Journal Of Proteomics[JOURNAL]
Sun
200 papers
Early regulatory networks driving somatic embryogenesis in Saccharum spp. L. revealed by time-resolved proteomics.
da Paschoa RP, Xavier LR, Corrêa CCG … +8 more , Vieira KDS, Pacheco DDR, Gomes LDES, da Silva CEA, Alves LEO, Pinto VB, Santa-Catarina C, Silveira V
J Proteomics · 2026 Apr · PMID 41539360 · Publisher ↗
The induction of somatic embryogenesis is controlled by various genes and proteins involved in hormonal pathways and stress responses, which act as key regulators of in vitro cellular reprogramming. In this study, we emp...
The induction of somatic embryogenesis is controlled by various genes and proteins involved in hormonal pathways and stress responses, which act as key regulators of in vitro cellular reprogramming. In this study, we employed a temporal proteomic approach to investigate the underlying molecular mechanisms governing sugarcane (Saccharum spp.) embryogenic callus formation in response to 2,4-dichlorophenoxyacetic acid (2,4-D) during induction. Proteomic profiling revealed 996 differentially accumulated proteins (DAPs) across at least one pairwise comparison among time points (0, 7, 14 and 21 days) during callus induction. These DAPs were classified into different clusters on the basis of their accumulation profile. Proteins involved in embryogenesis, histone epigenetic regulation, hormone responses and protein post-translational modification accumulate during callus induction. The predicted interactions between the TOPLESS protein and auxin response proteins (SKP1, CUL1 and CAND1) are associated with increased accumulation of the histone deacetylase HDT2 protein, a regulator of chromatin condensation, during embryogenic callus initiation. Moreover, proteomic analysis revealed a temporal reduction in methylation cycle enzymes during callus induction, whereas global DNA methylation showed only a slight, non-significant increase, suggesting that additional regulatory layers are present. The identified protein dynamics provide valuable targets for refining somatic embryogenesis protocols and advancing their biotechnological applications in sugarcane. SIGNIFICANCE: Genetic engineering and plant cloning usually involve the induction of embryogenic competence using 2,4-dichlorophenoxyacetic acid (2,4-D). This study presents protein-protein interaction (PPI) networks regulated during the induction of sugarcane callus using 2,4-D, in addition to the morphological aspects of the explant during the process. Proteomic analysis of time series shows the regulation of protein kinases and transcriptional regulators TOPLESS, CUL1, SKP1, CAND1, and ARGONAUTE kinases, revealing mechanisms of activation of induction and multiplication of embryogenic callus. Furthermore, the possible interaction between GH3.8 and SnRK/SAPK kinases suggests a link between hormonal responses.
Emphasizing the importance of interactions and networks in proteomics.
Armengaud J
J Proteomics · 2026 Mar · PMID 41535179 · Publisher ↗
Abstract loading — click title to view on PubMed.
Proteomic signatures in triple-negative breast cancer.
Kashyap S, Patidar V, Kumar A … +5 more , Sahu P, Dhiman M, Garg P, Jain A, Munshi A
J Proteomics · 2026 Mar · PMID 41512917 · Publisher ↗
An aggressive and heterogeneous malignancy, referred to as triple-negative breast cancer, is characterised by the absence of estrogen receptor, progesterone receptor, and human epidermal growth factor receptor 2. Treatme...
An aggressive and heterogeneous malignancy, referred to as triple-negative breast cancer, is characterised by the absence of estrogen receptor, progesterone receptor, and human epidermal growth factor receptor 2. Treatment options remain limited, relying primarily on chemotherapy due to the lack of well-defined therapeutic targets, which is linked with poor prognosis and high recurrence rates. Proteomics and other high-throughput technologies have significantly advanced TNBC research by enabling the identification of protein-based biomarkers with potential applications in diagnosis, prognosis, and treatment. Through protein biomarkers that affect immune checkpoints, cell-surface glycoproteins, and regulators of tumor microenvironment interactions, key protein signatures from tumor tissue, serum, and exosomal proteomics have been found to have the potential to predict chemotherapy response and disease progression. To develop new therapeutic approaches, these biomarkers are being investigated. Combining proteomics with other omics technologies, such as transcriptomics and genomics, enables the development of precision medicine approaches and provides deeper insights into the pathophysiology of TNBC. Clinically validated and newly developed protein biomarkers for diagnosis, prognosis, and treatment interventions are described in this review. The molecular mechanistic aspects have also been discussed. These biomarkers have the potential to aid in the classification, risk stratification, and development of personalized treatment approaches for TNBC. SIGNIFICANCE STATEMENT: Triple-negative breast cancer (TNBC) remains a highly aggressive and heterogeneous form of breast cancer, with very few treatment strategies. This review synthesizes past discoveries, current clinical applications, and future opportunities of proteomics in TNBC, making it highly relevant to the theme of this Special Issue on "Past, Present and Future of Proteomics." By consolidating evidence from human and other preclinical studies, it highlights how proteomic signatures have already transformed our understanding of TNBC biology and subtype classification, while also outlining their growing impact as diagnostic, prognostic, and therapeutic markers. Importantly, the review emphasizes the translational shift enabled by next-generation proteomic technologies to redefine precision medicine for TNBC. It showcases how proteomics can facilitate personalized medicine, drug repurposing, and rational combination therapies, and describes novel avenues such as single-cell proteomics and integrative immunoproteogenomics that are driving the field forward. Thus, this work not only consolidates what has been achieved but also provides perspectives on emerging technologies and innovative applications that could revolutionize biomarker discovery and clinical management of TNBC. It highlights proteomics as a critical pillar in shaping the future of cancer diagnostics and therapeutics, directly aligning with the scope and intent of the special issue.
Combining information on degradomics and gene expression data in prospecting metastatic melanoma proteolytic signatures.
Salardani M, Chaves AFA, Cardili L … +4 more , Uno M, Serrano SMT, Chammas R, Zelanis A
J Proteomics · 2026 Mar · PMID 41482208 · Publisher ↗
Melanoma is an aggressive skin cancer with a high metastatic potential, influenced by both genetic and environmental factors. Proteases play a key role in shaping the tumor microenvironment and enabling transformed cells...
Melanoma is an aggressive skin cancer with a high metastatic potential, influenced by both genetic and environmental factors. Proteases play a key role in shaping the tumor microenvironment and enabling transformed cells to actively colonize distant sites (metastasis). We performed proteomic mapping of protease cleavage sites in formalin-fixed paraffin-embedded tissue samples and profiled potentially active proteases in samples from melanoma patients with distinct prognostic outcomes. Although protein abundance alone did not indicate potential markers of disease progression, the observed cleaved fragments may serve for monitoring potentially active proteases in patient samples in targeted proteomics analysis. The findings provide valuable insights into melanoma biology and potential therapeutic prospects.
Proteomic comparison of human brain tissue preservation methods.
Plantera L, Didio A, Ceglarek U … +1 more , Bechmann I
J Proteomics · 2026 Mar · PMID 41478533 · Publisher ↗
This study investigated the impact of tissue preservation methods on protein profiles analyzed by reversed-phase liquid chromatography-high-resolution mass spectrometry (LC-HRMS) using data-independent acquisition (DIA)....
This study investigated the impact of tissue preservation methods on protein profiles analyzed by reversed-phase liquid chromatography-high-resolution mass spectrometry (LC-HRMS) using data-independent acquisition (DIA). Proteomic profiles from formalin-fixed, formalin-fixed and paraffin-embedded (FFPE), and fresh-frozen human brain tissues (cortex and hippocampus, n = 6) were compared, including an FFPE-specific protein extraction kit (n = 4). Formalin-fixed samples more closely resembled fresh-frozen profiles than FFPE or FFPE-Kit samples, while still showing high correlation and overlap with FFPE tissues in principal component analyses. A core set of 1753 proteins was consistently detected across all sample preparation methods. A total of 35 proteins were identified exclusively in fresh-frozen samples, but without functional enrichment. Quantitative comparisons to the proteome of fresh-frozen tissue revealed an underrepresentation of cellular processes, energy metabolism, signaling, and transport related to protein properties such as length, location, and hydrophobicity. In contrast, neuronal development and phagosome-related pathways were overrepresented in fixed tissues. In a pilot study comparing low (Braak 0-II, n = 4) and high (Braak IV-VI, n = 4) Alzheimer's disease (AD) stages using formalin-fixed samples, we identified 12 potential protein biomarkers, primarily nucleosomal proteins and carboxypeptidase M (CPM). These findings suggest that formalin-fixed brain tissue provides reliable proteomic information, making it a valuable resource for neurodegenerative disease research. SIGNIFICANCE: Proteomics offers enormous potential for investigating the molecular regulation of the human brain. Valuable tissue samples are often preserved in formalin or additionally with paraffin for later analysis. The potential value of these preserved samples for proteomic analysis has already been recognized. However, tissue preservation poses a challenge for proteome analysis. Consequently, several studies have compared different protein extraction protocols for fixed samples. In addition, studies have been published comparing protein extraction from FFPE samples with fresh-frozen samples. To our knowledge, this is the first study to compare protein extraction across all three tissue preservation methods with subsequent functional analysis using samples obtained from the same donors, thereby eliminating inter-donor variability and enabling a direct comparison of preservation effects. This study validates a protein extraction protocol from formalin-fixed samples, laying the groundwork for future research into potential biomarkers in formalin-fixed samples.
Assessing systemic effects of Bothrops jararaca venom in the lungs in a mouse model by label-free proteomics using DDA and DIA.
Silva ALT, de Barros BCSC, da Silva JPC … +4 more , Carvalho IS, Santoro ML, Chaves AFA, Serrano SMT
J Proteomics · 2026 Mar · PMID 41456809 · Publisher ↗
Snakebite envenomation is a critical yet underexplored public health issue, particularly in tropical and subtropical regions. Bothrops jararaca venom induces severe local and systemic effects, including pulmonary injury,...
Snakebite envenomation is a critical yet underexplored public health issue, particularly in tropical and subtropical regions. Bothrops jararaca venom induces severe local and systemic effects, including pulmonary injury, however, the molecular mechanisms underlying lung tissue damage remain poorly understood. This study employed label- free quantitative proteomics to map protein alterations in the lung tissue in a mouse model of envenomation. Using Data-Dependent Acquisition (DDA) and Data-Independent Acquisition (DIA) approaches combined with different sample preparation methods, we provide a comprehensive proteomic profile of venom-induced pulmonary damage. Our findings reveal significant changes in proteins involved in inflammatory responses, extracellular matrix remodeling, oxidative stress, and blood coagulation. Comparative analyses highlight the superior performance of DIA over DDA, with DIA offering deeper proteome coverage, enhanced detection of low-abundance proteins, and improved resolution of venom-induced alterations. This benchmark study underscores the potential of DIA as a robust tool for elucidating complex, systemic, mammalian molecular responses to animal toxins. By bridging the gap between proteomic methodologies and pathophysiological insights, our findings contribute to a deeper understanding of viperid snake venom-induced lung injury and give insights for improved clinical management strategies. SIGNIFICANCE: Bothrops snakebites remain a major neglected health problem, causing severe local and systemic complications. While the impact of viperid venoms on muscle and kidney tissues is well documented, the effects on the lungs - an organ critically involved in systemic envenomation outcomes - remain poorly understood. Our study provides the first comprehensive proteomic characterization of lung responses to B. jararaca venom in a murine model, revealing alterations in pathways related to inflammation, extracellular matrix remodeling, oxidative stress, and coagulation. These molecular insights fill an important knowledge gap by showing that proteomic disturbances occur even in the absence of overt lung pathology, highlighting the lungs as a key systemic target of envenomation. Moreover, by demonstrating that antivenom administration mitigates many of these changes, our findings underscore both the therapeutic efficacy of antivenom and the need to better understand its broader systemic footprint. This work advances both toxinology and proteomics by linking molecular-level disturbances to clinically relevant systemic outcomes.
Salivary proteomics and metabolic responses to resistance training with and without blood flow restriction in young adults.
Alencar GZ, Pessôa Filho DM, Santos KO … +6 more , Macedo AG, Vitti HB, Gasparino GN, Thomassian LTG, Faria MH, Magalhães AC
J Proteomics · 2026 Mar · PMID 41453684 · Publisher ↗
Blood flow restriction (BFR) has been applied as alternative strategy to reproduce the effects of conventional high-load intensity training (HI) while training with low-loads (LI). Therefore, the aim of this research was...
Blood flow restriction (BFR) has been applied as alternative strategy to reproduce the effects of conventional high-load intensity training (HI) while training with low-loads (LI). Therefore, the aim of this research was to evaluate the salivary proteomic and metabolic responses to different resistance training in young adults.Ten participants were selected and underwent to training with LI (30 %1RM - one repetition maximum) plus BFR vs. HI (70 %1RM) without BFR, at 48 h-interval. Stimulated saliva was collected before and immediately after the sessions, while breath-by-breath oxygen uptake (VO) was measured during and after each session. Arterial blood samples for lactate concentration measurement (in EqO) were taken at 1 minute of resting between each exercise. For HI, there was an increase in two actin cytoplasmic isoforms and two immunoglobulin isoforms and a decrease of six hemoglobin isoforms. For LI-BFR, there was an increase in two hemoglobin isoforms, and the same immunoglobulin isoforms (t-test, p < 0.05). No differences were significant between HI and LI + BRF training regarding the total energy demand (in mlO), absolute oxygen values (mlO) for oxidative response (VO), glycolytic (EqO), and oxygen debt (VO) (p > 0.05). Both HI and LI + BFR protocols modulated immune system activity and exhibited divergent hemoglobin patterns. SIGNIFICANCE: The current study, which identified protein from saliva samples, a non-invasive method, and analyzed physiological markers, enabled the comparison of different resistance exercise protocols. Although no significant differences were observed in the metabolic responses to each protocol, which highlights the potential of LI + BRF to reproduce a high-intensity training stimulus, the changes in salivary protein profiles indicate specific functional adaptations that may become evident over time.
MALDI Deamidation Score (MDS): A fast and flexible method for assessing deamidation in ZooMS data and its application to the Denisova Cave bone assemblage.
Yang F, Rodríguez Palomo I, Anila Bhuvanendran Nair B … +1 more , Brown S
J Proteomics · 2026 Feb · PMID 41330471 · Publisher ↗
Estimating deamidation from ZooMS spectra has frequently been achieved using the q2e method due to its high-throughput capacity and ease of use. Despite this, q2e only works with spectral data in txt format, operates slo...
Estimating deamidation from ZooMS spectra has frequently been achieved using the q2e method due to its high-throughput capacity and ease of use. Despite this, q2e only works with spectral data in txt format, operates slowly, and employs a genetic algorithm for fitting, which is stochastic and less interpretable. Furthermore, q2e only estimates deamidation at the peptide level and does not generate a sample-wide summary. The introduction of the Parchment Glutamine Index (PQI) presented an alternative method. Initially designed for a large ZooMS dataset of parchment, it utilises weighted least squares and a linear mixed-effects model (LME) to generate a peptide deamidation estimation and a sample level index, respectively. To address the limitations of q2e and expand the applicability of PQI to a wider range of archaeological tissues and MALDI-TOF-derived data (such as ZooMS data on bone collagen), we developed the MALDI Deamidation Score (MDS), an iteration of the PQI method optimised for handling large-scale datasets. MDS is more streamlined for analysing multi-species data with customisable peptide lists, offering dramatically reduced processing time. Using the published Denisova Cave ZooMS assemblage, we demonstrate that different peptides exhibit varying deamidation patterns over time, making the use of a single peptide to represent overall deamidation potentially biased. Such information is invaluable for investigating key questions such as protein preservation and site formation processes. SIGNIFICANCE: We introduce the MALDI Deamidation Score (MDS), a new model that estimates deamidation at both peptide and sample levels from MALDI-derived datasets. MDS streamlines multi-species analyses with customisable peptide lists and markedly reduces processing time, enabling robust and large-scale deamidation estimation. Before MDS, deamidation in ZooMS has often been inferred from a single peptide common to Eurasian terrestrial mammals. Applied to the published Denisova Cave ZooMS assemblage, MDS reveals peptide-specific temporal deamidation patterns, showing that single-peptide proxies can be biased as peptides differ in deamidation rates and may be subject to different taphonomic processes. These results have broad relevance for studies of protein preservation and site-formation processes related to molecular taphonomy across archaeological and paleontological contexts. Looking ahead, as MDS allows a customisable peptide list, it has the potential to extend deamidation analysis of ZooMS data beyond terrestrial mammals to marine mammals and non-mammalian vertebrates (e.g., birds), and to different proteinaceous material such as keratin. It also has the potential to be compatible with different instruments used in peptide mass fingerprinting, such as MALDI-TOF, MALDI-FTICR, and TIMS-TOF. We believe that MDS will contribute greatly to our understanding of deamidation on different peptide sequences under various environmental and burial conditions.
Sulfur metabolism regulates endoplasmic reticulum stress survival through the interaction between cystathionine beta-synthase and Sec14 protein.
Nieto-Zaragoza E, Espinoza-Simón E, Ramirez-Robles D … +3 more , Ríos-Castro E, Garza-Domínguez R, Torres-Quiroz F
J Proteomics · 2026 Feb · PMID 41325883 · Publisher ↗
The gasotransmitter hydrogen sulfide (HS) is implicated in a myriad of biological processes, including disease causing alterations. Besides acting as an antioxidant molecule, HS reacts with thiol groups from cysteine res...
The gasotransmitter hydrogen sulfide (HS) is implicated in a myriad of biological processes, including disease causing alterations. Besides acting as an antioxidant molecule, HS reacts with thiol groups from cysteine residues found in proteins. This post-translational modification (PTM), called S-persulfidation, plays an essential role during endoplasmic reticulum (ER) stress. Here we demonstrated that yeast cystathionine beta-synthase (Cys4), is the main responsible for ER HS-mediated homeostasis. We also found that during ER stress, Cys4 interacts with specific proteins that we identified with at least one cysteine residue modified by hydrogen sulfide. Finally, we focused on one interactor with reported tunicamycin sensitivity, the phospholipid transfer protein Sec14. In addition to Cys4 immunoprecipitation, we confirmed this interaction by pulling down Sec14 interactors. Deleting CYS4 generated the accumulation of lipid droplets inside the cytosol, similar to Sec14. For the first time, we described a set of protein-protein interactions of Cys4 during ER stress with cysteines susceptible to S-persulfidation, leaving an open question about the role and regulation of the rest of the interactors. SIGNIFICANCE: In this study, we identified several interactor partners of yeast cystathionine beta synthase and analyzed cysteine residues with cysteine S-persulfidations. Although yeast have multiple HS producing enzymes, Cys4 seems to play a predominant role during ER stress. Temporal and spatial generation of HS is becoming significant in the field, and our findings contribute to that understanding. Besides, Cys4/Sec14 complex found here, seven different Cys4 complexes that may be regulated by HS were also reported. Because the biogenesis of this PMT is still controversial, findings like these support the hypothesis of interaction mediated biogenesis. HS producing enzymes specificity would help control their signaling across the cell. Finally, all Cys4 interactors with modified cysteines, including Sec14, are excellent targets to study how this PTM regulates enzyme functioning. Structural and functional assays with cysteine mutants in these proteins will shed light on new regulatory mechanisms.
Opt-TMT: An optimized and scaled-down TMT labeling strategy for limited sample.
Martins M, Nogueira FCS, Junqueira M … +1 more , Nugue G
J Proteomics · 2026 Feb · PMID 41318025 · Publisher ↗
Mass spectrometry-based proteomics has evolved and currently requires minimal sample quantities. However, manufacturers' isobaric labeling protocols, such as Tandem Mass Tag (TMT), are still designed for larger sample am...
Mass spectrometry-based proteomics has evolved and currently requires minimal sample quantities. However, manufacturers' isobaric labeling protocols, such as Tandem Mass Tag (TMT), are still designed for larger sample amounts, leading to significant costs and limiting research possibilities. Here, we present an optimized isobaric labeling protocol (Opt-TMT) that maintains high labeling efficiency while substantially reducing reagent consumption and sample requirements. We achieved consistent labeling efficiency even with peptide quantities as low as 6-15 μg per channel by adjusting reaction conditions, including volume reduction and increased peptide concentration. Importantly, our protocol reduces reagent costs by up to 90 % compared to the commercial protocol, while maintaining labeling efficiency above 99 %. This cost-effective approach addresses key challenges in proteomic research, especially for studies involving limited biological material or post-translational modification analyses. The Opt-TMT method provides a practical solution for researchers seeking to maximize the utility of isobaric labeling while minimizing resource expenditure, without compromising analytical quality. SIGNIFICANCE: The Opt-TMT protocol provides a major advancement for proteomics by making isobaric labeling both cost-effective and scalable to very limited sample amounts. By reducing reagent costs up to 90 % without compromising labeling efficiency (>99 %), this approach enables high-quality quantitative proteomics for studies where material is scarce, such as patient-derived samples, biopsies, or post-translational modification analyses. Importantly, Opt-TMT broadens access to TMT-based workflows for laboratories with limited resources, while preserving analytical robustness. This work contributes a practical and impactful methodological improvement that directly benefits both fundamental and applied proteomics research.
Enhanced proteome profiling of human cerebrospinal fluid using a commercial plasma enrichment strategy.
Borràs E, Anastasi F, Pastor O … +2 more , Suárez-Calvet M, Sabidó E
J Proteomics · 2026 Feb · PMID 41308871 · Publisher ↗
Cerebrospinal fluid (CSF) is a valuable liquid biopsy for identifying protein biomarkers in neurological diseases, yet its proteome profiling faces challenges due to the large dynamic range of protein abundances. In this...
Cerebrospinal fluid (CSF) is a valuable liquid biopsy for identifying protein biomarkers in neurological diseases, yet its proteome profiling faces challenges due to the large dynamic range of protein abundances. In this study, we assessed the effectiveness of a commercial enrichment strategy, initially developed for plasma samples, in enhancing the detection of low-abundance proteins in human CSF. We demonstrate significant improvements in protein identification and coverage depth while maintaining high reproducibility and low coefficients of variation. These findings underscore the potential of this enrichment strategy to facilitate rapid and sensitive CSF analysis, advancing biomarker discovery in neurological research. SIGNIFICANCE: This article highlights the effectiveness of a commercial plasma enrichment strategy in enhancing the detection of low-abundance proteins in human CSF. The article shows improvements in proteome coverage and it underscores the potential of this strategy to facilitate rapid and sensitive CSF analysis.
Temporal proteomic profiling of mouse kidney reveals dynamic responses to Crotalus durissus terrificus envenomation.
Pimentel IOC, Santos WDS, Montoni F … +8 more , Chaves AFA, Eichler RADS, Lima IF, Souza-Siqueira T, Nishiyama-Jr MY, Oliveira LJ, Ferro ES, Iwai LK
J Proteomics · 2026 Feb · PMID 41297590 · Publisher ↗
Snakebite envenoming by Crotalus durissus terrificus causes significant morbidity, particularly acute kidney injury (AKI), though its molecular mechanisms remain poorly understood. This study provides the first comprehen...
Snakebite envenoming by Crotalus durissus terrificus causes significant morbidity, particularly acute kidney injury (AKI), though its molecular mechanisms remain poorly understood. This study provides the first comprehensive temporal proteomic atlas of renal responses to C. d. terrificus envenomation, combining TMT-based quantitative proteomics with multivariate bioinformatics and histopathological validation in a mouse model (0.5 LD50). We identified 2567 renal proteins, with 904 significantly altered (FDR ≤ 0.05), demonstrating a proteomic crisis that peaked at 12 h (400 increased, 451 decreased) and was already evident at 6 h (15 increased, 37 decreased). Changes at 1 h and 24 h were minimal at the single-protein level. These results delineate a precise biphasic progression: from acute phase at 6 h to 12 h, characterized by oxidative stress, mitochondrial dysfunction, and loss of key tubular transport proteins dominated by maladaptive repair and fibrotic signaling. Our temporal analysis defines distinct windows for intervention: an early opportunity for antioxidant therapy to counter acute injury, followed by a critical period where anti-fibrotic strategies are required to prevent the progression to irreversible kidney damage. SIGNIFICANCE: Snakebite envenomation by Crotalus durissus terrificus rattlesnake venom frequently leads to acute kidney injury (AKI), yet the molecular mechanisms driving nephrotoxicity remain poorly characterized. This study provides the first comprehensive temporal proteomic atlas of renal responses to envenomation, revealing that the most robust proteomic remodeling occurs between 6 h and 12 h, with hundreds of proteins significantly altered. These changes highlight mitochondrial dysfunction, oxidative stress, and tubular injury, exemplified by decrease of CUBN and AGT, alongside shifts in cytoskeletal and ribosomal pathways. Early (1 h) and late (24 h) effects were limited at the single-protein level and are reported as exploratory trends, such as NDRG2 (hypoxia response) and ITGA3 (fibrotic signaling). Histological validation confirmed progressive tubular damage and maladaptive repair, paralleling the proteomic signatures. Together, these findings delineate a critical window of maximal molecular disruption at 12 h, providing mechanistic insights into the progression from acute injury to maladaptive remodeling. The data suggest that therapeutic strategies targeting early oxidative stress (e.g., antioxidant interventions) or late fibrotic pathways (e.g., RAS modulation) could mitigate venom-induced damage. This work bridges molecular pathophysiology with clinical outcomes, informing future translational research.
Lunatin-1: A peptide derived from the venom of the Hadruroides lunatus scorpion modulates signaling pathways in HL60 tumor cells to induce cytotoxic effects.
Lima-Batista EM, Gómez-Mendoza DP, Moysés MN … +8 more , de Sousa Gomes K, Carvalho BC, de Lima ME, Souza-Fagundes EM, da Silva AM, Kjeldsen F, Verano-Braga T, Pimenta AMC
J Proteomics · 2026 Feb · PMID 41276073 · Publisher ↗
Lunatin-1 is a 13-residue cytotoxic peptide derived from the venom of the scorpion Hadruroides lunatus. This study investigated its early effects on cellular signaling in the human promyelocytic leukemia cell line HL-60...
Lunatin-1 is a 13-residue cytotoxic peptide derived from the venom of the scorpion Hadruroides lunatus. This study investigated its early effects on cellular signaling in the human promyelocytic leukemia cell line HL-60 using integrated proteomics and phosphoproteomics. Lunatin-1 regulated key mediators of apoptosis, such as caspase-2 (CASP2) and MEK1 (MAP2K1), and impacted major signaling pathways such as MAPK and PI3K/AKT. Lunatin-1 induced caspase-dependent and -independent apoptotic signaling, reduced AKT1 phosphorylation, and promoted BAX activation, consistent with mitochondrial apoptosis. These findings demonstrate that Lunatin-1 disrupts pro-survival signaling and activates multiple cell death pathways, highlighting its potential as a therapeutic candidate for hematologic malignancies. SIGNIFICANCE: This study provides a comprehensive analysis of the early molecular events triggered by Lunatin-1, a venom-derived peptide, in HL60 leukemia cells. Through integrated proteomic and phosphoproteomic approaches, we reveal that Lunatin-1 disrupts key survival pathways, notably MAPK and PI3K/AKT, and activates both caspase-dependent and -independent mechanisms of apoptosis. The peptide modulates proteins involved in DNA damage response, cell cycle regulation, and oxidative stress, offering insight into its multifaceted cytotoxic effects. These findings advance our understanding of venom-derived peptides as potential anticancer agents and underscore Lunatin-1's therapeutic promise for targeting resistant cancer cell populations.
Nitrate and silicate limitations induce metabolic reprogramming and lipid redistribution in Navicula incerta, enhancing biodiesel properties.
Encinas-Arzate JJ, De Jesús-Campos D, Márquez-Ríos E … +9 more , Hernández-Ortiz M, Morales-Amparano MB, López-Elías JA, Torres-Arreola W, Encarnación-Guevara S, Ramírez-Suárez JC, Carvallo-Ruiz MG, Bojórquez-Velázquez E, Huerta-Ocampo JÁ
J Proteomics · 2026 Jan · PMID 41276072 · Publisher ↗
Nutrient limitations alter microalgae metabolism and fatty acid biosynthesis, modifying the lipid profile and improving the chemical properties of the resulting biodiesel. This study investigated the effects of nitrate a...
Nutrient limitations alter microalgae metabolism and fatty acid biosynthesis, modifying the lipid profile and improving the chemical properties of the resulting biodiesel. This study investigated the effects of nitrate and silicate limitations on the proteomic and lipid profiles in Navicula incerta and its biodiesel potential. Proteomic analysis revealed 287 differentially abundant proteins (DAPs) out of 558 identified, with silicate-limited conditions showing the highest number of DAPs (212) and nitrogen-limited conditions showing 125 DAPs (log2FC > |0.57|, p-value <0.05). These changes underpin two distinct survival strategies: nitrogen limitation forced a broad metabolic shutdown, while silicate limitation prompted a strategic reallocation of resources, maintaining core biosynthesis and enhancing internal recycling. Both stresses induced a convergent lipid remodeling characterized by decreases in saturated fatty acids and increases in monounsaturated and polyunsaturated fatty acids. This shift optimizes membrane fluidity for stress resistance and enhances key biodiesel properties, confirming the potential of N. incerta as a sustainable source of high-quality biodiesel. These findings highlight the diatom's metabolic flexibility in optimizing resource allocation for survival, a trait that can be harnessed to tailor lipid profiles for advanced biofuel applications. Future work should focus on the impact, efficiency, and economic feasibility of cultivating N. incerta under nutrient stress. SIGNIFICANCE: Understanding the relationship between nitrogen and silicate concentrations and protein accumulation is crucial for harnessing the potential of microalgae in various industries and addressing environmental challenges. The proteomic analysis and lipid profiles obtained in N. incerta under nitrogen and silicate limitation demonstrate remarkable metabolic flexibility in response to nutrient limitations, optimizing resource allocation to ensure survival under nutrient stress. Nitrogen limitation drives the accumulation of carbohydrates and dry biomass, along with lipid mobilization and a shift toward unsaturated fatty acids, enhancing energy efficiency and membrane functionality. Silicate limitation, while having a milder effect, prioritizes resource conservation and the redistribution of existing reserves. These adaptive responses highlight the diatom's ability to maintain critical cellular functions under adverse conditions and reveal its potential for biodiesel production.
Proteome dynamics of chilli pepper fruits during development and ripening from two Mexican cultivars of Capsicum annuum L.
Gomez-Zepeda D, Cervantes-Hernández F, Martínez O … +2 more , Ochoa-Alejo N, Ordaz-Ortiz JJ
J Proteomics · 2026 Jan · PMID 41260332 · Publisher ↗
Chilli pepper (Capsicum annuum L., Solanaceae family), a horticultural crop native to the Americas, is esteemed for its flavour and bioactive compounds. To enhance our understanding of the molecular basis of chilli peppe...
Chilli pepper (Capsicum annuum L., Solanaceae family), a horticultural crop native to the Americas, is esteemed for its flavour and bioactive compounds. To enhance our understanding of the molecular basis of chilli pepper fruit development and ripening, we characterised proteome dynamics from early fruit set to ripening in two Mexican cultivars. Protein profiles were analysed using label-free quantitative (LFQ) LC-MS proteomics with data-independent acquisition (DIA), resulting in the quantification of 421 proteins, predominantly involved in primary and secondary metabolism. The developmental stage was the primary factor driving proteome variation, with limited influence from cultivar differences. Clustering and relative quantification revealed intricate patterns of protein abundance across fruit maturation. Proteins associated with carotenoid and capsaicinoid biosynthesis exhibited temporal regulation consistent with their roles in determining fruit colour and pungency. This study provides insights into the molecular changes underlying chilli pepper fruit growth, development, and ripening and offers a proteomic overview for understanding some biochemical traits that define chilli pepper fruit characteristics. SIGNIFICANCE: Understanding the molecular basis of fruit growth, development, and ripening is crucial for enhancing crop quality and nutritional value. In chilli pepper, traits such as the production of valuable secondary metabolites, pigmentation, and pungency arise from finely regulated metabolic processes during fruit maturation. Here, we investigated these processes from a proteomics perspective, complemented with clustering and functional enrichment analyses. The findings reveal that developmental stage, rather than genotype, is the dominant factor shaping the fruit proteome, underscoring a conserved maturation program. Proteins involved in primary metabolism and specialised biosynthetic pathways, including those for carotenoids and capsaicinoids, show dynamic regulation consistent with their roles in fruit quality traits. These results contribute to the understanding of the molecular processes involved in fruit growth, development, and ripening and provide a proteomic framework for studying trait formation in Capsicum annuum and related Solanaceae crops.
Dinuclear Cu-complexes disrupt cellular pathways and rewire the breast cancer proteome.
Ghasemishahrestani Z, de Oliveira SSC, Dos Santos Moraes Francisco R … +7 more , Ramos LFC, Dos Santos RM, Domont GB, Rey NA, Dos Santos ALS, Nogueira FCS, Pereira MD
J Proteomics · 2026 Jan · PMID 41260331 · Publisher ↗
Cancer's global burden highlights the urgent need for more effective therapies. Metal-based drugs, particularly Cu-complexes, offer promising alternatives due to copper's diverse biological functions. This study investig...
Cancer's global burden highlights the urgent need for more effective therapies. Metal-based drugs, particularly Cu-complexes, offer promising alternatives due to copper's diverse biological functions. This study investigates the antitumor potential of two novel dinuclear Cu-complexes, [Cu(μ-CHCOO)(L)(OH)]·2HO (R9) and [Cu(μ-OH)(HL)(OH)]ClO·2HO (R10), in MCF-7 breast cancer cells. Both compounds exhibited greater cytotoxicity than cisplatin, with IC values of 1.01 ± 0.09 μM (R9) and 1.27 ± 0.14 μM (R10), while showing selectivity toward cancer cells, as indicated by higher IC values in healthy MCF10A cells. Treated MCF-7 cells showed increased granularity, mitochondrial membrane depolarization, and elevated reactive oxygen species. At IC concentrations, cell cycle analysis revealed Sub-G1 accumulation and DNA fragmentation (TUNEL assay), indicating apoptosis via intrinsic pathways, supported by caspase 9 activation. Label-free proteomics revealed distinct mechanisms for R10 compared to cisplatin. In R10-treated cells, key downregulated pathways included glycolysis, the TCA cycle, oxidative phosphorylation, PI3K-Akt signaling, and the ubiquitin-proteasome system. Apoptosis-related proteins such as structural proteins (ACTB, ACTG1, SPTAN1, TUBA4A), mitochondrial apoptotic factors (AIFM1), nuclear envelope components (LMNA), and stress-response regulators (JUN, EIF2S1) were dysregulated. Proteomics data is available via ProteomeXchange with identifier PXD064464. These findings support the potential of Cu-complexes as effective antitumor agents with mechanisms distinct from cisplatin, offering superior efficacy through apoptosis induction. SIGNIFICANCE: Breast cancer remains one of the leading causes of cancer-related mortality among women, highlighting the need for more effective and selective therapeutic agents. While platinum-based drugs are widely used, their limitations call for novel alternatives. In this study, we demonstrate that two newly synthesized dinuclear copper(II) complexes, R9 and R10, exhibit strong cytotoxicity against MCF-7 breast cancer cells with higher selectivity compared to cisplatin. Through functional and proteomic analyses, we show that these compounds induce intrinsic apoptosis, disrupt cytoskeletal integrity, and modulate key signaling pathways such as PI3K-Akt and RAS-ERK. Our proteomic results reveal distinct molecular signatures for R10, underscoring its unique mechanism of action. Therefore, copper-based complexes represent promising candidates for breast cancer treatment, and proteomics provides critical insight into their therapeutic potential.
A fast TMT-based proteomic workflow reveals neural enrichment in neurospheres of hiPSC-derived neural stem cells.
de Lima Muniz P, Martins MR, Goto-Silva L … +6 more , Souza LRQ, Valadares W, Nogueira FCS, Rehen S, Nugue G, Junqueira M
J Proteomics · 2026 Jan · PMID 41253251 · Publisher ↗
Three-dimensional (3D) neural spheroids, or neurospheres, generated from human induced pluripotent stem cell (hiPSC)-derived neural stem cells (NSCs) more accurately recapitulate the microenvironmental cues of neural tis...
Three-dimensional (3D) neural spheroids, or neurospheres, generated from human induced pluripotent stem cell (hiPSC)-derived neural stem cells (NSCs) more accurately recapitulate the microenvironmental cues of neural tissue compared to traditional two-dimensional (2D) monolayers. However, comparative omics-based characterizations of these models remain limited. Here, we present a streamlined and scalable TMT-based quantitative proteomics workflow to contrast the proteomic landscapes of hiPSC-derived NSCs cultured in 2D monolayers versus 3D neurospheres. A total of 1576 proteins were identified in an unfractionated LC-MS/MS of 68 min, with 542 showing significant differential abundance between groups. Neurospheres exhibited enrichment in neural-related pathways, such as synaptic signaling, neurotrophin signaling, cytoskeletal organization and vesicle trafficking, while monolayers enriched for multipotency features, such as general metabolic activity. Cell-type enrichment analyses confirmed increased neuronal identity in neurospheres, including elevated levels of markers associated with neuronal maturation. Our results demonstrate that 3D culture of NSCs induces a proteomic shift toward a more mature neural phenotype, which was validated by immunofluorescence microscopy. This rapid, multiplexed proteomic approach enables high-content molecular profiling suitable for drug screening and personalized medicine applications. SIGNIFICANCE: The present work contributes to the molecular and biological understanding of iPSC-derived neurospheres by exploring the proteome of this model. Neurospheres are a culture model of great potential and applicability in neurobiology research and personalized medicine, which still lacks a robust omic characterization. By studying neurospheres, we also work with a 3D culture model generated in vitro, avoiding the use of primary neural cells culture and animal models. Our fast method is relevant to single-cell proteomics, personalized medicine and screening assays.
The dynamics of ubiquitination and its role within the proteome of extracellular vesicles.
Morales-Tarré O, Popa-Navarro X, Paradela A … +4 more , Hernández-Ortiz M, Arrieta O, Corrales F, Encarnación-Guevara S
J Proteomics · 2026 Jan · PMID 41241127 · Publisher ↗
Ubiquitination is a multifaceted post-translational modification that plays a crucial role in regulating the degradation of unnecessary cellular proteins and is involved in various cellular processes, including protein e...
Ubiquitination is a multifaceted post-translational modification that plays a crucial role in regulating the degradation of unnecessary cellular proteins and is involved in various cellular processes, including protein export via extracellular vesicles. We investigate how alterations in the intracellular levels of ubiquitinated proteins affect vesicle protein content in BEAS-2B cells. We increased the intracellular levels of ubiquitinated proteins by inhibiting proteasomal degradation with MG-132 and by blocking deubiquitinating enzymes using PR-619. Using centrifugation and ultracentrifugation, were isolate various vesicle types, specifically the largest vesicles (enriched in plasma membrane-derived microvesicles) and the smallest vesicles (enriched in endosomal exosomes). High-resolution mass spectrometry-based proteomics was utilized to quantify their protein content. The content of extracellular vesicles changed in response to both treatments, reflecting cellular changes and the export of stress signals. The increase in intracellular levels of ubiquitinated proteins induced metabolic stress in the cells, generally leading to a reduction in protein translation, an enhanced response to oxidative stress, changes in membrane transport, and alterations in cell-microenvironment interactions. The modifications observed in the vesicular proteome suggest that ubiquitination plays a significant role in regulating protein export. This regulation can be mastered for diagnostic purposes and for describing cells and tissues through liquid biopsies. SIGNIFICANCE: Ubiquitination is one of the most abundant post-translational modifications in cells, and its role, beyond marking proteins for degradation, is not fully understood. Characterizing the effect of this modification on protein export to extracellular vesicles can shed light on how a cell selects its contents to influence its microenvironment, send signals to distant tissues, or interact with the immune system. This is particularly relevant in the context of pathologies such as cancer, which hijacks the cellular vesicle-producing machinery and adapts it to its needs to influence the remodeling of its surroundings. Understanding how a cell regulates the specific contents of its vesicles may point the way toward the development of treatments or superior diagnostic and classification tools.
Systematic comparison of the effects of various fixatives on the stability of the cellular proteome.
Chen Y, Zou X, Wang L … +6 more , Gao Y, Fu H, Liu B, Jiang H, Tan M, Zhai L
J Proteomics · 2026 Jan · PMID 41241126 · Publisher ↗
Proteomics research represents a critical area within modern biomedical science. Fixatives, as essential components in proteomic analysis, play a pivotal role in maintaining proteome stability and analytical accuracy, wh...
Proteomics research represents a critical area within modern biomedical science. Fixatives, as essential components in proteomic analysis, play a pivotal role in maintaining proteome stability and analytical accuracy, while also exerting a substantial influence on experimental outcomes. However, there remains a limited understanding of how various fixatives affect proteome stability. In this study, we conducted a systematic comparison of commonly used fixation agents-specifically formaldehyde, paraformaldehyde, methanol, and ethanol-to evaluate how they affect the stability of the cellular proteome. Our results show that different fixatives lead to notably different levels of proteome stability. Importantly, formaldehyde solution and paraformaldehyde produce cross-linking effects that can significantly reduce protein solubility and hinder the efficiency of enzymatic digestion. Additionally, we analyzed the proteomic profiles of both drug-treated and untreated samples under different fixation conditions to better understand how these conditions may affect the quality and interpretation of mass spectrometry data. These results provide a scientific basis for selecting the most appropriate fixative in proteomics research. Our study also contributes to improving the compatibility between fixatives and mass spectrometry technologies, offering dependable technical support for biological and biomedical research. SIGNIFICANCE: We conducted a systematic comparison of commonly used fixation agents-specifically formaldehyde, paraformaldehyde, methanol, and ethanol-to evaluate how they affect the stability of the cellular proteome. These results provide a scientific basis for selecting the most appropriate fixative in proteomics research. Our study also contributes to improving the compatibility between fixatives and mass spectrometry technologies, offering dependable technical support for biological and biomedical research.
Differences between protein cargo in outer membrane vesicles released from Mannheimia haemolytica A2 in the presence and absence of bovine lactoferrin.
Avalos-Gómez C, Aguilar-Chaparro MA, Ríos-Castro E … +3 more , Marin-Flamand E, Sánchez-Mendoza AE, de la Garza M
J Proteomics · 2026 Jan · PMID 41236000 · Publisher ↗
Pneumonic mannheimiosis (PM) is a respiratory disease that causes significant economic losses in the ruminant livestock industry. Due to the lack of effective commercial products and the growing problem of bacterial anti...
Pneumonic mannheimiosis (PM) is a respiratory disease that causes significant economic losses in the ruminant livestock industry. Due to the lack of effective commercial products and the growing problem of bacterial antibiotic resistance, recent studies have focused on identifying new therapeutic strategies. Mannheimia haemolytica, the primary bacterial pathogen in ovine PM, naturally releases outer membrane vesicles (OMVs) whose protein cargo varies depending on environmental conditions. Lactoferrin (LF) is a glycoprotein of the mammalian innate immune system with bacteriostatic and bactericidal properties. In this study, we evaluated the effect of bovine LF on the protein composition of M. haemolytica OMVs. A total of 766 proteins were identified, including cytoplasmic, outer membrane (OM), and cell envelope proteins, most of which are related to metabolic processes. The presence of LF in the culture medium led to differential regulation of 162 proteins, affecting pathways such as general metabolism, aminoacyl-tRNA biosynthesis, RNA degradation, and biosynthesis of secondary metabolites. Notably, a decrease was observed in several lipoproteins (Lpps), OM proteins (OMPs)-including the LF-binding protein OmpA-and two components of the Tol-Pal system associated with pathogenicity. In addition, LF treatment was associated with a tendency to increase both the size and number of OMVs. These observations provide valuable insights into the use of LF-modified OMVs as a foundation for alternative prophylactic or therapeutic options against PM. SIGNIFICANCE: This work focuses on the analysis of protein cargo in Mannheimia haemolytica A2 OMVs, when bacteria grow in the presence of bovine lactoferrin (LF). This glycoprotein from the innate immune system caused stress in the bacteria which led to more OMVs released and differences in protein cargo present in OMVs, including decrease of several proteins related to pathogenicity. The results in vitro suggest that treatment with LF could reduce the damage caused by OMVs to their host cells, and being LF an alternative for the prevention and treatment of pneumonic mannheimiosis.
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