Expert Review of Proteomics最新文献_第2页

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

Omics and rare diseases: challenges, applications, and future perspectives. 组学和罕见疾病：挑战、应用和未来展望。

IF 3.8 3区生物学

Expert Review of Proteomics Pub Date : 2025-03-01 Epub Date: 2025-02-20 DOI: 10.1080/14789450.2025.2468300

Daniela Braconi, Haidara Nadwa, Giulia Bernardini, Annalisa Santucci

{"title":"Omics and rare diseases: challenges, applications, and future perspectives.","authors":"Daniela Braconi, Haidara Nadwa, Giulia Bernardini, Annalisa Santucci","doi":"10.1080/14789450.2025.2468300","DOIUrl":"10.1080/14789450.2025.2468300","url":null,"abstract":"Introduction: Rare diseases (RDs) are a heterogeneous group of diseases recognized as a relevant global health priority but posing aspects of complexity, such as geographical scattering of affected individuals, improper/late diagnosis, limited awareness, difficult surveillance and monitoring, limited understanding of natural history, and lack of treatment. Usually, RDs have a pediatric onset and are life-long, multisystemic, and associated with a poor prognosis.Areas covered: In this work, we review how high-throughput omics technologies such as genomics, transcriptomics, proteomics, metabolomics, epigenomics, and other well-established omics, which are increasingly more affordable and efficient, can be applied to the study of RDs promoting diagnosis, understanding of pathological mechanisms, biomarker discovery, and identification of treatments.Expert opinion: RDs, despite their challenges, offer a niche where collaborative efforts and personalized treatment strategies might be feasible using omics technologies. Specialized consortia fostering multidisciplinary collaboration, data sharing, and the development of biobanks and registries can be built; multi-omics approaches, including so far less exploited omics technologies, along with the implementation of AI tools can be undertaken to deepen our understanding of RDs, driving biomarker discovery and clinical interventions. Nevertheless, technical, ethical, legal, and societal issues must be clearly defined and addressed.","PeriodicalId":50463,"journal":{"name":"Expert Review of Proteomics","volume":" ","pages":"107-122"},"PeriodicalIF":3.8,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143434310","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

Proteomic interrogation of the human olfactory system: the road ahead. 人类嗅觉系统的蛋白质组学研究：未来之路。

IF 3.8 3区生物学

Expert Review of Proteomics Pub Date : 2025-03-01 Epub Date: 2025-03-11 DOI: 10.1080/14789450.2025.2476966

Elena Anaya-Cubero, Paz Cartas-Cejudo, Marina De Miguel, Leire Extramiana, Silvia Romero-Murillo, Mercedes Lachén-Montes, Joaquín Fernández-Irigoyen, Enrique Santamaría

引用次数: 0

Emerging protein sequencing technologies: proteomics without mass spectrometry? 新兴的蛋白质测序技术：没有质谱的蛋白质组学？

IF 3.8 3区生物学

Expert Review of Proteomics Pub Date : 2025-03-01 Epub Date: 2025-04-06 DOI: 10.1080/14789450.2025.2476979

A S Deshpande, A Lin, I O'Bryon, J A Aufrecht, E D Merkley

{"title":"Emerging protein sequencing technologies: proteomics without mass spectrometry?","authors":"A S Deshpande, A Lin, I O'Bryon, J A Aufrecht, E D Merkley","doi":"10.1080/14789450.2025.2476979","DOIUrl":"10.1080/14789450.2025.2476979","url":null,"abstract":"Introduction: Liquid chromatography-tandem mass spectrometry (LC-MS/MS) has been a leading method for proteomics for 30 years. Advantages provided by LC-MS/MS are offset by significant disadvantages, including cost. Recently, several non-mass spectrometric methods have emerged, but little information is available about their capacity to analyze the complex mixtures routine for mass spectrometry.Areas covered: We review recent non-mass-spectrometric methods for sequencing proteins and peptides, including those using nanopores, sequencing by degradation, reverse translation, and short-epitope mapping, with comments on bioinformatics challenges, fundamental limitations, and areas where new technologies will be more or less competitive with LC-MS/MS. In addition to conventional literature searches, instrument vendor websites, patents, webinars, and preprints were also consulted to give a more up-to-date picture.Expert opinion: Many new technologies are promising. However, demonstrations that they outperform mass spectrometry in terms of peptides and proteins identified have not yet been published, and astute observers note important disadvantages, especially relating to the dynamic range of single-molecule measurements of complex mixtures. Still, even if the performance of emerging methods proves inferior to LC-MS/MS, their low cost could create a different kind of revolution: a dramatic increase in the number of biology laboratories engaging in new forms of proteomics research.","PeriodicalId":50463,"journal":{"name":"Expert Review of Proteomics","volume":" ","pages":"89-106"},"PeriodicalIF":3.8,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143659453","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

Mass spectrometry-based ligand binding assays in biomedical research. 生物医学研究中基于质谱的配体结合分析。

IF 3.8 3区生物学

Expert Review of Proteomics Pub Date : 2025-03-01 Epub Date: 2025-02-23 DOI: 10.1080/14789450.2025.2467263

Tobias Meisinger, Amelie Vogt, Robin Kretz, Helen S Hammer, Hannes Planatscher, Oliver Poetz

{"title":"Mass spectrometry-based ligand binding assays in biomedical research.","authors":"Tobias Meisinger, Amelie Vogt, Robin Kretz, Helen S Hammer, Hannes Planatscher, Oliver Poetz","doi":"10.1080/14789450.2025.2467263","DOIUrl":"10.1080/14789450.2025.2467263","url":null,"abstract":"Introduction: Ligand binding assays combining immunoaffinity enrichment steps with mass spectrometry (MS) readout have gained attention as a highly specific and sensitive tool for protein quantification. These techniques typically combine enzymatic fragmentation of the sample or enriched protein with capture on the protein or peptide-level for quantification. Antibodies ensure specific target recognition, while MS offers quantitative accuracy with isotopically labeled internal standards. This dual approach supports a broad dynamic range, enabling protein measurements from picomolar to nanomolar levels. These methods have diverse applications, from quantifying signaling proteins in basic research to biomarker monitoring in clinical trials and analyzing the pharmacokinetics of therapeutic proteins.Areas covered: This review delves into the diverse workflows of immunoaffinity-MS, shedding light on the innovative strategies employed, their practical applications, efficacy, and inherent limitations in the realm of protein quantification.Expert opinion: Immunoaffinity-MS has transformed protein analysis, but widespread adoption is hindered by complex workflows, high instrument costs, and limited capture molecule availability. Efforts to enhance automation, standardize workflows, and advance technological innovation aim to overcome these barriers. Improvements in mass spectrometer sensitivity, advances in recombinant capture technologies, and support from public initiatives are poised to further improve the reliability and accessibility of this method.","PeriodicalId":50463,"journal":{"name":"Expert Review of Proteomics","volume":" ","pages":"123-140"},"PeriodicalIF":3.8,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143442646","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

AlphaFold and what is next: bridging functional, systems and structural biology. AlphaFold和下一步是什么：连接功能，系统和结构生物学。

IF 3.8 3区生物学

Expert Review of Proteomics Pub Date : 2025-02-01 Epub Date: 2025-02-12 DOI: 10.1080/14789450.2025.2456046

Kacper Szczepski, Łukasz Jaremko

{"title":"AlphaFold and what is next: bridging functional, systems and structural biology.","authors":"Kacper Szczepski, Łukasz Jaremko","doi":"10.1080/14789450.2025.2456046","DOIUrl":"10.1080/14789450.2025.2456046","url":null,"abstract":"Introduction: The DeepMind's AlphaFold (AF) has revolutionized biomedical and biocience research by providing both experts and non-experts with an invaluable tool for predicting protein structures. However, while AF is highly effective for predicting structures of rigid and globular proteins, it is not able to fully capture the dynamics, conformational variability, and interactions of proteins with ligands and other biomacromolecules.Areas covered: In this review, we present a comprehensive overview of the latest advancements in 3D model predictions for biomacromolecules using AF. We also provide a detailed analysis its of strengths and limitations, and explore more recent iterations, modifications, and practical applications of this strategy. Moreover, we map the path forward for expanding the landscape of AF toward predicting structures of every protein and peptide, and their interactions in the proteome in the most physiologically relevant form. This discussion is based on an extensive literature search performed using PubMed and Google Scholar.Expert opinion: While significant progress has been made to enhance AF's modeling capabilities, we argue that a combined approach integrating both various in silico and in vitro methods will be most beneficial for the future of structural biology, bridging the gaps between static and dynamic features of proteins and their functions.","PeriodicalId":50463,"journal":{"name":"Expert Review of Proteomics","volume":" ","pages":"45-58"},"PeriodicalIF":3.8,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143015483","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

Oncoproteins E6/E7 of the human papillomavirus types 16 & 18 synergize in modulating oncogenes and tumor suppressor proteins in colorectal cancer. 人乳头瘤病毒16型和18型的癌蛋白E6/E7协同调节结直肠癌的癌基因和肿瘤抑制蛋白。

IF 3.8 3区生物学

Expert Review of Proteomics Pub Date : 2025-02-01 Epub Date: 2025-02-03 DOI: 10.1080/14789450.2025.2455104

Queenie Fernandes, Lubna Therachiyil, Shahd M Younis, Said Dermime, Ala-Eddin Al Moustafa

{"title":"Oncoproteins E6/E7 of the human papillomavirus types 16 & 18 synergize in modulating oncogenes and tumor suppressor proteins in colorectal cancer.","authors":"Queenie Fernandes, Lubna Therachiyil, Shahd M Younis, Said Dermime, Ala-Eddin Al Moustafa","doi":"10.1080/14789450.2025.2455104","DOIUrl":"10.1080/14789450.2025.2455104","url":null,"abstract":"Objective: Our study presents a novel analysis of the oncogenes and tumor suppressor proteins directly modulated by E6/E7 of high-risk HPV types 16 and 18, in colorectal cancer (CRC).Methods: HCT 116 (KRAS mutant) & HT-29 (TP53 mutant) cell models of CRC were transduced with E6/E7 of HPV16 and HPV18, individually and in combination. Further, we utilized a liquid chromatography mass spectrometry (LC-MS/MS) approach to analyze and compare the proteomes of both CRC cell models.Results: We generated six stably transduced cell lines. Our data revealed a significantly higher, HPV-induced modulation of oncogenes and tumor suppressor proteins in the TP53 mutant model, as compared to the KRAS mutant model (p ≤ 0.01). Less than 1% of the genes were commonly modulated by HPV, between both models. We also report that HT-29 cells, expressing E6/E7 of both HPV types, significantly reduced the suppression of oncogenes as compared to cells expressing E6/E7 of either HPV types individually (p-value ≤0.00001).Conclusion: Our data imply that HPV coinfections leads to the sustenance of a pro-oncogenic environment in CRC. HPV modulates different oncogenes/tumor suppressor proteins in CRC of varying mutational backgrounds, thus highlighting the importance of personalized therapies for such diseases with mutational heterogeneity.","PeriodicalId":50463,"journal":{"name":"Expert Review of Proteomics","volume":" ","pages":"71-84"},"PeriodicalIF":3.8,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143015490","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

Metabolomics studies in cushing's syndrome: recent developments and perspectives. 库欣综合征的代谢组学研究：最新进展和展望。

IF 3.8 3区生物学

Expert Review of Proteomics Pub Date : 2025-02-01 Epub Date: 2025-02-10 DOI: 10.1080/14789450.2025.2463324

Sowrabha Bhat, Vanya Kadla Narayana, T S Keshava Prasad

{"title":"Metabolomics studies in cushing's syndrome: recent developments and perspectives.","authors":"Sowrabha Bhat, Vanya Kadla Narayana, T S Keshava Prasad","doi":"10.1080/14789450.2025.2463324","DOIUrl":"10.1080/14789450.2025.2463324","url":null,"abstract":"Introduction: Exogenous Cushing's syndrome is the result of long-term exposure to glucocorticoids, while endogenous Cushing's syndrome occurs due to excessive production of glucocorticoids within the body. Cushing's syndrome remains a diagnostic challenge for the treating physician.Mass spectrometry, with its better resolution, detectability, and specificity, paved the way to understanding the cellular and molecular mechanisms involved in several diseases that facilitated the evolution of biomarkers and personalized medicine, which can be applicable to manage Cushing's syndrome as well.Areas covered: There are only a few reports of mass spectrometry-based metabolomic approaches to endogenous Cushing's syndrome of certain etiologies. However, the application of this approach in the diagnosis of exogenous Cushing has not been explored much. This review attempts to discuss the application of the mass spectrometry-based metabolomic approach in the evaluation of Cushing's syndrome.Expert opinion: Global metabolomics has the potential to discover altered metabolites and associated signaling and metabolic pathways, which may serve as potential biomarkers that would help in developing tools to accelerate precision medicine. Multi-omics approaches will provide innovative solutions to develop molecular tests for multi-molecule panel assays.","PeriodicalId":50463,"journal":{"name":"Expert Review of Proteomics","volume":" ","pages":"59-69"},"PeriodicalIF":3.8,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143384062","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