Journal Of Proteomics[JOURNAL]
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200 papers
Integrated analysis of the transcriptome and proteome reveals that ABI3BP is involved in the pathogenesis of osteoarthritis.
Yu J, Xiao L, Yan Z … +4 more , Chen X, Zhao S, Yu C, Dong Y
J Proteomics · 2026 Jan · PMID 41232761 · Publisher ↗
OBJECTIVE: Osteoarthritis (OA) is the most common degenerative joint disease mainly characterized by cartilage degradation, but the underlying molecular mechanisms remains unclear. This study aims to identify key genes,...
OBJECTIVE: Osteoarthritis (OA) is the most common degenerative joint disease mainly characterized by cartilage degradation, but the underlying molecular mechanisms remains unclear. This study aims to identify key genes, proteins, and pathways involved in OA progression using integrated transcriptomic and proteomic approaches. METHODS: Transcriptome and proteome profiles of lesioned (OA) and preserved (control) cartilage tissues were analyzed. Differentially expressed genes (DEGs) and differentially abundant proteins (DAPs) were identified, followed by functional enrichment analysis. Key candidates were validated using qRT-PCR and western blotting. The role of ABI3BP in chondrocyte senescence and catabolism was investigated by siRNA knockdown, SA-β-gal staining, and immunofluorescence for senescence markers (P16, P21). RESULTS: Omics analysis revealed 24 significantly altered genes/proteins, including upregulated ABI3BP, TGFBI, ANOS1, S100A4, and TNFAIP6, and downregulated METTL7A. Enriched pathways included extracellular matrix (ECM) organization, ECM-receptor interaction, and phenylalanine metabolism. ABI3BP was notably elevated in OA cartilage. Its knockdown mitigated IL-1β-induced ECM degradation and reduced the level of senescence-associated markers, suggesting a protective effect against OA progression. CONCLUSIONS: The results provided a comprehensive molecular profile of OA cartilage, highlighting ABI3BP as a regulator of chondrocyte senescence and ECM homeostasis. Targeting ABI3BP may offer a novel therapeutic strategy for OA treatment. SIGNIFICANCE OF THE STUDY: This study provides multi-omics insights into the molecular mechanisms of osteoarthritis (OA), particularly focusing on cartilage degeneration. By integrating transcriptomic and proteomic analyses, we identified key dysregulated genes/proteins (ABI3BP, TGFBI, ANOS1, S100A4, TNFAIP6, and METTL7A) and highlighted their roles in extracellular matrix (ECM) disruption, cellular senescence, and inflammatory responses. Notably, ABI3BP was found to be upregulated in OA cartilage and functionally linked to chondrocyte catabolism and senescence. Its knockdown ameliorated IL-1β-induced damage, suggesting its potential as a novel therapeutic target for OA. These findings deepen our understanding of OA pathogenesis and pave the way for future targeted interventions.
Decoding spliceosome inhibition: Isobaric tag-based proteomic profiling of pladienolide B treated human cell lines.
Lopez XIH, Martinez-Perez K, Thakurta SG … +2 more , Levi BP, Paulo JA
J Proteomics · 2026 Jan · PMID 41224195 · Full text
Pladienolide B (Pla-B) is a potent splicing modulator that has shown promise in cancer treatment, but its cellular effects remain incompletely understood. We investigated the dose-associated effect of Pla-B on human cell...
Pladienolide B (Pla-B) is a potent splicing modulator that has shown promise in cancer treatment, but its cellular effects remain incompletely understood. We investigated the dose-associated effect of Pla-B on human cell lines using isobaric tag-based quantitative proteomics and phosphoproteomics techniques. We quantified over 10,000 proteins and 19,000 phosphorylation events in SH-SY5Y cells, revealing dose-associated changes in protein abundance and phosphorylation status. Low Pla-B concentrations induced significant alterations in nuclear proteins, specifically those involved in transcription and cell division. Higher concentrations led to more extensive proteome remodeling, affecting chromatin-associated proteins and transcription. Phosphoproteome analysis uncovered alterations in the phosphorylation states of proteins including the splicing factor subunit SF3B, suggesting complex regulation of signaling pathways. Our findings reveal the detailed proteomic landscape of Pla-B's effects, offering insights into its role in the global proteome, which may guide future therapeutic applications and rational drug design.
Corrigendum to "Serum proteomics identifies biomarkers for predicting non-survivors in elderly COVID-19 patients" [Journal of Proteomics, volume 311 (2025) 105356].
Wang L, Tian W, Wang S … +6 more , Liu Y, Wang H, Xiao J, Yu Z, Xie L, Chen Y
J Proteomics · 2026 Jan · PMID 41207823 · Publisher ↗
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The protein cargo of extracellular vesicles. Recent advances in lung cancer research.
Morales-Tarré O, Navarro XP, Encarnación-Guevara S
J Proteomics · 2026 Jan · PMID 41207652 · Publisher ↗
Extracellular vesicles (EVs) are membranous microparticles produced by all living cells, from bacteria to humans. In recent years, interest in these vesicles has increased because they are linked to various biological fu...
Extracellular vesicles (EVs) are membranous microparticles produced by all living cells, from bacteria to humans. In recent years, interest in these vesicles has increased because they are linked to various biological functions, such as coagulation, the removal of undegraded proteins, intercellular signaling, stimulation and inactivation of T lymphocytes, and the transfer of antigens to APC. Since these vesicles carry specific characteristics of the parental cells, their characterization is a valuable opportunity to understand, through a liquid biopsy, the mechanisms involved in different pathologies, such as cancer. Lung cancer, is known to increase the production of extracellular vesicles, making their study particularly relevant in this group of diseases where biopsy collection is extremely difficult. Most research has centered on characterizing the nucleic acid content of vesicles due to their ability to alter gene expression in recipient cells. In contrast, the protein content of extracellular vesicles has been studied less extensively. Here, we describe the mechanisms of production for the main classes of extracellular vesicles and delve into their protein content. We also analyze recent progress in the proteomic characterization of extracellular vesicles in lung cancer research and explore their potential in diagnosis and the mechanisms underlying the disease's development. SIGNIFICANCE: This article highlights the advancements that the field of proteomics has brought to the characterization of extracellular vesicles derived from lung cancer. Given that lung cancer is the leading cause of cancer-related deaths, it is crucial to molecularly characterize this disease within the current landscape of biomedical research. We aim to draw the reader´s attention to the benefits of analyzing extracellular vesicles, as their protein content holds promise as an alternative liquid biopsy to achieve these objectives. By discussing existing findings and the challenges that remain, we hope to motivate researchers to utilize proteomics tools to develop new methodologies that can be consistently applied in clinical research and personalized patient care.
Quantitative proteomic analysis of cadmium chloride tolerance mechanisms in Aeromonas hydrophila.
Xie X, Zhang B, Chen X … +7 more , Tang J, Qiu Z, Shen C, Lian L, Gu G, Lin X, Ali F
J Proteomics · 2026 Jan · PMID 41192588 · Publisher ↗
Aeromonas hydrophila, an antibiotic-and multi-metal-resistant pathogen, threatens aquaculture, yet its adaptation to cadmium chloride (CdCl₂) remains poorly understood. A.hydrophilla was grown with CdCl₂ exposure, and da...
Aeromonas hydrophila, an antibiotic-and multi-metal-resistant pathogen, threatens aquaculture, yet its adaptation to cadmium chloride (CdCl₂) remains poorly understood. A.hydrophilla was grown with CdCl₂ exposure, and data-independent acquisition (DIA)-based proteomics was employed to identify the 253 upregulated and 163 downregulated proteins. GO and KEGG enrichment analyses revealed upregulated proteins involved in sulfate metabolism, siderophore- and iron transport, and other transition metal transport processes, while downregulated proteins were linked to amino acid metabolism, the tricarboxylic acid (TCA) cycle, and fatty acid metabolism. Gene Set Enrichment Analysis (GSEA) indicated positive enrichment of ribosome, RNA degradation, sulfur metabolism, and riboflavin metabolism, and negative enrichment of valine, leucine, and isoleucine degradation, two-component system, and bacterial chemotaxis. CdCl₂ tolerance assays of four gene-deletion mutants confirmed proteomics predictions: ΔAHA_3605 (uncharacterized protein) and ΔAHA_1796 (GGDEF-domain deletion) were significantly more sensitive to CdCl₂, suggesting a role for cyclic di-GMP (c-di-GMP) signaling in cadmium resistance. Collectively, these results provide novel insights into the adaptive strategies of A. hydrophila, revealing key molecular determinants of CdCl₂ stress tolerance. SIGNIFICANCE: Cadmium contamination increasingly co-selects for antibiotic-resistant pathogens in aquaculture, yet the molecular basis of cadmium tolerance in Aeromonas hydrophila-one of the most problematic Gram-negative fish pathogens-has been unknown. Here, we provide the first comprehensive, DIA-based quantitative proteome map of A. hydrophila under CdCl₂ stress, uncovering a tightly orchestrated stress response that simultaneously remodels metal acquisition, down-regulates energy-intensive metabolism (TCA cycle, branched chain amino acid and fatty acid degradation), and activates sulfur-riboflavin-ribosome pathways to repair oxidative damage. Functional validation using gene-deletion mutants demonstrated that loss of AHA_3605 (uncharacterized) or AHA_1796 (GGDEF domain protein) significantly increased CdCl₂ sensitivity, implicating cyclic di-GMP signaling in cadmium resistance. These findings advance our mechanistic understanding of heavy-metal adaptation in aquatic pathogens and offer proteome informed targets to disrupt metal-driven co-selection of multidrug-resistant A. hydrophila in aquaculture ecosystems.
Decoding bladder cancer aggressiveness: A proteomic, phosphoproteomic and metabolomic approach.
Feng Z, Zhang B, Liu Y … +4 more , Yang F, Lei Y, Liao S, Hou X
J Proteomics · 2026 Jan · PMID 41187894 · Publisher ↗
BACKGROUND: Bladder cancer (BC) is the most common malignancy of the urinary system. However, the median survival of patients with metastatic bladder cancer remains limited. Thus, there is an urgent imperative to develop...
BACKGROUND: Bladder cancer (BC) is the most common malignancy of the urinary system. However, the median survival of patients with metastatic bladder cancer remains limited. Thus, there is an urgent imperative to develop novel biomarkers for BC-targeted therapies and to conduct in-depth investigations into BC pathogenesis leveraging multi-omics technologies. RESULTS: Our results revealed that proteins co-upregulated in both proteomic and phosphoproteomic analysis, such as SLC4A7 and MYO9B, demonstrated potential utility in distinguishing MIBC from NMIBC. Upregulation of CPT2 and palmitic acid in MIBC patients highlighted the dysregulation of physiological control mechanisms and enhanced pro-tumorigenic effects of lipid metabolic pathways. CONCLUSIONS: Integrated multi-omics analysis reveals that key regulatory proteins such as SLC4A7 and MYO9B play pivotal roles in mediating the aggressive phenotypes of MIBC. Aberrant upregulation of CPT2 protein and metabolites like palmitic acid may drive malignant transformation from NMIBC to MIBC by promoting lipid metabolic reprogramming. SIGNIFICANCE: This study utilized LC-MS/MS to systematically profile the proteomic, phosphoproteomic, and metabolomic characteristics of MIBC, NMIBC, and adjacent noncancerous tissues, with the aim of identifying key molecules and metabolites driving bladder cancer progression. Our findings indicate that aberrant phosphorylation of regulatory proteins such as SLC4A7 and MYO9B may play a critical role in mediating the invasive phenotype of MIBC. In parallel, the upregulation of CPT2 and its associated metabolites (e.g., palmitic acid) suggests that lipid metabolic reprogramming, including enhanced β-oxidation and membrane phospholipid synthesis, may contribute to the malignant transition from NMIBC to MIBC. Overall, this study not only reveals potential molecules and metabolites driving bladder cancer progression but also provides a valuable reference for further exploration of pathways associated with bladder cancer invasiveness.
Comparative quantitative proteomics of tumoral and peritumoral tissues for distinguishing human glioblastoma from low-grade astrocytoma.
Xiong Z, Li C, Han Q … +3 more , Su Y, Cheng L, Zeng HL
J Proteomics · 2026 Jan · PMID 41161534 · Publisher ↗
Glioblastoma multiforme (GBM) and low-grade astrocytoma (LGA) are diffuse gliomas with distinct biological features and prognoses. However, the molecular mechanisms driving their differences are not fully understood. In...
Glioblastoma multiforme (GBM) and low-grade astrocytoma (LGA) are diffuse gliomas with distinct biological features and prognoses. However, the molecular mechanisms driving their differences are not fully understood. In this study, we performed a multi-dataset analysis integrating in-house quantitative proteomics data with high-quality external datasets to identify GBM-specific proteomic alterations between tumoral and peritumoral tissues relative to LGA. Our analysis revealed more pronounced proteomic differences between intra- and peritumoral tissues in GBM than in LGA. Proteins specifically dysregulated in GBM were predominantly linked to upregulated RNA splicing and spliceosome signaling. Through multi-dataset integration, we identified 73 GBM-specific upregulated proteins enriched in processes such as transcriptional regulation, hypoxia and necrosis, cytoskeleton organization, extracellular matrix remodeling, and immune response. Conversely, the 129 GBM-specific downregulated proteins were mainly involved in tumor suppression, G-protein signaling, calcium signaling, and neuronal gap junctions. Using these signature proteins, we developed a risk model based on CDK2, HDAC1, IGFBP2, SLC6A1, and TNR, which significantly predicted overall survival in glioma patients. This study delineates the proteomic landscape of GBM in comparison to LGA and offers a valuable resource for future mechanistic and clinical investigations. SIGNIFICANCE: Diffuse gliomas are a heterogeneous brain tumor that include both low-grade and high-grade variants, each characterized by distinct morphological and biological features. Glioblastoma multiforme (GBM) is the most common primary high-grade and malignant brain tumor, with a median survival of less than 15 months despite aggressive treatment, including surgery, radiotherapy, and chemotherapy. In contrast, low-grade astrocytoma (LGA) exhibits indolent growth and a less aggressive clinical course, resulting in significantly longer patient survival compared to GBM. The molecular mechanisms underlying the biological differences between LGA and GBM are incompletely understood, and there is an urgent need for new molecular biomarkers to enhance diagnosis and therapeutic options. In this study, we conducted a comprehensive multi-dataset analysis by integrating our in-house quantitative proteomics data with several high-quality external datasets. We analyzed tumor and peritumoral tissue samples from human GBM and LGA, and further identified the GBM-specifically regulated proteomic signatures and signaling pathways, which is crucial for understanding the molecular mechanisms driving the aggressive behavior of GBM and could serve as a foundation for developing novel diagnostic biomarkers and therapeutic targets. Future research should focus on validating these GBM-specific proteins in larger cohorts and exploring their functional roles in GBM progression. Additionally, integrating multi-omics data (e.g., genomics, transcriptomics, and metabolomics) with proteomics could provide a more comprehensive understanding of the molecular mechanisms underlying GBM.
Advancing post-genomics research in Mexico: Opportunities and strategies for the next decade.
Winkler R, Moreno-Ulloa A
J Proteomics · 2026 Jan · PMID 41138909 · Publisher ↗
The Mexican Proteomics Society (SMP) is the oldest proteomics organization in Latin America (LATAM), dedicated to advancing research in proteomics, metabolomics, and mass spectrometry (MS). As a non-profit, SMP organizes...
The Mexican Proteomics Society (SMP) is the oldest proteomics organization in Latin America (LATAM), dedicated to advancing research in proteomics, metabolomics, and mass spectrometry (MS). As a non-profit, SMP organizes symposia and academic events, promoting collaboration and education. Since its founding in 2005, SMP has held biennial meetings and workshops in proteomics and metabolomics, invited international experts and fostered a multidisciplinary community. In this perspective manuscript, we provide a brief overview of the SMP, highlighting positive and negative aspects related to the economy, funding, infrastructure, technology and innovation, agriculture, health, and other fields. We also offer an overview of the MS equipment-critical infrastructure for omics research development-available within research centers and universities nationwide. Moreover, we present statistics on the contributions of Mexican-affiliated researchers to published research articles across various omics disciplines comparing Mexico's output to that of other LATAM countries. We believe that with this perspective the community will capture the role of the SMP in the development of omics research in Mexico, what is the country's contribution in the field, what are the country needs and how the new SMP board will contribute to advancing the field. SIGNIFICANCE: Omics-based societies play a crucial role in education, scientific development, and fostering multi-institutional collaborations. Although there are various societies worldwide focused on mass spectrometry-based omics, such as proteomics and metabolomics, their presence and impact on academia can be difficult to track. Therefore, in this manuscript, we provide a brief overview of the Mexican Proteomics Society (SMP), highlighting its contributions to omics research, the opportunities envisioned by the 2025-elected SMP leadership to advance omics science nationwide, and insights into the strategic directions for the coming decade.
Comparative performance of Scribe and database search engines in metaproteomic profiling of a ground-truth microbiome dataset.
Rajczewski AT, Mehta S, Wagner R … +9 more , Gabriel W, Johnson J, Do K, Vintila S, Wilhelm M, Kleiner M, Searle BC, Griffin TJ, Jagtap PD
J Proteomics · 2026 Jan · PMID 41130385 · Full text
Mass spectrometry-based metaproteomics, the identification and quantification of thousands of proteins expressed by complex microbial communities, has become pivotal for unraveling functional interactions within microbio...
Mass spectrometry-based metaproteomics, the identification and quantification of thousands of proteins expressed by complex microbial communities, has become pivotal for unraveling functional interactions within microbiomes. However, metaproteomics data analysis encounters many challenges, including the search of tandem mass spectra against a protein sequence database using proteomics database search algorithms. We used a ground-truth dataset to assess a spectral library searching method against established database searching approaches. Mass spectrometry data collected by data-dependent acquisition (DDA-MS) was analyzed using database searching approaches (MaxQuant and FragPipe), as well as using Scribe with Prosit predicted spectral libraries. We used FASTA databases that included protein sequences from microbial species present in the ground-truth dataset along with background protein sequences, to estimate error rates and assess the effects on detection, peptide-spectral match quality, and quantification. Using the Scribe search engine resulted in more proteins detected at a 1 % false discovery rate (FDR) compared to MaxQuant or FragPipe, while FragPipe detected more peptides verified by PepQuery. Scribe was able to detect more low-abundance proteins in the microbiome dataset and was more accurate in quantifying the microbial community composition. This research provides insights and guidance for metaproteomics researchers aiming to optimize results in their analysis of DDA-MS data. SIGNIFICANCE OF THE STUDY: Metaproteomics requires a balance between high numbers of peptide and protein identification and confidence in the accuracy of the identifications made. We demonstrate the utility of the Scribe search engine for metaproteomics applications, as it was found to detect low-abundance proteins with accurate quantitation than other DDA-MS search engines. This tool has great utility for both novel metaproteomics studies as well as hypothesis-generating experiments using previously acquired open source proteomics raw data.
Proteomic exploration of the recently Re-classified forest cobra Naja species and the potential cytotoxic activity in cancer cell lines.
Motsa P, Muller B, Motadi LR … +2 more , Offor BC, Piater LA
J Proteomics · 2026 Jan · PMID 41115607 · Publisher ↗
The forest cobra (Naja melanoleuca) species represents one of the most widespread medically important elapid snakes across Africa. The immense tissue-damaging effect of cobra venoms is attributed to the cytotoxins (CTX),...
The forest cobra (Naja melanoleuca) species represents one of the most widespread medically important elapid snakes across Africa. The immense tissue-damaging effect of cobra venoms is attributed to the cytotoxins (CTX), which predominate in virtually all cobra venoms. In this study a bottom-up venomic approach was followed for deciphering the composition of the N. melanoleuca, N. subfulva, and N. savannula venom proteomes. The results revealed complex venoms that constituted predominantly of proteins belonging to the three-finger toxins (3FTxs) followed by phospholipase A (PLAs) and snake venom metalloproteinases (SVMPs). The cytotoxicity and selectivity of the crude venoms and fractions were evaluated against cancer and normal cell lines. The crude N. melanoleuca venom sample demonstrated weak/low cytotoxic activity across the different cell lines as corroborated by SI values of less than 2, thus highlighting its limited application against these cancer cells, while the N. subfulva venom demonstrated its highest cytotoxic activity against the HeLa cancer cell line with a moderate selectivity index of 2.04. It is crucial to emphasize that these findings are still in the preliminary stages, primarily based on in vitro studies, and there remains a significant gap to bridge before any therapeutic applications can be considered. SIGNIFICANCE: Biological significance: African forest cobra venom is a rich source of bioactive compounds such as cytotoxins, which cause tissue necrosis and descending paralysis. However, the venom has also been identified as a potential source of therapeutic agents, including anticancer agents. In this study, we evaluate the anticancer effects of the N. melanoleuca, N. subfulva, and N. savannula venoms and their fractions against the selected cell lines. The 3FTxs and PLAs, which are the most abundant protein families in the venoms, are predominantly responsible for the cytotoxic effects. In conclusion, this research study highlights the important role of forest cobra venoms as potential resources that researchers can further exploit to investigate the molecules responsible for the anticancer effect and investigate their mechanisms of action.
Hypersensitivity and L-Asparaginase: A structural analysis of the interaction with HLA-DRB1*07:01.
de Lima JY, de Castro Andreassa E, Santos MDM … +2 more , Carvalho PC, de Souza TACB
J Proteomics · 2026 Jan · PMID 41110826 · Publisher ↗
L-Asparaginase derived from Escherichia coli (EcA) is extensively employed in the treatment of acute lymphoblastic leukemia (ALL); however, immunogenic responses frequently result in therapeutic failure. This study aims...
L-Asparaginase derived from Escherichia coli (EcA) is extensively employed in the treatment of acute lymphoblastic leukemia (ALL); however, immunogenic responses frequently result in therapeutic failure. This study aims to identify residues involved in EcA immunogenicity and to propose structural modifications that may reduce antigenic potential or facilitate the development of targeted therapeutic strategies to inhibit such interactions. To achieve this, we investigate the sites of interaction of HLA-DRB1*07:01 allele and EcA by crosslinking mass spectrometry (XL-MS) using recombinantly expressed proteins. Circular dichroism (CD) spectroscopy confirmed the proper folding of the expressed enzymes, ensuring their structural integrity. Additionally, XL-MS allowed us to experimentally determine the structure of HLA-DRB1*07:01, which was previously unknown. Structural analysis and sequence alignment revealed immunogenic epitopes on the enzyme surface, particularly near the active site and at K288, a highly reactive residue. Our findings highlight key immunogenic sites on EcA, particularly residues 53-58, 283-289, and K288, which represent promising targets for reducing immunogenicity while preserving enzymatic function. These proposed modifications should be experimentally validated to ensure enzyme activity is maintained while effectively mitigating immune responses. SIGNIFICANCE: Hypersensitivity to Escherichia coli-derived L-asparaginase (EcA) remains one of the main challenges in the treatment of acute lymphoblastic leukemia (ALL), often forcing patients to interrupt a therapy that could be lifesaving. In this study, we mapped at the structural level how EcA interacts with the HLA-DRB1*07:01 allele, one of the main genetic factors associated with these adverse reactions. By identifying specific regions of the enzyme that trigger the immune response, especially residue K288, we offer a foundation for targeted modifications that may reduce immunogenicity without affecting enzymatic activity. These findings provide a concrete path toward developing safer EcA variants and bring us closer to more effective and personalized treatments.
Enhancing glycopeptide annotation and glycan localization using electron activated dissociation through a multiplexed parallel reaction monitoring design of experiments.
Salim H, Almey R, Pont L … +3 more , Benavente F, Dhaenens M, Giménez E
J Proteomics · 2026 Jan · PMID 41106808 · Publisher ↗
We present an optimized electron activated dissociation (EAD) methodology, based on hot electron capture dissociation, for liquid chromatography-tandem mass spectrometry characterization of N- and O-glycopeptides, using...
We present an optimized electron activated dissociation (EAD) methodology, based on hot electron capture dissociation, for liquid chromatography-tandem mass spectrometry characterization of N- and O-glycopeptides, using recombinant human erythropoietin as a model glycoprotein. Applying a full factorial design of experiments (DoE) approach, we first optimized LC-MS parameters (i.e., ion spray voltage, ion source temperature, and active gradient time) to enhance glycopeptide ionization efficiency while reducing in-source fragmentation. A second DoE was then applied to fine-tune EAD-specific parameters. Multiplexed parallel reaction monitoring was performed to efficiently and comprehensively optimize the electron beam current, reaction time, and electron kinetic energy of the EAD set-up. Finally, the optimized EAD parameters, initially determined using one glycoform per glycopeptide, were successfully applied in data-dependent acquisition mode to detect the overall glycoform composition of each studied glycopeptide. Byonic, Fragpipe and Mascot softwares, and several peak picking softwares were used to evaluate the potential of our optimized EAD set-up, and compare with collision induced dissociation (CID). The results confirmed that EAD improved confidence in glycan localization, while CID enabled the identification of a greater number of glycoforms but with less confident glycan assignments. SIGNIFICANCE: The current manuscript introduces a novel and efficient optimization strategy for electron activated dissociation (EAD) parameters, based on hot electron capture dissociation, using a synergistic combination of design of experiments (DoE) and multiplexed parallel reaction monitoring (PRM) on the ZenoTOF 7600 instrument. The PRM-DoE approach enables rapid and systematic optimization of LC-MS conditions and simultaneous evaluation of key EAD parameters across target glycopeptide glycoforms in a drastically reduced number of experimental runs, significantly saving experimental time and resources. This approach provides the glycoproteomics field with a comprehensive method for achieving improved glycan site localization confidence over conventional collision induced dissociation, as demonstrated by applying a data-dependent acquisition method. The proposed strategy advances the analytical toolkit for LC-MS/MS glycoprotein analysis and potentially other post-translational modifications.
SequenceAssembler: A tool for protein sequence assembly from mass spectrometry data.
Calomeno CVAQ, Brum H, Brant RSC … +6 more , Santos MDM, Muñoz-Gómez LM, da Costa Neves-Ferreira AG, Valente RH, Batista M, Carvalho PC
J Proteomics · 2026 Jan · PMID 41072654 · Publisher ↗
Accurate sequencing of complete proteoforms-that is, all molecular variants generated by post-translational modification or sequence change-is essential for advancing our understanding of biological systems, guiding biop...
Accurate sequencing of complete proteoforms-that is, all molecular variants generated by post-translational modification or sequence change-is essential for advancing our understanding of biological systems, guiding biopharmaceutical development, and enabling new biotechnological applications. We present SequenceAssembler (SA), a user-friendly software post-identification tool designed to assemble full-length protein sequences by integrating both peptide-spectrum matching (PSM) and de novo sequencing data. SA is compatible with widely used proteomics tools, including Novor Cloud, PEAKS Studio, and PatternLab for Proteomics, from which it efficiently aggregates input data. Our software offers an accessible and intuitive interface, enhancing its usability. We demonstrated SA's effectiveness by analyzing bovine serum albumin and the monoclonal antibody trastuzumab, each subjected to multiple enzymatic digestions followed by high-resolution mass spectrometry. The results were consistent with those of established tools like Stitch, with performance varying depending on threshold parameters. Notably, SA distinguishes itself through its user-friendly graphical interface, one-click installation, and streamlined workflow, making it an attractive solution for a wide range of proteomics researchers. The software is freely available for academic use at http://patternlabforproteomics.org/sa. SIGNIFICANCE: SequenceAssembler fills a critical gap in proteomics by unifying peptide-spectrum matching and de novo sequencing into a single assembly platform, enabling reconstruction of full-length proteins. The intuitive graphical interface lowers barriers to adoption in core laboratories, minimizing manual steps and enhancing reproducibility. By streamlining sequence assembly workflows, SequenceAssembler empowers rapid protein sequencing to broad protein research applications.
Two decades of the Mexican Proteomics Society: the history and evolution of proteomics and metabolomics in Mexico.
Huerta-Ocampo JÁ, Winkler R, Moreno-Ulloa A … +1 more , Encarnación-Guevara S
J Proteomics · 2026 Jan · PMID 41067688 · Publisher ↗
The establishment of the Mexican Proteomics Society (Sociedad Mexicana de Proteómica, SMP) has provided a platform for researchers in proteomics and metabolomics to share ideas and collaborate on research. This initiativ...
The establishment of the Mexican Proteomics Society (Sociedad Mexicana de Proteómica, SMP) has provided a platform for researchers in proteomics and metabolomics to share ideas and collaborate on research. This initiative promotes scientific knowledge in México and facilitates the integration of national researchers into international projects. Founded twenty years ago, the SMP is the oldest proteomics society in Latin America. It is a non-profit organization that advocates for research in proteomics, metabolomics, and MS within the country. This review seeks to trace the development of the field by highlighting the contributions of researchers, laboratories, institutions, and organizations such as the SMP that have played a role in establishing and advancing this science in México. However, we are an enthusiastic and diverse community that, through imagination, collaboration, and determination, will continue to advance proteomics, metabolomics, and related fields in México. SIGNIFICANCE: The Mexican Proteomics Society (Sociedad Mexicana de Proteómica, SMP) was established 20 years ago to foster proteomics in México. The organization of a biannual symposium has since evolved into a reliable academic event in proteomics, metabolomics, and mass spectrometry (MS), where international experts present their discoveries to our community, and vendors present their latest products. We encourage students and professionals to learn through hands-on workshops on protein electrophoresis, proteomics, metabolomics, and open-access computer tools for analyzing omics data. Additionally, SMP has hosted the Ibero-American Symposium on Mass Spectrometry, the Pan-American Human Proteome Organization (Pan-HUPO) meeting, and most recently, the Human Proteome Organization World Congress (HUPO-2022). This commentary does not offer a comprehensive overview of proteomics in México; instead, it follows its evolution by emphasizing the contributions of researchers, laboratories, and institutions that have played a significant role in establishing and expanding this field in México. It also endeavors to offer a comprehensive understanding of the current state of proteomics in México. The challenges, opportunities, and perspectives related to the SMP's role in advancing proteomics in the country will be discussed in a parallel commentary included in this special issue entitled "Advancing post-genomics research in México: Opportunities and strategies for the next decade".
Antiobesogenic effect of hydrolysates and peptide fractions of porcine collagen after in vitro gastrointestinal digestion.
González-Noriega JA, Valenzuela-Melendres M, Hernández-Mendoza A … +9 more , Astiazarán-García H, Islava-Lagarda T, Tortoledo-Ortiz O, de la Garza AL, Gutierrez-Pacheco SL, Alvarez-Armenta A, Ríos-Castro E, Huerta-Ocampo JA, Peña-Ramos EA
J Proteomics · 2026 Jan · PMID 41067687 · Publisher ↗
The present study evaluated the angiotensin-converting enzyme inhibitory activity (ACEi) of a porcine skin collagen hydrolysate (PSCH) and its peptide fractions before and after a simulation of gastrointestinal digestion...
The present study evaluated the angiotensin-converting enzyme inhibitory activity (ACEi) of a porcine skin collagen hydrolysate (PSCH) and its peptide fractions before and after a simulation of gastrointestinal digestion and their ability to reduce lipid accumulation in adipocytes (LAA). Before digestion, peptide fractions <1 kDa (PF4) had the highest (p < 0.05) ACEia (85.45 %), followed by PSCH (53.54 %). Post-digestion, PF4 (IC: 124.49 μg/mL) decreased its activity; thus, DPF4 (digested PF4) had an ACE IC of 204.56 μg/mL, while fraction <1 kDa from digested hydrolysate (FDH) showed the lowest activity (IC: 313.81 μg/mL). Peptides were identified by LC-MS/MS and homology database search and aligned to peptides widely recognized as ACE inhibitors. Nine peptides were identified as potential ACE inhibitors through docking with the active site cavity of this enzyme (mainly GAXGPXGPQ and GPPGPA), and interaction with Zn (II). Subsequently, adding 600 μg/mL of FDH in preadipocytes reduced 71 % LAA, while DPF4 was less effective (45.5 % reduction). The addition of digested peptide fractions into differentiated adipocytes had a similar (p > 0.05) reduction of LAA of 22-39 %. Therefore, regardless of their differences as ACE inhibitors, digested FDH and DPF4 have a similar potential as anti-obesogenic adjuvants. SIGNIFICANCE: In this study, we evaluated the angiotensin-converting enzyme inhibitory activity of a porcine skin collagen hydrolysate and its peptide fractions before and after a simulation of gastrointestinal digestion and their ability to reduce lipid accumulation in adipocytes. Peptides were identified by LC-MS/MS and homology database search and aligned to peptides widely recognized as ACE inhibitors. Nine peptides were identified as potential ACE inhibitors through docking with the active site cavity of this enzyme (mainly GAXGPXGPQ and GPPGPA), and interaction with Zn (II). Subsequently, adding digested peptide fractions into differentiated adipocytes resulted in a reduction of lipid accumulation in adipocytes.
Interspecific and intraspecific variability in venom composition of Naja naja and Naja kaouthia (Reptilia: Elapidae) populations from different habitats in Bangladesh.
Chowdhury MAW, Müller J, Al Haidar IK … +9 more , Rahman MM, Noman M, Ghose A, Sayeed AA, Amin R, Sanz L, Faiz MA, Kuch U, Calvete JJ
J Proteomics · 2026 Jan · PMID 41052712 · Publisher ↗
The spectacled cobra (Naja naja) and monocled cobra (Naja kaouthia), widespread venomous snakes in South and Southeast Asia, occur in diverse habitats and cause neurotoxic envenoming. Despite reported venom variability o...
The spectacled cobra (Naja naja) and monocled cobra (Naja kaouthia), widespread venomous snakes in South and Southeast Asia, occur in diverse habitats and cause neurotoxic envenoming. Despite reported venom variability of these two cobras across their range, no comparative study has been conducted from the interconnected but distinct habitats of Bangladesh. Using venomics and antivenomics, we analysed 26 individual venom samples of N. kaouthia and 17 of N. naja from Bangladesh across age groups and locations, respectively. Significant interspecific and intraspecific venom variability was observed, with geographically connected populations showing minimal divergence, while isolated populations (separated by river barriers or distinct ecosystems) exhibited pronounced compositional differences. Ontogenetic differences in venom composition between adult N. kaouthia and their juvenile offspring were detected. Commercially available Incepta polyvalent antivenom, produced against India's "Big Four" (including southern Indian N. naja), demonstrated poor efficacy against Bangladeshi cobra venoms. Collectively, our analyses demonstrate the existence of multi-dimensional variation in cobra venoms of Bangladesh that is influenced by biotic and abiotic factors. We emphasize the urgent need for region-specific antivenoms incorporating venom from ecologically distinct populations and age groups of both species across South Asia to improve snakebite treatment efficacy as well pre-clinical assessments to address biogeographic and ontogenetic venom diversity. SIGNIFICANCE: Snakebite envenoming is a major neglected tropical disease and a leading occupational health hazard especially for rural populations in many low-and middle-income countries. As differences in snake venom composition between and within species can greatly affect the clinical course of envenoming and the efficacy of treatment, detailed knowledge of this variability is highly important for public health planning and the development of better antidotes. In Bangladesh, the monocled cobra (Naja kaouthia) and the spectacled cobra (Naja naja) belong to the medically most important and most widely distributed common snake species, but data on the variability of their venoms in this country has been limited and its relation to climatic and other environmental factors remained unexplored. Here we report on the analysis of 43 individual venom samples from 26 N. kaouthia and 17 N. naja from different age groups and geographical localities in Bangladesh, using venomics and antivenomics methods. Our findings show that the venoms of these cobras are highly diverse qualitatively and quantitatively, with significant inter- and intraspecific, geographic and ontogenetic variability and differences in their reactivity with a commercial antivenom. The observed geographical variability appears to be influenced by climatic and other environmental variables of different habitats in Bangladesh. When designing improved antivenoms, geographically appropriate and more diverse venom samples, also from different age groups of the snakes, should be included to cover this variability and ensure that the clinically significant toxins of all cobra venom varieties in Bangladesh are well neutralized by the antivenoms.
Integration of proteomic and transcriptomic data of the venom and venom gland from Tityus jaimei.
Escobar A, Salazar MH, Hernández-Ortiz M … +5 more , Clement H, Encarnación-Guevara S, Cleghorn J, Acosta H, Corzo G
J Proteomics · 2026 Jan · PMID 41046910 · Publisher ↗
This work presents a comprehensive transcriptomic and proteomic analysis of the venom gland and venom of Tityus jaimei, a recently described scorpion species of medical relevance in Panama and Costa Rica. High-throughput...
This work presents a comprehensive transcriptomic and proteomic analysis of the venom gland and venom of Tityus jaimei, a recently described scorpion species of medical relevance in Panama and Costa Rica. High-throughput RNA sequencing (RNA-seq) and tandem mass spectrometry (MS/MS) enabled the identification of a diverse repertoire of venom proteins. Notably, this is the first report of proteins belonging to the nucleotide pyrophosphatase/phosphodiesterase and knottins families in the venom proteome of a scorpion from the genus Tityus. In addition, several known venom protein families were identified, including hyaluronidases, voltage-gated sodium and potassium channel toxins, lipolysis-activating peptides (LVPs), cysteine-rich secretory proteins (CRISPs), metalloproteinases, peptidylglycine alpha-hydroxylating monooxygenases (PHMs), serine proteases, alpha-amylases, single insulin-like growth factor-binding domain proteins, non-disulfide-bridged peptides (NDBPs), chitinases, cyclotide trypsin inhibitors, and calcin-like peptides. The identification of 16 distinct families in the venom of Tityus jaimei offers novel insights into its composition and the diversity of Tityus venoms in Central America. Finally, the use of IA to protein domain search for protein annotation. SIGNIFICANCE T JAIMEI: Here a comprehensive transcriptomic and proteomic analysis of the venom gland and venom of Tityus jaimei, a recently described scorpion species of medical relevance in Panama and Costa Rica, is presented. Nucleotide pyrophosphatase/phosphodiesterase and knottins families in the venom proteome of a scorpion from the genus Tityus are for the first time reported. Sixteen distinct protein families in the venom of Tityus jaimei were found, and they offer novel insights into its composition and the diversity of Tityus venoms in Central America.
Extruded Limnospira platensis with enzyme supplementation shifts the broiler muscle proteome toward enhanced energy metabolism pathways.
Spínola MP, Maslov DR, Rubić I … +5 more , da Costa MM, Mrljak V, Lordelo M, de Almeida AM, Prates JAM
J Proteomics · 2026 Jan · PMID 41033654 · Publisher ↗
Limnospira platensis (Spirulina) is known for its nutritional and bioactive profile, but its high-level dietary inclusion effects in broilers, particularly post-extrusion and enzyme pre-treatment, remain underexplored. W...
Limnospira platensis (Spirulina) is known for its nutritional and bioactive profile, but its high-level dietary inclusion effects in broilers, particularly post-extrusion and enzyme pre-treatment, remain underexplored. We investigated how 15 % L. platensis raw (MA), extruded (MAE) or extruded with pancreatin (0.20 %) and lysozyme (0.01 %) (MAEM) affects the pectoralis major proteome of Ross 308 broilers. Birds were fed until day 35, then muscle proteins were prepared by filter-aided sample preparation, TMT 6-plex labelling and analysed by LC-MS/MS. Statistical analysis identified 26 differentially abundant proteins (p < 0.05, ≥ 2 peptides). MAEM samples clustered separately, showing increased abundance of NDUFA10 (Complex I; + 1.30-fold), COX5B (Complex IV; + 1.25-fold) and glycogen phosphorylase (+ 1.40-fold). Enrichment analysis revealed up-regulation of ATP synthesis, oxidative phosphorylation and glycogen catabolism in L. platensis groups, whereas control diets featured proteins linked to fatty-acid β-oxidation and myofibrillar assembly. These results indicate that extrusion combined with enzyme treatment enhances nutrient bioavailability and shifts the broiler muscle proteome toward energy-metabolism pathways without compromising performance. Data are available via ProteomeXchange (PXD064230). SIGNIFICANCE: The incorporation of Spirulina (Limnospira platensis) as a sustainable alternative to conventional feed ingredients is gaining attention in poultry nutrition. However, its specific effects on broiler's muscle proteome, as well as the impact of higher Spirulina inclusion levels on animal performance, remain largely unexplored. Herein, we investigated how extruded L. platensis, with and without enzyme supplementation, influences muscle protein expression. Results revealed a metabolic shift toward enhanced mitochondrial ATP production and glycogen metabolism when L. platensis was incorporated into the diets, suggesting improved energy efficiency and nutrient utilisation. These findings provide valuable insight into the biological mechanisms underlying muscle development in broilers fed microalgae-based diets. More broadly, they highlight the potential of combining pre-treated microalga ingredients as a strategy to optimise animal performance and health in the framework of poultry production.
Molecular signature of early obesity-associated insulin resistance: Adipocyte-derived extracellular vesicle proteins reveal stage-specific candidates for metabolic dysfunction.
Delgadillo-Velázquez J, Bojórquez-Velázquez E, Ruiz-May E … +5 more , Carvajal-Millan E, Aguirre-García M, Alday-Noriega E, Huerta-Ocampo JÁ, Astiazaran-Garcia H
J Proteomics · 2026 Jan · PMID 41033653 · Publisher ↗
Visceral obesity is closely related to insulin resistance (IR), a key process in developing metabolic diseases. Adipocyte-derived extracellular vesicles (AdEVs) have emerged as mediators of intercellular communication, c...
Visceral obesity is closely related to insulin resistance (IR), a key process in developing metabolic diseases. Adipocyte-derived extracellular vesicles (AdEVs) have emerged as mediators of intercellular communication, carrying signals reflecting adipose tissue's functional state. This study aimed to perform a comparative proteomic analysis of AdEVs to propose a molecular fingerprint of specific biomarker candidates for IR in early-onset obesity. AdEVs were isolated from epididymal adipocytes of 16-week-old male Wistar rats on a high-fat diet (HFD) and controls and analyzed by mass spectrometry coupled to a multi-software protein identification bioinformatics strategy. For relative quantification using the label-free method, more than 1200 proteins were identified, with 431 being overrepresented and unique to HFD, associated explicitly with energy metabolism, cellular stress, and insulin signaling. Based on biological plausibility, and/or the best log2FC and p-value scores, six proteins were proposed as part of the IR molecular fingerprint: Atp5f1b, Anxa6, Myo1c, GLUT4, Anxa5, and Aoc3. Phosphoproteomic analysis revealed key modifications in phosphorylated proteins such as CaATPase (S663), PLIN (S130), and PPM1H (S260,265). The results suggest that AdEVs reflect early mitochondrial alterations related to IR, which could be employed as potential non-invasive biomarker candidates for metabolic dysfunction and follow-up in early overweight or obesity. Significance In this study, we demonstrate that adipocyte-derived extracellular vesicles (AdEVs) encapsulate a stage-resolved molecular signature that reflects key pathophysiological events underlying the early development of insulin resistance in obesity. These vesicles carry proteins linked to lipotoxicity, mitochondrial and endoplasmic reticulum stress, and impaired vesicular trafficking, offering mechanistic insight into how local adipocyte dysfunction may trigger systemic metabolic impairment. This EV-based proteomic fingerprint advances our understanding of insulin resistance pathogenesis and identifies potential biomarker candidates for early metabolic risk stratification.
Comparative proteomic analysis of residual proteins in waterlogged ancient leather.
Tang L, Yang H, Wu Z … +3 more , Bao L, Zhou Y, Wang H
J Proteomics · 2026 Jan · PMID 40992725 · Publisher ↗
Leather artifacts hold significant historical and cultural value in human civilization. During long-term preservation, ancient relics, especially waterlogged leather artifacts, are susceptible to protein degradation. The...
Leather artifacts hold significant historical and cultural value in human civilization. During long-term preservation, ancient relics, especially waterlogged leather artifacts, are susceptible to protein degradation. Therefore, analyses of the structure and protein composition of these ancient relics are crucial for their effective conservation. However, comprehensive research in this field is scarce and urgently needed. In this study, systematic investigations of the structures of fresh vegetable-tanned leather, dried leather artifacts, and waterlogged leather artifacts were performed from multiple perspectives. Compared with fresh vegetable-tanned leather and dry leather artifacts, the deterioration of waterlogged leather artifacts resulted in a darkened color, increased brittleness, and reduced fiber structure. Infrared analyses revealed that the characteristic peaks of the amide II and III bands were nearly absent in waterlogged leather artifacts. The species of the leather artifacts were analyzed using enzyme-linked immunosorbent assay (ELISA). Furthermore, comparative proteomic analysis revealed a markedly reduced repertoire of protein species in waterlogged leather artifacts compared with fresh vegetable-tanned leather. In particular, the number of peptides derived from type I collagen and other structural proteins was substantially diminished. This loss of collagen- and structure-related peptides, together with extensive fiber disintegration, underlies the pronounced morphological deterioration observed in waterlogged leather. By integrating species identification through ELISA with proteomic profiling, we establish a strategy that enables rapid, sensitive, and specific characterization of leather proteins. SIGNIFICANCE: This study integrated stereomicroscopy, scanning electron microscopy (SEM), and fourier transform infrared spectroscopy (FTIR) to systematically characterize morphological and microstructural differences between fresh vegetable-tanned leather and archaeological waterlogged leather artifacts. To further unravel residual proteins, comparative proteomic profiling was implemented to identify compositional shifts in collagenous proteins resulting from prolonged waterlogged burial conditions. A multidisciplinary approach was used to assess the characteristics of waterlogged leather artifacts.
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