Expert Review of Proteomics最新文献

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 : 2025-04-20 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":"https://doi.org/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":"1-9"},"PeriodicalIF":3.8,"publicationDate":"2025-04-20","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

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 : 2025-04-18 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":"https://doi.org/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 DNA 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 acid research. In the future, IMAC should be integrated with other 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":""},"PeriodicalIF":3.8,"publicationDate":"2025-04-18","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

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

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