for quality control and simultaneously monitor and quantify multiple quality attributes of therapeutic proteins, such as monoclonal antibodies and other biologics. The combination of Multi-Attribute Method with the analysis of intact proteins by mass spectrometry could replace the vast majority of traditional control techniques and become the essential platform to ensure the quality and safety of therapeutic proteins in the near future. SIGNIFICANCE: This review demonstrates the great importance of proteomics for the biopharmaceutical industry, both in the development of new drugs and in the production of recombinant proteins. Advances in mass spectrometry, along with liquid chromatography, will soon become a fundamental tool for quality control of therapeutic proteins.
Comprehensive S-acylation profiling of the porcine epididymis and exosomes reveals a role in cargo sorting and long-distance trafficking.
Cao H, Liu X, Li L … +10 more , Liu S, Gao H, Dong Q, Nie H, Li Y, Gong Y, Jin T, Wang Y, Qin W, Dong W
J Proteomics · 2026 Jun · PMID 41864562 · Publisher ↗
The epididymis orchestrates sperm maturation through microenvironmental regulation and epididymosome-mediated cargo delivery. Despite emerging evidence implicating protein S-acylation in vesicular trafficking, its compar...
The epididymis orchestrates sperm maturation through microenvironmental regulation and epididymosome-mediated cargo delivery. Despite emerging evidence implicating protein S-acylation in vesicular trafficking, its compartment-specific dynamics and functional implications in epididymal physiology remain poorly characterized. Here, we employed acyl-biotin exchange-based 4D proteomics to decode the S-acylation proteomic of porcine caput/cauda epididymidis and their exosomes. Comparative analysis identified 2780 and 2084 S-acylated proteins in caput and cauda tissues, respectively, with 317 upregulated and 579 downregulated S-acylated proteins in cauda versus caput. Functional enrichment revealed S-acylation-dependent regulation of signal transduction, vesicle trafficking, and immune pathways, particularly through lysosomal activity, AMPK signaling, and glutathione metabolism. Exosomal profiling demonstrated conserved S-acylated protein signatures between caput and cauda derived exosomes, with 114 S-acylated proteins shared among caput tissue and both exosomal populations, implicating long-distance transport of caput-specific cargoes. Validation identified 5 caput-enriched S-acylated proteins, including evolutionarily conserved OCLN, CDH1, PDZK1, BAG5, and SCRN1, which were detected in S-acylated forms within caput-derived exosomes and cauda exosomes, but absent in cauda tissue. This study reveals a potential role of S-acylation in mediating exosomal cargo trafficking during porcine epididymis. Our findings advance understanding of post-testicular sperm functionalization and highlight S-acylation as a potential therapeutic target for male infertility. SIGNIFICANCE: This study provides the comprehensive S-acylation proteomic atlas of the porcine epididymis and its exosomes, revealing how this reversible lipid modification spatiotemporally regulates exosome-mediated protein trafficking to support sperm maturation. We demonstrate that S-acylation governs key pathways including vesicle transport, immune regulation, and metabolic signaling in the epididymal microenvironment. Crucially, we identify a cohort of caput-enriched S-acylated proteins that are packaged into exosomes and transported distally to the cauda region, suggesting a previously unrecognized mechanism for long-distance intercellular communication. These findings establish S-acylation as a central regulator of epididymal function and offer molecular insights into post-testicular sperm maturation. The identified S-acylated proteins and associated pathways may serve as diagnostic biomarkers or therapeutic targets for male infertility, particularly in cases of defective sperm functionalization.
Peptidomics assessment of plant-based meat analogs produced by high-moisture extrusion: Analytical strategies, challenges, and future perspectives.
Martinez Vargas EK, Šalaševičienė A, Ertbjerg P
J Proteomics · 2026 Jun · PMID 41861950 · Publisher ↗
The global shift toward plant-based diets has increased the demand for sustainable and nutritionally equivalent alternatives to animal meat. High-moisture extrusion (HME) technology enables the transformation of plant pr...
The global shift toward plant-based diets has increased the demand for sustainable and nutritionally equivalent alternatives to animal meat. High-moisture extrusion (HME) technology enables the transformation of plant proteins into fibrous, meat-like textures; however, the molecular changes induced by this process remain largely understudied. Peptidomics, a large-scale mass-spectrometry-based analysis of peptides, offers a promising approach to investigate protein modifications, digestibility, and bioactive peptide generation in plant-based meat analogs (PBMAs). Particular attention is given to LC-MS/MS workflows, acquisition strategies (data-dependent and data-independent acquisition), and sample preparation challenges associated with complex processed food matrices. This review summarizes current advances in the application of peptidomics to HME-derived matrices and highlights knowledge gaps that limit the current understanding of extrusion-induced molecular transformations. Integrating peptidomics into the design of PBMAs can benefit product optimization for both texture and nutritional functionality. SIGNIFICANCE: Understanding how high-moisture extrusion (HME) alters plant protein structure and digestibility is crucial for advancing nutritionally equivalent and sustainable alternatives to animal meat. This review synthesizes current evidence on the use of peptidomics to elucidate the molecular transformations and peptide release dynamics occurring during extrusion and subsequent digestion of plant-based meat analogs (PBMAs). Specifically, it addresses current gaps in the peptidomics literature regarding extrusion-processed plant proteins, method selection for complex food matrices, and the linkage between peptide profiles, processing conditions, and digestibility outcomes. By integrating principles of protein chemistry, digestion modeling, and emerging computational tools, the review positions peptidomics as a bridge between processing parameters, structural organization, and nutritional functionality. This mechanistic perspective deepens our understanding of extrusion-induced modifications and establishes a conceptual framework for designing PBMAs with optimized texture, digestibility, and bioactive potential, thereby expanding the predictive and hypothesis-driven application of proteomic sciences to sustainable food innovation.
Structural diversity of lipid A modulates neutrophil proteome and secretome responses.
Pittaluga Villarreal JR, Kim D, Yoon SH … +5 more , Bhushan V, Issara-Amphorn J, Pederson J, Manes NP, Nita-Lazar A
J Proteomics · 2026 Jun · PMID 41819446 · Full text
Neutrophils (PMNs) are central effector cells of the innate immune system, deploying antimicrobial functions such as degranulation, ROS production, and release of antimicrobial mediators. However, the neutrophil reprogra...
Neutrophils (PMNs) are central effector cells of the innate immune system, deploying antimicrobial functions such as degranulation, ROS production, and release of antimicrobial mediators. However, the neutrophil reprogramming in response to structurally distinct lipopolysaccharide (LPS) stimuli remains incompletely defined. Here, we integrated functional profiling with quantitative high-resolution proteomics to compare human PMN responses to two LPS preparations differing primarily in lipid A acylation: hexaacylated LPS from Escherichia coli (ECO-LPS) and tetra-acylated LPS from Francisella tularensis (FT-LPS). Principal component analysis (PCA) revealed that inter-donor variability was the dominant source of variation. ECO-LPS induced clear activation phenotypes and robust, time-dependent proteome remodeling, including early loss of L-selectin and progressive depletion of granule-associated proteins concomitant with increased abundance of inflammatory signaling proteins. In contrast, FT-LPS treated PMNs were indistinguishable from controls at the cellular proteome level. In the secretome, ECO-LPS treatment caused enrichment of neutrophil degranulation and granule lumen components, consistent with intracellular depletion of granules. FT-LPS elicited limited secretory changes, suggesting a restrained activation or primed state without coordinated intracellular remodeling. Together, our results demonstrate that lipid A acylation is a key determinant of neutrophil activation state and provide a resource for defining proteomic signatures associated with LPS sensing. SIGNIFICANCE: Neutrophils are essential first- responder cells of the innate immune system, and their activation is classically studied using targeted sets of surface markers and functional readouts, while the proteome- and secretome-level dynamics remain less well defined. By applying quantitative DIA proteomics to both the intracellular proteome and the secretome of primary human neutrophils, this study reveals how lipid A structure dictates the depth and coordination of neutrophil activation. The data demonstrate that hexaacylated LPS drives coordinated depletion of degranulation-associated proteins with a concomitant appearance in the secretome. In contrast, tetra-acylated LPS fails to induce comparable intracellular remodeling and instead produces only subtle secretory responses consistent with restrained activation. These findings refine our mechanistic understanding of how structurally distinct endotoxins differentially regulate neutrophil effector functions, emphasize the donor-intrinsic proteomic variation, and provide a reference that can guide future studies of attenuated innate sensing and neutrophil-focused therapeutic approaches.
Small extracellular vesicles in clinical Cancer research - A quantitative proteomics perspective.
Pandey D, Tiwari V, Ghosh D
J Proteomics · 2026 Jun · PMID 41806951 · Publisher ↗
'Small extracellular vesicles (sEVs) are nanosized, membrane-enclosed sacs released by diverse cell types. They play a critical role in cell-cell communication through their cargo, which includes a wide range of proteins...
'Small extracellular vesicles (sEVs) are nanosized, membrane-enclosed sacs released by diverse cell types. They play a critical role in cell-cell communication through their cargo, which includes a wide range of proteins, lipids, and nucleic acids. Physiologically, sEVs circulate in various body fluids such as blood, urine, and saliva, making them accessible for diagnostic via non-invasive isolation techniques. Recent advances in high-throughput proteomics have significantly enhanced our ability to characterize the protein content of sEVs. Importantly, multiple studies on human fluids have identified specific protein markers across different cancer types, encompassing molecules involved in inflammation, cellular adhesion, immunity, and lipoprotein regulation. Interestingly, some of these proteins are consistently detected across multiple cancer types and sample sources, suggesting the existence of a shared "oncogenic signature" that may be transferred via sEVs. Among body fluids, urine and saliva are particularly promising for easy, non-invasive diagnostics. However, these sample types remain underexplored as compared to the serum, leaving substantial opportunities for future research. Taken together, these findings position sEVs as a powerful tool with significant potential for advancing precision cancer care. SIGNIFICANCE: Living cells release nanosized membrane-enclosed vesicles called small extracellular vesicles (sEVs) into the extracellular environment. sEVs contain protein cargo molecules that critically take part in cell-cell communications. Quantitative proteomics identified potential sEV associated biomarkers for early cancer diagnosis and therapy. sEV Proteins associated with cell adhesion and inflammation, lipoproteins and immunoglobulins are potential molecules that were majorly identified. Interestingly, some of these proteins such as APOA4, SAA4, ITIH4, SERPINC1 and VWF were consistently identified across multiple cancer types and sample sources, highlighting their potential as future biomarkers.
Transmutation learning: Breaking the reference database barrier to unlock single-cell proteomics.
Martins AAM, Melo RM, Sales L … +4 more , Dos Santos MDM, Yates JR, Muotri AR, Carvalho PC
J Proteomics · 2026 Jun · PMID 41802595 · Publisher ↗
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A multi-omics comparison unveils convergent and divergent antidepressant mechanisms of fluoxetine and St. John's wort extract.
Zhang J, Cai Y, Zhang P … +11 more , Hao X, Guo B, Zhang W, Wu Y, Sun J, Xu X, Li W, Zhang B, Zhang S, Zhang W, Kong D
J Proteomics · 2026 May · PMID 41796893 · Publisher ↗
Fluoxetine (Flx), a selective serotonin reuptake inhibitor, and St. John's Wort extract (SJW), a herbal remedy, are common treatments for depression. However, a comprehensive comparison of their molecular mechanisms rema...
Fluoxetine (Flx), a selective serotonin reuptake inhibitor, and St. John's Wort extract (SJW), a herbal remedy, are common treatments for depression. However, a comprehensive comparison of their molecular mechanisms remains elusive. This study aimed to systematically elucidate and compare their therapeutic actions using an integrated proteomics and metabolomics approach. Behavioral and pharmacological effects of both treatments were assessed through behavioral tests. Proteomics and metabolomics analyses were performed on cortical tissue to identify differentially expressed proteins and metabolites. Furthermore, Mass Spectrometry Imaging (MSI) was employed to visualize the spatial distribution of key metabolites within the cortex. Bioinformatic analysis and integrated multi-omics analysis were used to map the signaling pathways and key molecular targets. Both Flx and SJW induced behavioral changes in locomotor activity as observed through behavioral tests. Multi-omics analysis revealed that both treatments share common regulatory patterns involving neuroplasticity-related pathways and Nicotinate and nicotinamide metabolism. Flx showed a more focused effect on synaptic plasticity. In contrast, SJW exhibited a broader modulation involving inflammatory pathways and amino acid metabolism. MSI analysis confirmed the localized accumulation of key differential metabolites, such as N-Acetyl-l-aspartate, ADP and l-Glutamine. Integrated analysis identified Rhoa, Scn1a, and Camk2a as key shared hub proteins. SIGNIFICANCE: Flx and SJW are widely used antidepressants in clinical practice. This multi-omics study deciphers the convergent and divergent molecular modulations of Flx and SJW, providing insight into their potential mechanisms relevant to depression treatment. While both promote neuroplasticity, Flx's action is more centered on synaptic remodeling, whereas SJW possesses additional strong anti-inflammatory and amino acid metabolism-modulating properties. These findings provide a detailed molecular basis for their clinical efficacy and suggest distinct therapeutic strengths.
Quantitative proteomics of intracellular and axenic amastigote-like forms of Trypanosoma cruzi under replicative and non-replicative conditions.
Melo RM, de Souza AR, Dos Santos Júnior ACM … +10 more , Lopes TZZ, Santana JM, Bastos ID, Motta FN, de Souza JMF, Charneau S, de Sousa MV, Fontes W, de Lima BD, Ricart CAO
J Proteomics · 2026 May · PMID 41765178 · Publisher ↗
Trypanosoma cruzi, the etiologic agent of Chagas disease, has a complex life cycle that involves both arthropods and mammals. Amastigotes are the T. cruzi life forms capable of replication in mammalian hosts. Here we rep...
Trypanosoma cruzi, the etiologic agent of Chagas disease, has a complex life cycle that involves both arthropods and mammals. Amastigotes are the T. cruzi life forms capable of replication in mammalian hosts. Here we report a quantitative LC-MS/MS-based proteomics of intracellular amastigotes (AI) and amastigote-like forms produced in axenic cultures. AI were purified from T. cruzi-infected HeLa cells using DEAE-cellulose, whereas three different axenic amastigote-like forms were produced as follows. Incubation of trypomastigotes in DMEM, pH 5.0, for 9 h led to AD5 forms. Further incubation of AD5 cells for 18 h at pH 7.2 in DMEM or LIT media produced AD7 and AL7 cells, respectively. AD5 cells were non-replicative, whereas AD7 and AL7 cells displayed active replication. Proteomic analysis confirmed the efficiency of the AI isolation method. Further comparison of AI, AD5, AD7 and AL7 proteomes suggested the relevance of ubiquitination, phosphorylation and kinetoplast-associated proteins in amastigote replication and highlighted similarities between amastigote-like forms and intracellular amastigotes. In contrast, substantial differences in protein translation and energy metabolism distinguished axenic amastigote-like forms from intracellular amastigotes. Together, these results demonstrate that axenic amastigote-like forms only partially reflect the proteomic landscape of intracellular amastigotes. SIGNIFICANCE: In this study we have adapted a previously published method for intracellular Trypanosoma cruzi amastigote purification, highlighting the great enrichment of the protozoan proteins at the proteomic level. Comparing the intracellular amastigotes with axenic amastigote-like grown life forms, we showed differences in the replication process, mainly related to energy, amino acid metabolism and translation. This study also revealed important processes for amastigote cell division, such as protein phosphorylation, ubiquitination and kDNA associated proteins, that are likely conserved on both intracellular and amastigote-like forms. We expect that this study can provide a guideline of axenic amastigote-like form replication biology for future T. cruzi experiments.
Integrative Astral-DIA proteomics and transcriptomics reveal candidate salt-tolerance genes in the halophyte Hordeum marinum.
Zhou H, Zhang B, Li L … +2 more , Wu D, Kuang L
J Proteomics · 2026 May · PMID 41763645 · Publisher ↗
Sea barleygrass (Hordeum marinum) is a halophytic wild barley with exceptional salt tolerance. However, the molecular genetic basis that confers its super salt tolerance remains to be elucidated. Here, we applied high-re...
Sea barleygrass (Hordeum marinum) is a halophytic wild barley with exceptional salt tolerance. However, the molecular genetic basis that confers its super salt tolerance remains to be elucidated. Here, we applied high-resolution Astral-DIA quantitative proteomics using root samples of sea barleygrass accession H559 exposed to 300 mM NaCl for 2 and 7 days. Among 9032 quantified proteins, 1875 and 2052 proteins showed significant changes in abundance after 2 and 7 days of salt treatment, respectively. KEGG enrichment indicated that proteins with increased abundance were predominantly associated with carbon metabolism, MAPK signaling and calcium signaling, whereas proteins with decreased abundance were enriched for protein processing in the endoplasmic reticulum, protein folding and vesicle-mediated transport. Subcellular-localization analysis indicated coordinated activity of key ion transporters (e.g., SOS1, V-ATPase subunits and KEA2) involved in Na extrusion, vacuolar sequestration and K uptake. Integration with the root transcriptomes of H559 revealed convergent enrichment of the glutathione-metabolism pathway, highlighting its pivotal role in maintaining redox homeostasis and regulating ions. Collectively, our results suggest that H. marinum maintains a low root Na/K ratio through synergistic ion-homeostasis and antioxidant defenses, a strategy that constitutes the key determinant of its superior salt tolerance. These findings provide mechanistic insights and candidate genes for developing salt-tolerant crops. SIGNIFICANCE: Soil salinization is a major global threat to agriculture, yet the molecular mechanisms enabling extreme salt tolerance in halophytic species remain poorly understood. Hordeum marinum, a close wild relative of cultivated barley, represents an invaluable genetic reservoir for improving salt tolerance in crops. By integrating high-resolution Orbitrap Astral-DIA proteomics with transcriptome profiling, this study uncovers the temporal ion-homeostasis and antioxidant mechanisms that underpin the exceptional salt tolerance of halophyte H. marinum. We identify key early-acting Na-detoxification components (SOS1, V-ATPases), prolonged K-retention regulators (e.g., KEA2), and glutathione-centered redox pathways as core determinants of its stress tolerance. These findings significantly advance our understanding of halophyte stress biology and provide high-confidence candidate genes and pathways that can be exploited for engineering or breeding salt-tolerant cereal crops.
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