Expert Review of Proteomics最新文献

Extracellular vesicle proteomics in brain solid tumors: future strategy for personalized medicine. 脑实体瘤的细胞外囊泡蛋白质组学：个性化医疗的未来策略。

IF 3.8 3区生物学

Expert Review of Proteomics Pub Date : 2025-06-01 Epub Date: 2025-06-04 DOI: 10.1080/14789450.2025.2514841

Sonia Spinelli, Andrea Garbarino, Marco Pavanello, Giovanni Candiano, Isabella Panfoli, Maurizio Bruschi

{"title":"Extracellular vesicle proteomics in brain solid tumors: future strategy for personalized medicine.","authors":"Sonia Spinelli, Andrea Garbarino, Marco Pavanello, Giovanni Candiano, Isabella Panfoli, Maurizio Bruschi","doi":"10.1080/14789450.2025.2514841","DOIUrl":"10.1080/14789450.2025.2514841","url":null,"abstract":"Introduction: Brain solid tumors are a leading cause of cancer-related mortality at all ages. The updated 2021WHO Central Nervous System tumor classification is based on genomic diagnostics. Nonetheless, extracellular vesicles (EVs) proteomics is a platform for protein biomarker discovery in brain tumor patient management. Tumor metabolic reprogramming, also through epigenetic mechanisms, is central to cancer. EVs transfer proteins and nucleic acids that relay the metabolic and redox state of the parent cells.Areas covered: This review addresses the biomarker discovery and translation focusing on recent (from 2022 to 2024 PubMed) proteomic studies of EVs in brain tumor patients, selected for their focus on metabolic aspects. The most treatable adult brain tumor is isocitrate dehydrogenase-mutated glioma. Minimally invasive collection of EVs from cerebrospinal fluid or prospectively blood allows proteomic and metabolic analysis of the parent tumor cells.Expert opinion: The CSF EVs express key CNS tumor biomarkers and therapy targets undetectable in whole CSF and relay the brain tumor metabolic adaptations. Metabolic dependencies can represent potential therapy targets. The clinical implications of biomarker EV proteomic discovery represent a promising platform for diagnostic and prognostic purposes in brain solid tumors, a leading cause of cancer-related mortality at all ages.","PeriodicalId":50463,"journal":{"name":"Expert Review of Proteomics","volume":" ","pages":"217-224"},"PeriodicalIF":3.8,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144188428","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Shaping the future of precision medicine: plasma proteomics to uncover insights in thrombosis. 塑造精准医学的未来：血浆蛋白质组学揭示血栓形成的见解。

IF 3.8 3区生物学

Expert Review of Proteomics Pub Date : 2025-06-01 Epub Date: 2025-06-13 DOI: 10.1080/14789450.2025.2517146

Emil Johansson, Maria Jesus Iglesias, Jacob Odeberg, Fredrik Edfors

{"title":"Shaping the future of precision medicine: plasma proteomics to uncover insights in thrombosis.","authors":"Emil Johansson, Maria Jesus Iglesias, Jacob Odeberg, Fredrik Edfors","doi":"10.1080/14789450.2025.2517146","DOIUrl":"10.1080/14789450.2025.2517146","url":null,"abstract":"Introduction: Advances in various proteomics technologies, especially high-throughput and reproducibility, have enabled the systematic exploration of the circulating thrombosis proteome. This includes dissecting biological systems and pathways imperative to thrombosis, such as platelet activation, coagulation cascade, complement system, and endothelial cells. These insights strengthen our understanding of the cause and effect of thrombosis and improve precision medicine by identifying better biomarkers and biomarker panels, which may aid clinicians in decision-making in venous thromboembolism (VTE) and other thrombotic patients. This progress has the potential to reduce thrombosis-related morbidity and mortality, ultimately improving patient quality of life.Areas covered: This review highlights recent advances and applications of mass spectrometry and affinity-based proteomics in thrombosis over the past three years (2022-2024), focusing on the thrombotic proteome signature related to VTE.Expert opinion: Plasma proteomics, predominantly driven by mass spectrometry and affinity-based proteomics, has shown promise in identifying novel disease biomarkers and pathways. With the recent advances in the field, proteomics holds the potential to revolutionize precision medicine. As thrombosis is an intravascular disease, analysis of the blood proteome can capture environmental, genetic, and epigenetic contributors to risk variation in thrombosis, revealing novel protein biomarkers for diagnosis and risk prediction and new biological pathways.","PeriodicalId":50463,"journal":{"name":"Expert Review of Proteomics","volume":" ","pages":"237-254"},"PeriodicalIF":3.8,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144235822","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

The potential of proteomics for in-depth molecular investigations of progressive supranuclear palsy. 蛋白质组学对进行性核上性麻痹的深入分子研究的潜力。

IF 3.8 3区生物学

Expert Review of Proteomics Pub Date : 2025-06-01 Epub Date: 2025-06-17 DOI: 10.1080/14789450.2025.2519466

Silvia Romero-Murillo, Seojin Lee, Joaquín Fernández-Irigoyen, Ivan Martinez-Valbuena, Enrique Santamaría

{"title":"The potential of proteomics for in-depth molecular investigations of progressive supranuclear palsy.","authors":"Silvia Romero-Murillo, Seojin Lee, Joaquín Fernández-Irigoyen, Ivan Martinez-Valbuena, Enrique Santamaría","doi":"10.1080/14789450.2025.2519466","DOIUrl":"10.1080/14789450.2025.2519466","url":null,"abstract":"Introduction: Progressive supranuclear palsy (PSP) is a rare neurodegenerative disorder. The lack of comprehension about the pathogenesis of the disease, its heterogeneity, and the complex clinical evaluation in early stages, limit the development of effective treatments for PSP patients and highlight the need of further research on the field.Areas covered: In this work, we review the current knowledge of the physio- and neuropathology of PSP, its clinical features, diagnosis markers, and treatment options. We also compare the proteomic-based studies done to date in brain tissues as well as in cerebrospinal fluid and other non-cerebral samples, briefly describing the proteomic approach used and the biological findings obtained in each study.Expert opinion: PSP is a complex neurodegenerative disorder marked by tau aggregation, glial dysfunction, and neuroinflammation. Although advances in neuroimaging and biofluid biomarkers have improved PSP diagnostic accuracy, no disease-modifying therapies are currently available. Promising avenues such as tau PET tracers, seed amplification assays, and advanced proteomic-based approaches are enhancing our ability to detect disease-specific tau pathology and hold the potential to provide novel biomarkers for earlier and more precise clinical diagnosis and treatment development that could transform the landscape of PSP.","PeriodicalId":50463,"journal":{"name":"Expert Review of Proteomics","volume":" ","pages":"225-235"},"PeriodicalIF":3.8,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144287009","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Immobilized metal ion affinity chromatography: waltz of metal ions and biomacromolecules. 固定化金属离子亲和层析：金属离子与生物大分子的华尔兹。

IF 3.8 3区生物学

Expert Review of Proteomics Pub Date : 2025-05-01 Epub Date: 2025-05-26 DOI: 10.1080/14789450.2025.2492764

Rui Yan, Yan-Ming Xu, Andy T Y Lau

{"title":"Immobilized metal ion affinity chromatography: waltz of metal ions and biomacromolecules.","authors":"Rui Yan, Yan-Ming Xu, Andy T Y Lau","doi":"10.1080/14789450.2025.2492764","DOIUrl":"10.1080/14789450.2025.2492764","url":null,"abstract":"Introduction: Immobilized metal ion affinity chromatography (IMAC) is an effective method developed in the 1980s for the separation and purification of proteins. The system consists of a solid-phase matrix, a linking ligand, and a metal ion. The method is based on the ability of metal ions to bind specifically to certain specific amino acid residues of proteins, thereby selectively enriching and purifying proteins.Areas covered: This review aims to describe current knowledge of fundamental principle of IMAC and summarize the supports, chelating ligands, and metal ions of IMAC. In addition, how IMAC technology is used in proteomics and nucleic acids research are highlighted.Expert opinion: Over the past decades, IMAC has been extensively utilized as a predominant technique for protein enrichment in a variety of biological and medical research, such as disease diagnosis, tumor biomarker identification, protein purification, and nucleic acids research. In the future, IMAC should be integrated with other emerging proteomics technologies to promote the applications of metalloproteomes in disease diagnosis, metallodrug development, and clinical translation.","PeriodicalId":50463,"journal":{"name":"Expert Review of Proteomics","volume":" ","pages":"185-198"},"PeriodicalIF":3.8,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144006586","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Utilization of high-resolution mass spectrometry and data-independent analysis to track the monoclonal antibody spatial stability. 利用高分辨率质谱和数据独立分析来跟踪单克隆抗体的空间稳定性。

IF 3.8 3区生物学

Expert Review of Proteomics Pub Date : 2025-05-01 Epub Date: 2025-04-20 DOI: 10.1080/14789450.2025.2492763

Valerie Prochazkova, Michal Rosulek, Michael Karpisek, Vaclav Matousek, Petr Novak, Zdenek Kukacka

{"title":"Utilization of high-resolution mass spectrometry and data-independent analysis to track the monoclonal antibody spatial stability.","authors":"Valerie Prochazkova, Michal Rosulek, Michael Karpisek, Vaclav Matousek, Petr Novak, Zdenek Kukacka","doi":"10.1080/14789450.2025.2492763","DOIUrl":"10.1080/14789450.2025.2492763","url":null,"abstract":"Objectives: Chemical cross-linking coupled with mass spectrometry (CXMS) offers the distance constraints critical for building the structural model of protein and protein complexes and understanding dynamics of biological systems. Originally developed for protein structural models, CXMS has evolved into method for studying protein complex formation, ligand-induced conformational changes, and quantitative structural analysis using isotopically labeled cross-linkers.Methods: In this study we tested the potential of isotopically labeled MS-cleavable cross-linker to track the stability of the therapeutic monoclonal antibodies.Results: A novel isotopically labeled MS-cleavable cross-linker was synthesized, and its reactivity was successfully tested on peptide and protein standards. Further, the novel cross-linker was utilized to test the stability of selected therapeutical monoclonal antibodies, bevacizumab and trastuzumab, adopting the data-independent acquisition.Conclusion: This study reports the advantages of using combination of 13C isotopically labeled MS-cleavable cross-linkers and data-independent mass spectrometry analysis for the automated identification of cross-linked products and thus monitoring the structural rearrangement of protein structure.","PeriodicalId":50463,"journal":{"name":"Expert Review of Proteomics","volume":" ","pages":"199-207"},"PeriodicalIF":3.8,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144027266","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Optimization of bottom-up proteomic sample preparation by design of experiments for absolute quantification of 257 proteins in human plasma using UPLC-MRM-MS. UPLC-MRM-MS绝对定量257种人血浆蛋白的实验设计优化自下而上蛋白质组学样品制备

IF 3.8 3区生物学

Expert Review of Proteomics Pub Date : 2025-05-01 Epub Date: 2025-05-22 DOI: 10.1080/14789450.2025.2504994

Kari Arnarson, Kristrun Y Holm, Valdis Gunnarsdottir Thormar, Finnur F Eiríksson, Yassene Mohammed, Christoph H Borchers, Sigridur K Bodvarsdottir, Margret Thorsteinsdottir

{"title":"Optimization of bottom-up proteomic sample preparation by design of experiments for absolute quantification of 257 proteins in human plasma using UPLC-MRM-MS.","authors":"Kari Arnarson, Kristrun Y Holm, Valdis Gunnarsdottir Thormar, Finnur F Eiríksson, Yassene Mohammed, Christoph H Borchers, Sigridur K Bodvarsdottir, Margret Thorsteinsdottir","doi":"10.1080/14789450.2025.2504994","DOIUrl":"10.1080/14789450.2025.2504994","url":null,"abstract":"Introduction: Targeted protein absolute quantification using mass spectrometry holds promise for identifying biomarkers for diagnosis, prognosis, and personalized medicine. However, complex and time-consuming workflows, particularly during sample preparation, present significant bottlenecks. Addressing these challenges is critical for the applicability of absolute quantification of proteins in clinical research settings.Areas covered: We explore optimization strategies for protein digestion in bottom-up proteomics sample preparation. Design of experiments (DoE), a statistical approach for systematically evaluating multiple experimental factors, was used for simultaneous optimization of digestion time, temperature, enzyme-to-protein substrate ratio, and denaturing agent. Furthermore, the lower limit of quantification (LLOQ) for our platform was improved by using the Waters Xevo TQ-XS UPLC-MRM-MS. The integration of automated sample preparation into the workflow enabled reproducible absolute quantification of 257 proteins in human plasma.Expert opinion: We successfully reduced protein digestion time from 18 hours (overnight) to 4 hours while maintaining relative digestion efficiency. We improved the sensitivity of the assay via the optimized workflow and were able to quantify proteins that previously fell below the LLOQ. These advancements, combined with automation, provide a practical, efficient, and reproducible workflow suitable for clinical research.","PeriodicalId":50463,"journal":{"name":"Expert Review of Proteomics","volume":" ","pages":"209-216"},"PeriodicalIF":3.8,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144112575","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Novel activity assay for botulotoxin A1 detection using functionalized chips and matrix-assisted laser desorption/ionization mass spectrometry. 利用功能化芯片和基质辅助激光解吸/电离质谱法检测肉毒毒素A1的新活性测定。

IF 3.8 3区生物学

Expert Review of Proteomics Pub Date : 2025-04-01 Epub Date: 2025-03-24 DOI: 10.1080/14789450.2025.2482933

Zuzana Kalaninova, Josef Dvorak, Jiri Dresler, Michael Volny, Petr Novak, Petr Pompach

{"title":"Novel activity assay for botulotoxin A1 detection using functionalized chips and matrix-assisted laser desorption/ionization mass spectrometry.","authors":"Zuzana Kalaninova, Josef Dvorak, Jiri Dresler, Michael Volny, Petr Novak, Petr Pompach","doi":"10.1080/14789450.2025.2482933","DOIUrl":"10.1080/14789450.2025.2482933","url":null,"abstract":"Background: Botulinum neurotoxins (BoNTs) are a group of neurotoxins produced by Clostridium bacteria. Their effect on neuro-muscular connections through cleaving proteins of the SNARE complex results in blocking acetylcholine signal transduction. The FDA-approved mouse bioassay, which involves exposing live mice to potentially contaminated food, is the most widely used method. However, this assay is costly, time-consuming, and raises ethical concerns. Therefore, there is a need for alternative assays that can enzymatically measure the activity of BoNTs.Research design and methods: We present an approach that combines the EndoPep-MS assay with protein affinity chips fabricated using ion soft-landing technology. Toxic activity is indirectly assessed by monitoring the N- and C-terminal fragments of the substrate peptide. This new method employs a protein array with affinity molecules targeting either the BoNT/A1 or the substrate peptide. Both variants enable in-situ reaction and detection of substrate peptides via MALDI-ToF MS on the protein chip.Results: This method demonstrated successful detection of active BoNT/A1 in both buffer and complex matrices, achieving a detection limit of 0.5 ng/mL.Conclusions: This study reports the in-situ detection of botulotoxin A1 using functionalized MALDI chips. The advantages of the MALDI chip technology include speed, robustness, cost-effectiveness, and possible automatization.","PeriodicalId":50463,"journal":{"name":"Expert Review of Proteomics","volume":" ","pages":"177-184"},"PeriodicalIF":3.8,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143659457","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Acoustic ejection mass spectrometry: the potential for personalized medicine. 声射质谱法：个性化医疗的潜力。

IF 3.8 3区生物学

Expert Review of Proteomics Pub Date : 2025-04-01 Epub Date: 2025-04-12 DOI: 10.1080/14789450.2025.2491356

Chang Liu

{"title":"Acoustic ejection mass spectrometry: the potential for personalized medicine.","authors":"Chang Liu","doi":"10.1080/14789450.2025.2491356","DOIUrl":"https://doi.org/10.1080/14789450.2025.2491356","url":null,"abstract":"Introduction: The emergence of personalized medicine (PM) has shifted the focus of healthcare from the traditional 'one-size-fits-all' approach to strategies tailored to individual patients, accounting for genetic, environmental, and lifestyle factors. Acoustic ejection mass spectrometry (AEMS) is a novel technology that offers a robust and scalable platform for high-throughput MS readout. AEMS achieves analytical speeds of one sample per second while maintaining high data quality, broad compound coverage, and minimal sample preparation, making it an invaluable tool for PM.Areas covered: This article explores the potential of AEMS in critical PM applications, including therapeutic drug monitoring (TDM), proteomics, metabolomics, and mass spectrometry imaging. AEMS simplifies conventional workflows by minimizing sample preparation, enhancing automation compatibility, and enabling direct analysis of complex biological matrices.Expert opinion: Integrating AEMS with orthogonal separation techniques such as differential mobility spectrometry (DMS) further addresses challenges in isomer discrimination, expanding the platform's analytical capabilities. Additionally, the development of high-throughput data processing tools could further enable AEMS to accelerate the development of personalized medicine.","PeriodicalId":50463,"journal":{"name":"Expert Review of Proteomics","volume":"22 4","pages":"141-147"},"PeriodicalIF":3.8,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144038715","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Recent implementations of data-independent acquisition for cancer biomarker discovery in biological fluids. 在生物流体中发现癌症生物标志物的数据独立采集的最新实现。

IF 3.8 3区生物学

Expert Review of Proteomics Pub Date : 2025-04-01 Epub Date: 2025-04-27 DOI: 10.1080/14789450.2025.2491355

Annie Ha, Michael Woolman, Matthew Waas, Meinusha Govindarajan, Thomas Kislinger

{"title":"Recent implementations of data-independent acquisition for cancer biomarker discovery in biological fluids.","authors":"Annie Ha, Michael Woolman, Matthew Waas, Meinusha Govindarajan, Thomas Kislinger","doi":"10.1080/14789450.2025.2491355","DOIUrl":"https://doi.org/10.1080/14789450.2025.2491355","url":null,"abstract":"Introduction: Cancer is the second-leading cause of death worldwide and accurate biomarkers for early detection and disease monitoring are needed to improve outcomes. Biological fluids, such as blood and urine, are ideal samples for biomarker measurements as they can be routinely collected with relatively minimally invasive methods. However, proteomics analysis of fluids has been a challenge due to the high dynamic range of its protein content. Advances in data-independent acquisition (DIA) mass spectrometry-based proteomics can address some of the technical challenges in the analysis of biofluids, thus enabling the ability for mass spectrometry to propel large-scale biomarker discovery.Areas covered: We reviewed principles of DIA and its recent applications in cancer biomarker discovery using biofluids. We summarized DIA proteomics studies using biological fluids in the context of cancer research over the past decade, and provided a comprehensive overview of the benefits and challenges of DIA-MS.Expert opinion: Various studies showed the potential of DIA-MS in identifying putative cancer biomarkers in a high-throughput manner. However, the lack of proper study design and standardization of methods across platforms still needs to be addressed to fully utilize the benefits of DIA-MS to accelerate the biomarker discovery and verification processes.","PeriodicalId":50463,"journal":{"name":"Expert Review of Proteomics","volume":"22 4","pages":"163-176"},"PeriodicalIF":3.8,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144063077","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Unravelling disease complexity: integrative analysis of multi-omic data in clinical research. 揭示疾病复杂性：临床研究中多组学数据的综合分析。

IF 3.8 3区生物学

Expert Review of Proteomics Pub Date : 2025-04-01 Epub Date: 2025-04-13 DOI: 10.1080/14789450.2025.2491357

Ornella Cominetti, Loïc Dayon

{"title":"Unravelling disease complexity: integrative analysis of multi-omic data in clinical research.","authors":"Ornella Cominetti, Loïc Dayon","doi":"10.1080/14789450.2025.2491357","DOIUrl":"https://doi.org/10.1080/14789450.2025.2491357","url":null,"abstract":"Introduction: A holistic view on biological systems is today a reality with the application of multi-omic technologies. These technologies allow the profiling of genome, epigenome, transcriptome, proteome, metabolome as well as newly emerging 'omes.' While the multiple layers of data accumulate, their integration and reconciliation in a single system map is a cumbersome exercise that faces many challenges. Application to human health and disease requires large sample sizes, robust methodologies and high-quality standards.Areas covered: We review the different methods used to integrate multi-omics, as recent ones including artificial intelligence. With proteomics as an anchor technology, we then present selected applications of its data combination with other omics layers in clinical research, mainly covering literature from the last five years in the Scopus and/or PubMed databases.Expert opinion: Multi-omics is powerful to comprehensively type molecular layers and link them to phenotype. Yet, technologies and data are very diverse and still strategies and methodologies to properly integrate these modalities are needed.","PeriodicalId":50463,"journal":{"name":"Expert Review of Proteomics","volume":"22 4","pages":"149-162"},"PeriodicalIF":3.8,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144063158","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0