J. Proteome Res. [JOURNAL]
Sun
200 papers
MS-Based Crevicular Fluid Proteomics for the Study of Periodontal and Peri-Implant Conditions: A Systematic Review.
Souza LPSS, Dias DR, Cesar GPS … +3 more , Bianco DA, Araújo MG, Matarazzo F
J Proteome Res · 2026 Jul · PMID 42339612 · Publisher ↗
This systematic review aimed to evaluate the current literature on mass spectrometry (MS)-based proteomic analysis of the crevicular fluid in different periodontal and peri-implant conditions, and to summarize methodolog...
This systematic review aimed to evaluate the current literature on mass spectrometry (MS)-based proteomic analysis of the crevicular fluid in different periodontal and peri-implant conditions, and to summarize methodological differences among studies. A search of electronic databases was conducted and clinical studies using MS-based proteomics in gingival (GCF) and/or peri-implant crevicular fluid (PICF) were considered for inclusion. The findings were synthesized and methodological variations described. A modified QUADOMICS tool was applied for risk of bias assessment. Thirteen studies; five longitudinal and eight cross-sectional were analyzed. Patients ranged from 10 to 190, with 42 to 3070 human proteins identified. Sample preparation and preanalytical procedures differed among studies. Protein identification, characterization and quantification were conducted using different algorithms and computer software against different databases. Different strategies were used to select distinctive proteins. Six studies attempted at biomarker development using different protein selection and validation criteria. While six studies presented moderate quality, seven were considered to be low quality. The present findings emphasize the need for methodological harmonization, including standardized protocols for GCF/PICF collection, harmonized proteomic workflows, multicenter longitudinal validation studies, and targeted mass spectrometry approaches for biomarker verification before they can be translated into the clinical practice.
Quantitative and Site-Specific Profiling of Protein O-GlcNAcylation in Carboplatin-Treated Cancer Cells.
Xie Q, Zhang C, Chen G … +2 more , Li X, Hao Y
J Proteome Res · 2026 Jun · PMID 42333547 · Publisher ↗
Platinum (Pt)-based chemotherapeutics are widely used for cancer treatment in clinical trials. It has been reported that protein O-linked β--acetylglucosamine (O-GlcNAc) modification occurs on several important proteins...
Platinum (Pt)-based chemotherapeutics are widely used for cancer treatment in clinical trials. It has been reported that protein O-linked β--acetylglucosamine (O-GlcNAc) modification occurs on several important proteins implicated in regulating cancer cell response to Pt drugs. However, the O-GlcNAc proteomic landscape during this process remains poorly characterized. Herein, we report quantitative profiling of O-GlcNAcylation sites with carboplatin exposure, by using a chemoenzymatic labeling-assisted chemoproteomic approach. A total of 244 O-GlcNAcylated sites, many of which occur on essential genome stability regulators, are quantified. Furthermore, we discover that the cellular O-GlcNAc level is elevated upon carboplatin treatment and suppression of O-GlcNAcylation renders cancer cells more sensitive to carboplatin. These results establish a valuable resource for elucidating the functional role of O-GlcNAcylation in carboplatin response and suggest potential insights into cancer chemotherapy. The chemoproteomic strategy should be generally applicable for monitoring O-GlcNAc dynamic changes in various pharmacological processes.
High-Throughput Olink Proteomics Elucidates the Immuno-Neurological Landscape of Gastric Cancer.
Li X, Wang Q, Luo S … +5 more , Guo Z, Xu Y, Fu X, You F, Jiang Y
J Proteome Res · 2026 Jul · PMID 42329880 · Publisher ↗
Gastric cancer (GC) ranks as the third leading cause of cancer-related mortality globally. A comprehensive and precise proteomic study of GC tissues can yield detailed insights into its pathogenesis. This study employed...
Gastric cancer (GC) ranks as the third leading cause of cancer-related mortality globally. A comprehensive and precise proteomic study of GC tissues can yield detailed insights into its pathogenesis. This study employed the highly sensitive Olink technology to quantify the levels of 1034 selected proteins in tumor tissues, paired adjacent tissues, and normal tissues from Chinese GC patients. Through an examination of expression changing trends and differential expression across these tissue types, it was determined that the protein profile of tumor tissue exhibits distinct characteristics, whereas the protein profiles of adjacent and normal tissues are more similar. The 124 differentially expressed proteins (DEPs) are predominantly associated with inflammation, immunity, and neurology, with major contributions from protein families such as chemokines, interleukins, and CLECs. We also employed machine learning algorithms to identify potential biomarkers, including CCN4, FNDC1, and PGF. Furthermore, validation results obtained through transcriptome data and ELISA demonstrated a concordance with findings from Olink analysis. To the best of our knowledge, this study represents the inaugural proteomic investigation of GC tissue utilizing high-throughput Olink technology. It reveals distinctive proteomic characteristics at the tissue level and offers significant insights for the identification and validation of novel biomarkers.
Comprehensive Analysis of Proteomic Variations Influenced by Culture Conditions in Human Mesenchymal Stromal Cells.
Fukuta T, Tomioka R, Ueda H … +1 more , Kadota K
J Proteome Res · 2026 Jul · PMID 42322301 · Publisher ↗
Proteomics, a powerful approach allowing the broad analysis of protein expression levels in samples, has been used to characterize mesenchymal stromal cells (MSCs) used in regenerative medicine, focusing on the influence...
Proteomics, a powerful approach allowing the broad analysis of protein expression levels in samples, has been used to characterize mesenchymal stromal cells (MSCs) used in regenerative medicine, focusing on the influence of their tissue of origin, culture media, and passage number. However, the proteomic signatures arising from comprehensive alterations in culture conditions remain to be characterized. Here, we evaluated the effects of major culture parameters, including cell seeding density, detachment methods, media composition, and passage number, on both the cellular and supernatant proteomic profiles of human MSCs. Among the evaluated parameters, the 15-passage condition exerted the most significant impact on the cell samples, with the most significant proteome remodeling, including decreased DNA replication-related proteins and increased lipid metabolism-related proteins. Regarding the supernatant samples, significant differences were found between xeno-free media and serum-containing media, with serum-containing media showing higher secretion of the insulin growth factor-binding protein (IGFBP) family. Further, functional changes included reduction in thrombospondin-1, which is associated with MSC migration. These findings demonstrate that culture conditions significantly influence the characteristics of MSCs used in regenerative medicine, and that a wide proteomics evaluation of both the cells and supernatant is crucial for understanding these characteristics.
Quantitative Global Proteomics of Formalin-Fixed Paraffin-Embedded Tumors Identifies Dimethylated G3BP1 at Arginine 460 as a Robust Pharmacodynamic Biomarker of Methylthioadenosine Phosphorylase-Selective Protein Arginine Methyltransferase 5 Inhibition.
Tu A, Wiseman EJ, Sweet SM … +8 more , Urosevic J, Loizou J, Barnicle A, Richardson C, Abhishek S, Chain DC, Kim YJ, Chambers AG
J Proteome Res · 2026 Jul · PMID 42321016 · Publisher ↗
MTA-cooperative inhibition of protein arginine methyltransferase 5 (PRMT5) is synthetic lethal with methylthioadenosine phosphorylase (MTAP)-deficient cancers. PRMT5's enzymatic activity can be assessed by measuring symm...
MTA-cooperative inhibition of protein arginine methyltransferase 5 (PRMT5) is synthetic lethal with methylthioadenosine phosphorylase (MTAP)-deficient cancers. PRMT5's enzymatic activity can be assessed by measuring symmetric dimethylarginine (SDMA) modification levels of protein substrates. However, conventional assays that attempt to measure total SDMA levels lack the specificity to measure individual PRMT5 substrates, and thus potentially reduce selectivity and sensitivity. This study aims to identify and characterize specific DMA peptides that can serve as clinical pharmacodynamic (PD) biomarkers for PRMT5 inhibition in formalin-fixed paraffin-embedded solid tumors, leveraging data-independent acquisition-mass spectrometry (DIA-MS)-based global proteomics without additional DMA enrichment. We evaluated 145 DMA peptides in xenograft models treated by a novel MTAP-selective PRMT5 inhibitor, AZD3470. Arginine dimethylation of G3BP1 at residue R460 (G3BP1(R460)) was identified as the primary PD biomarker for PRMT5 inhibition due to its high abundance and significant post-treatment reduction that correlated with dose. The global proteomics assay with a limit of detection/quantification characterized the quantitative performance and allowed for confident detection of G3BP1(R460). Using this quantitative assay, more than 90% reduction in G3BP1(R460) modification at 100 mg/kg was reproducibly detected in MTAP-null xenograft models. Our findings suggested that the DIA-MS proteomics assay can provide high specificity and sensitivity in the detection of PRMT5 inhibition.
Integrated Proteomic Profiling of Whole-Cell and Multi-Post-Translational Modifications Unveils Regulatory Networks in Macrophage Inflammatory Responses.
Yuan G, Zhi L, Wang J … +7 more , Wang J, Zhu B, Han X, Liu J, Cai L, Jie H, Yan Z
J Proteome Res · 2026 Jul · PMID 42316966 · Publisher ↗
The RAW264.7/THP1 cells have been extensively employed as macrophage models in inflammation research. However, comprehensive comparisons of their expression profiles remain largely unexplored. In this study, we conducted...
The RAW264.7/THP1 cells have been extensively employed as macrophage models in inflammation research. However, comprehensive comparisons of their expression profiles remain largely unexplored. In this study, we conducted a systematic bioinformatics analysis to characterize the whole-cell proteome, phosphoproteome, acetylome, and ubiquitinome profiles of lipopolysaccharide-stimulated RAW264.7/THP1 cells. Through comparative temporal analysis of differentially regulated proteins (classified as rapid, persistent, or slow dysregulation patterns), we identified IGF2, COPZ1, and GTF2B, exhibiting persistent downregulation in both cell models. Additionally, we observed that nearly all dysregulated proteins within each modification type exhibited significant enrichment in the other two modification types, forming a highly interconnected protein-protein interaction network. Notably, VIMENTIN demonstrated significant downregulation across three modification types (phosphorylation at Ser56/214, acetylation at Lys235, and ubiquitination at Lys139), with coordinated downregulation observed in both cell lines. It was also shown that VIMENTIN mutation at Ser56, Lys235, and Lys139 dramatically reduces the expression of CDK1, which may help the inflammation response by averting mitotic catastrophe and changing the macrophage cell cycle. These findings provide valuable molecular insights into species-specific macrophage responses and establish an important reference data set for discovering novel inflammatory proteins and investigating macrophage-associated diseases using these experimental models. Notably, our work delineates vimentin-centered regulatory networks that may offer novel diagnostic biomarkers and therapeutic targets for inflammatory diseases.
Donor-Independent Metabolomics Enables Bloodstain Age Determination at Crime Scenes.
Nielsen KL, Lassen JK, M Løber IM … +7 more , Skovbo F, Frisch K, Czaja TP, Khakimov B, Engelsen SB, Johannsen M, Villesen P
J Proteome Res · 2026 Jul · PMID 42316882 · Publisher ↗
Determining when bloodstains were deposited remains an unsolved challenge in forensic science, limiting investigators' ability to reconstruct events and verify suspect timelines. Here, we develop a metabolomics-based app...
Determining when bloodstains were deposited remains an unsolved challenge in forensic science, limiting investigators' ability to reconstruct events and verify suspect timelines. Here, we develop a metabolomics-based approach combining liquid chromatography-mass spectrometry (LC-MS) with machine learning to estimate bloodstain age independent of donor-specific variation. Through untargeted analysis and degradation studies, we identified 51 time-dependent biomarkers and transformed their intensities into stable ratios that normalize for individual differences and blood volume. Using samples collected under controlled environmental conditions, we achieve high accuracy for forensically relevant timeframes with prediction errors of ∼7 h for fresh bloodstains and near-perfect classification of samples as recent (<60 h) or aged (>60 h). Validation on two independent data sets confirms strong performance under typical indoor conditions, while highlighting sensitivity to extreme environmental fluctuations. By addressing key biological and technical sources of variability that have hindered translation to practice, this study establishes a robust analytical framework for bloodstain age estimation. The approach offers a practical foundation for future operational implementation and has the potential to substantially improve forensic timeline reconstruction.
Seed Compositional Profiling of 21 Industrial Hemp Varieties and Comparative Proteomic Analysis of Wild and Cultivated L. Genotypes.
Tamang KR, Mooney BP, Mawhinney TP … +7 more , Asiamah J, Sharma S, Padyana S, Carson C, Koirala P, Mahdi S, Valliyodan B
J Proteome Res · 2026 Jul · PMID 42315114 · Publisher ↗
Industrial hemp is a nutritious crop with wide implications. We conducted a comprehensive study of amino acid, fatty acid, and sugar profiles, which have a profound impact on human nutrition and animal feed. We found tha...
Industrial hemp is a nutritious crop with wide implications. We conducted a comprehensive study of amino acid, fatty acid, and sugar profiles, which have a profound impact on human nutrition and animal feed. We found that variety significantly influences the nutritional profile of hemp. Furthermore, we found glutamic acid, arginine, and aspartic acid to be the primary amino acids; linoleic acid was the major fatty acid, and fructose and sucrose were the dominant sugars. Proteomic analysis identified 240 differential proteins (DEPs) in wild and cultivated dual-type varieties and 648 in wild and fiber-type hemp varieties. We found that all the varieties shared common proteins, indicating a strong seed proteomic profile in the domesticated and wild-type varieties. Notably, most of the differentially expressed proteins were downregulated in cultivated types compared to their wild counterparts. Overall, this study elucidates the nutritional and proteomic profiles of diverse hemp varieties, providing fundamental insights into the molecular and genetic changes associated with the domestication and cultivation of hemp.
Proteomics Evidence Consistent with a Ginger-Flavored Alcoholic Beverage Found in the Corrosion of a 1500-1046 BCE Chinese Bronze Vessel.
Junglas KS, Pires E, Goodburn-Brown D … +3 more , Cheng AY, von Przychowski A, da Costa Carvalho L
J Proteome Res · 2026 Jul · PMID 42314157 · Publisher ↗
During the Shang (ca. 1500-1046 BCE) and early Western Zhou (1046-978 BCE) periods in China, elite rituals involved offerings of food and drink presented to ancestors in elaborately cast bronze vessels. Although later te...
During the Shang (ca. 1500-1046 BCE) and early Western Zhou (1046-978 BCE) periods in China, elite rituals involved offerings of food and drink presented to ancestors in elaborately cast bronze vessels. Although later texts describe these practices in detail, direct biomolecular evidence for vessel contents remains scarce. We analyzed corrosion from eight unprovenanced Chinese ritual bronzes at the Museum Rietberg (Zurich, Switzerland) using powder X-ray diffraction to characterize crystalline inorganic phases and nanoLC-MS/MS to target preserved proteins. Only one vessel (a -type) yielded diagnostic peptides preserved within a copper carbonate matrix, matched to proteins from ginger () and a fermentation mold (). Serpin-domain-containing protein signals were also detected and are interpreted more cautiously. To our knowledge, this study provides the first direct proteomic evidence consistent with a fermented beverage residue associated with ancient Chinese recipes and supports the traditional interpretation of this vessel type in drink preparation and/or consumption. More importantly, we show that corroded, unprovenanced bronze vessels can preserve archeologically informative proteins, highlighting the value of proteomics for extending the scientific and curatorial significance of museum collections.
Evaluation of FASP for Mass Spectrometry-Based Untargeted Metabolomics Analysis of Urine Samples.
Mousa MK, Carvalho LB, Giddey AD … +6 more , Figueiredo A, Al-Hroub H, Semreen MH, Uddin M, Santos HM, Soares NC
J Proteome Res · 2026 Jul · PMID 42314122 · Publisher ↗
Filter-Aided Sample Preparation (FASP) is a well-established method in proteomics, yet its potential for the parallel recovery of metabolites remains largely unexplored. Herein, we evaluate the performance of FASP as a s...
Filter-Aided Sample Preparation (FASP) is a well-established method in proteomics, yet its potential for the parallel recovery of metabolites remains largely unexplored. Herein, we evaluate the performance of FASP as a straightforward workflow for the simultaneous isolation of protein and corresponding metabolite fractions from a single urine sample. The FASP-based LC-MS/MS approach for both proteomics and metabolomics analysis identified 3,163 nonredundant peptides corresponding to 957 unique protein groups. The metabolomic profile comparison of three urine fractions, specifically FASP-concentrated, FASP flow-through, and raw samples, resulted in the identification of 176 common metabolites. Next, as a proof-of-concept, the FASP protocol was applied to compare the metabolomic profiles of clinical urine samples from healthy individuals (n = 13) and patients with Ta bladder cancer (n = 12). The metabolomic modulation was consistent with previously reported findings, highlighting perturbations in phenylacetate, purine, and tryptophan metabolism, as reflected by changes in metabolites such as adenosine monophosphate (AMP), phenylacetic acid, glutamine, cytosine, and l-tryptophan. FASP protocol can be effectively adapted for the concurrent profiling of both proteomic and metabolomic fractions from urine samples. Thus, FASP-based workflow represents a viable alternative for single-step sample preparation, facilitating subsequent quantitative multiomics data integration.
Metabolic Reprogramming in Renal Cell Carcinoma: A Scoping Review with Quantitative Integration of Metabolomic Studies.
Amaro F, Carvalho M, Bastos ML … +2 more , Guedes de Pinho P, Pinto J
J Proteome Res · 2026 Jul · PMID 42313837 · Publisher ↗
A deeper understanding of renal cell carcinoma (RCC)-specific molecular alterations is crucial for improving diagnosis, predicting outcomes, and advancing therapeutic development. Metabolomics enables systematic profilin...
A deeper understanding of renal cell carcinoma (RCC)-specific molecular alterations is crucial for improving diagnosis, predicting outcomes, and advancing therapeutic development. Metabolomics enables systematic profiling of small molecules and provides direct functional readouts of tumor biology, offering a powerful route to characterize metabolic reprogramming and identify clinically actionable biomarkers. We conducted a scoping review of 45 RCC metabolomic studies using tissue, urine, blood, and cell line models and performed a quantitative synthesis specific to each matrix using the Amanida package, focusing on the metabolites reported most consistently across the studies. Tissue analysis demonstrated consistent metabolic reprogramming in metabolites related to the core energy and amino acid pathways. Urine studies identified significantly altered metabolites with potential utility as noninvasive biomarkers. Blood-based and in vitro data sets were too limited and heterogeneous to support quantitative synthesis. Across studies, consistent dysregulation in metabolites associated with glutathione, lipid, inositol phosphate, and purine/pyrimidine pathways highlights underexplored metabolic processes with potential diagnostic and therapeutic relevance. Taken together, the data indicate consistent tissue metabolic signatures reflecting RCC biology and identify urinary metabolites as strong candidates for biomarker validation. Standardized analytical and reporting frameworks, coupled with validation in larger, well-characterized cohorts, are needed to accelerate clinical implementation of RCC metabolomic biomarkers and metabolism-informed targets.
Integrated Lipidomic, Transcriptomic, and Metabolomic Analyses Reveal the Regulatory Mechanism Underlying Venom Synthesis in Parotoid Glands of .
Wang Y, Yu X, Peng J … +1 more , Wang H
J Proteome Res · 2026 Jul · PMID 42313667 · Publisher ↗
The parotoid gland secretion of the medicinal toad () is the primary source of Chansu, a valuable traditional medicine. However, the lack of understanding regarding the biological regulation of venom synthesis limits the...
The parotoid gland secretion of the medicinal toad () is the primary source of Chansu, a valuable traditional medicine. However, the lack of understanding regarding the biological regulation of venom synthesis limits the optimization of farming practices and quality control. Here, we integrated histology, lipidomics, transcriptomics, and untargeted metabolomics to delineate the regulatory mechanisms governing venom accumulation and biosynthesis, aimed at guiding aquaculture management. Histological results revealed that the parotoid gland is a highly regionalized organ, where structural maturity is positively correlated with toxin storage capacity, providing a morphological basis for determining optimal harvest timing. This structure is underpinned by a distinct lipid profile: high levels of triglycerides supply essential energy for massive venom production, while enriched ceramides and sphingomyelin form a specialized barrier to ensure high-quality venom encapsulation. Transcriptome analysis indicated that the upregulation of steroid and primary bile acid biosynthesis genes (e.g., , , , , and ) drives the synthesis of bioactive bufadienolides. Furthermore, we identified key enzymatic regulators─including CYP450s (, , ) and acetylases (, )─as potential genetic markers for identifying high-yielding venom. Collectively, these findings provide a scientific basis for establishing standardized farming protocols, advancing molecular breeding strategies for this important medicinal species, and achieving sustainable exploitation of toad venom.
Multi-Omics Analysis Identifies Paxillin as a Biomarker of Doxorubicin Resistance via Cytoskeletal Remodeling and Immune Exhaustion.
Liu Y, Yao Z, Li Y … +2 more , Qing H, Xu W
J Proteome Res · 2026 Jul · PMID 42313513 · Publisher ↗
Chemotherapy resistance remains a primary cause of treatment failure in breast cancer, yet the global proteomic landscape driving this phenotype has not been completely understood. In this study, we employed a systematic...
Chemotherapy resistance remains a primary cause of treatment failure in breast cancer, yet the global proteomic landscape driving this phenotype has not been completely understood. In this study, we employed a systematic multiomics approach, integrating quantitative proteomics of doxorubicin-resistant cells with transcriptomic and proteomic data from large-scale clinical cohorts (TCGA and FUSCC). Our analysis revealed a fundamental functional dichotomy in resistant cells, where a downregulation of metabolic processes contrasts with a robust upregulation of cytoskeletal and focal adhesion complexes. Through machine learning and interaction network analyses, we identified the focal adhesion scaffold paxillin (PXN) as a central hub driving resistance and a robust prognostic marker for poor recurrence-free survival in chemotherapy-treated patients. Mechanistically, PXN orchestrates a "cell adhesion-mediated drug resistance" program by an extracellular matrix-focal adhesion-cytoskeleton axis, driving extensive extracellular matrix remodeling and stiffening via the upregulation of cross-linking enzymes and protease inhibitors. This structural remodeling reprograms the tumor microenvironment, inducing an immunosuppressive state where PXN-high tumors exhibit increased CD8 T cell infiltration, but these lymphocytes are functionally exhausted and fail to execute cytotoxic responses. In summary, our findings reveal a novel resistance axis where PXN connects the intracellular cytoskeleton and extracellular matrix remodeling. This reprograms the tumor microenvironment and immune cell cytotoxicity, highlighting PXN as a critical target for overcoming chemoresistance.
Optimized Simultaneous N/O-Glycopeptide Enrichment Strategy Identifies Lung Cancer Diagnostic Biomarkers in Serum.
Zhou Z, Zhao J, Zhang J … +5 more , Wu P, Yang Y, Li W, Peng C, Qiang Z
J Proteome Res · 2026 Jul · PMID 42313501 · Publisher ↗
Glycoproteins, degradable into glycopeptides, are crucial in lung cancer (LC), yet efficient methods to enrich them from LC serum for biomarker discovery remain lacking. We mixed microcrystalline cellulose with cationic...
Glycoproteins, degradable into glycopeptides, are crucial in lung cancer (LC), yet efficient methods to enrich them from LC serum for biomarker discovery remain lacking. We mixed microcrystalline cellulose with cationic and anionic fillers was packed into the DeepGP column. Comparing DeepGP, MAX, HILIC, and PBA in HeLa cells showed DeepGP's superior glycopeptide coverage, which was then applied to profile N/O-glycoproteins in 18 serum samples, with biomarker identification via MetaboAnalyst and N-glycan analysis using GlycanFinder. A total of 4801 glycopeptides (4021 N- and 780 O-glycopeptides) were quantified using MAX, HILIC, DeepGP, and PBA, with DeepGP identifying the most O-glycopeptides in HeLa cells. Applying DeepGP to LC serum enabled quantification of 10,482 N- and 11,110 O-glycopeptides. Proteomic analysis highlighted changes in transcription, post-translational modifications, protein turnover, and chaperone functions, with pathway enrichment revealing complement/coagulation cascades, cholesterol metabolism, and cancer-related proteoglycan signaling. MetaboAnalyst identified four site-specific glycopeptides (AACT-N106-H7N6S4F1, HEMO-N187-N4H5F1S1, ITIH3-N580-N5H6S3, IGG1-N180-N5H3F1) as potential biomarkers with AUC > 0.88. Thus, this establishes a refined strategy of DeepGP to simultaneously enrich N/O glycopeptides, enhancing the potential of glycopeptides as diagnostic and prognostic biomarkers for LC in clinical settings in the future.
MPOInt: An Epigenetics-Driven Workflow for Integrative Multi-Level Proteomics.
Schaefer Z, Sokolik CC, Parker IK
J Proteome Res · 2026 Jul · PMID 42312483 · Publisher ↗
Proteomics provides key insights into systems regulating cell behavior and can elucidate key epigenetic states influencing biological functions in health and disease. Integrating different modalities of proteomics (total...
Proteomics provides key insights into systems regulating cell behavior and can elucidate key epigenetic states influencing biological functions in health and disease. Integrating different modalities of proteomics (total, phospho, epi) allows for a comprehensive understanding of how systems change in response to a stimulus. A current limitation is that these data are often captured individually with a limited scope of how systems regulating biological processes interact. Integrative analyses are essential to accurately depict biological states but often require custom, time-consuming bioinformatics processing. The MPOInt pipeline and its associated R package provide highly flexible analysis modules that can be easily combined to develop a multidimensional view of the input data with minimal barrier to entry, and is capable of integrating histone proteome data with known epigenetic effectors. Using this tool and pre-existing clinical data, we identify several pathways that may be targets in driving the growth of aggressive cancers, including treatment-resistant estrogen receptor-positive breast cancer. Overall, MPOInt adds clinical context to data that is traditionally difficult to interpret and generates a unique network centered around epigenetic factors for each collection of data.
A Combined Omics Approach to Elucidate the Molecular Interplay behind a Beneficial Interaction.
Lampens A, Vandecasteele M, Braem M … +7 more , Vuylsteke M, Xu X, Pauwels J, Van Dingenen J, De Smet I, Gevaert K, Goormachtig S
J Proteome Res · 2026 Jul · PMID 42308052 · Publisher ↗
Plants rely on complex signaling networks to interact with beneficial plant growth-promoting rhizobacteria (PGPR). Among these microbes, RHG1 is recognized by roots via specific receptor-like kinases (RLKs), but the mo...
Plants rely on complex signaling networks to interact with beneficial plant growth-promoting rhizobacteria (PGPR). Among these microbes, RHG1 is recognized by roots via specific receptor-like kinases (RLKs), but the molecular mechanisms underlying the plant growth-promotion effect remain largely unknown. To investigate these mechanisms, we used an integrative approach combining proteomics and phosphoproteomics. Our phosphoproteome analysis revealed that RHG1 triggers a range of signaling events, involving two RLKs (LysM RLK1-INTERACTING KINASE 1 [LIK1] and an uncharacterized RLK, AT5G49770). Notably, via the proteome analysis, we revealed that upon RHG1 treatment, defense proteins are downregulated early. Later on, developmental processes, such as ribosome biogenesis and maturation, might lead to enhanced cell division and/or activity to promote growth. Our findings suggest that RHG1 triggered phosphorylation-based signaling pathways, resulting in the timely modulation of defense and developmental processes, which eventually lead to plant growth promotion. Our data, combined with that of previous reports, suggest that RHG1 activates a broad network of regulatory mechanisms that extend beyond a single pathway. Understanding the mechanisms behind such beneficial plant-microbe interactions can pave the way for more effective commercialization of PGPR-based agricultural products.
Development of an Spiked Lipoprotein Lipase Activity Assay in Serum and Plasma for Evaluation of Substrate and Donor-Specific Lipase Activity.
Rees JC, Sultan JA, Gardner MS … +2 more , Kuklenyik Z, Barr JR
J Proteome Res · 2026 Jul · PMID 42307472 · Publisher ↗
Lipoprotein lipase (LPL) is a membrane-bound, water-soluble enzyme that hydrolyzes triglycerides (TAG) into diacylglycerides (DAG), monoacylglycerides (MAG), and free fatty acids (FFA), enabling lipid uptake and energy d...
Lipoprotein lipase (LPL) is a membrane-bound, water-soluble enzyme that hydrolyzes triglycerides (TAG) into diacylglycerides (DAG), monoacylglycerides (MAG), and free fatty acids (FFA), enabling lipid uptake and energy distribution across tissues. We developed and validated a mass spectrometry-based in vitro assay to quantify LPL activity and assess interindividual variation in serum and plasma samples. Assay conditions were optimized for LPL concentration, calcium chloride concentration, and incubation time to maximize enzymatic activity. Samples were incubated with and without exogenous LPL and analyzed using targeted lipidomics to quantify changes in TAG, DAG, and FFA species. The assay demonstrated high reproducibility in quality control plasma over 10 days. We observed consistent reductions in TAG species and corresponding increases in DAG and FFA species, which varied according to fatty acid composition. Notably, LPL showed reduced catalytic efficiency for TAG and DAG species containing long-chain polyunsaturated fatty acids (PUFAs). Application of the assay to serum samples from 31 healthy volunteers confirmed these substrate-specific patterns, demonstrating the assay's potential to probe LPL function in physiological and pathophysiological states.
Glycoproteome Profiling of Human Serum for Hepatocellular Carcinoma Biomarker Discovery.
Sajid MS, Varghese RS, Saleem S … +3 more , Zhang X, Kroemer A, Ressom HW
J Proteome Res · 2026 Jul · PMID 42304605 · Publisher ↗
Hepatocellular carcinoma (HCC) typically develops in a cirrhotic background, where elevated serum α-fetoprotein (AFP), a commonly used HCC biomarker, performs inconsistently. We implemented an integrated serum intact gly...
Hepatocellular carcinoma (HCC) typically develops in a cirrhotic background, where elevated serum α-fetoprotein (AFP), a commonly used HCC biomarker, performs inconsistently. We implemented an integrated serum intact glycoproteomics strategy that profiles N-linked and O-linked glycopeptides in parallel. This strategy couples prevalence-aware filtering with multialgorithm feature selection to prioritize glycoform-resolved markers distinguishing HCC from cirrhosis. Serum from HCC ( = 20) and cirrhosis ( = 20) underwent high-abundance protein depletion, proteolysis, glycopeptide enrichment, and high-resolution liquid chromatography-mass spectrometry/MS (LC-MS/MS). Intact glycopeptides were filtered to a high-confidence quantitative matrix requiring ≥70% feature presence, with statistically significant low-prevalence features recovered by chi-square testing and incorporated into the final modeling pool. Candidate prioritization integrated SelectKBest, SVM-RFE, Elastic Net, Transformer-RFE, and Random Forest, with discrimination assessed by ROC analysis. This workflow delivered broad N/O glycoproteome coverage and a candidate of 11 intact glycopeptide features spanning both glycosylation classes. Multiple candidates exhibited pronounced group-associated detectability and/or significant abundance differences, and prioritized markers exceeded clinically measured AFP in univariate ROC comparisons within this cohort. Network-level interpretation (PPI and IPA) revealed an immune/complement-centered module and enrichment of pathways encompassing the complement system, neutrophil degranulation, O-linked glycosylation, sphingolipid metabolism, and nuclear receptor signaling (LXR/RXR activation and androgen signaling).
Coupling Far-Western Blotting with Peptide Microarrays Reveals Novel E-Cadherin Spore-Surface Ligands in .
Lopez-Garcia OK, Pizarro-Guajardo M, Kocurek KI … +2 more , Rezenom YH, Paredes-Sabja D
J Proteome Res · 2026 Jul · PMID 42299067 · Publisher ↗
is an anaerobic spore-forming bacterium and the leading cause of nosocomial diarrhea. A major clinical challenge is infection recurrence, affecting 20-30% of patients, mainly driven by spore persistence. The mechanisms...
is an anaerobic spore-forming bacterium and the leading cause of nosocomial diarrhea. A major clinical challenge is infection recurrence, affecting 20-30% of patients, mainly driven by spore persistence. The mechanisms underlying spore persistence in the gut remain poorly understood. Recently, our group showed that E-cadherin acts as a spore receptor mediating adherence to intestinal epithelial cells (PMID: 36448839), but the identity of the E-cadherin-binding proteins remains unknown. Here, far-Western blotting coupled with MS/MS-identified E-cadherin-binding spore ligands. The spore surface proteins CotE (CDIF27147_01458) and CdeM (CDIF27147_01682), along with two uncharacterized proteins, CDIF27147_03838 and CDIF27147_02282, interact with E-cadherin. Peptide microarray analysis mapped discrete E-cadherin-binding regions within these proteins, corresponding to 9-20 residue motifs, predicted to be surface-exposed by AlphaFold. However, competitive E-cadherin pull-down assays using synthetic peptides of these motifs did not reduce E-cadherin binding to spores. Comparative genomics showed that these ligands and motifs are conserved across all five classical clades (C1-C5). Similar levels of E-cadherin binding were observed in spores from all five classical clades. Collectively, this work identifies CDIF27147_03838 and CDIF27147_02282 as novel E-cadherin ligands and suggests additional roles for CotE and CdeM, expanding insights into spore-host interactions.
Characterization and Identification of Potential Allergenic Proteins in L. Pollen.
He X, Wang M, Guo L … +10 more , Yang Z, Ma F, Zhang W, Wilson G, Wang W, Ma J, Sa Y, Yang L, Chen G, Ma X
J Proteome Res · 2026 Jul · PMID 42297733 · Publisher ↗
L. pollen (SJP) is an emerging cause of urban seasonal allergies such as asthma and rhinitis. This study systematically evaluated the allergenicity of SJP using both and experiments. , a mouse model was employed in...
L. pollen (SJP) is an emerging cause of urban seasonal allergies such as asthma and rhinitis. This study systematically evaluated the allergenicity of SJP using both and experiments. , a mouse model was employed in which SJP induced typical allergic symptoms, including sneezing and rubbing behavior, elevated serum IgE and IL-4 levels, and reduced IFN-γ levels. , IgE immunoblotting and ELISA using sera from allergic patients identified five potential allergenic protein bands separated by SDS-PAGE. LC-MS analysis further revealed a novel potential allergen, a 35 kDa protein belonging to the cytochrome f family, designated as Sop j 1. Structural comparison by CD spectroscopy and AlphaFold, combined with matching molecular weight and IgE reactivity profiles, confirmed that this cytochrome f protein is indeed Sop j 1. Recombinant Sop j 1 was produced and structurally validated. Western blot and inhibition ELISA demonstrated its specific binding to IgE in patient sera and its ability to inhibit IgE binding to native SJP. These findings indicate that Sop j 1 is a key allergenic protein in SJP with high IgE sensitization rates in the studied population, which will facilitate the development of precise diagnostics and treatments.
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