Expert Review of Proteomics最新文献_第2页

Two decades of advances in sequence-based prediction of MoRFs, disorder-to-order transitioning binding regions. 二十年来基于序列预测morf的进展，无序到有序过渡结合区。

IF 3.8 3区生物学

Expert Review of Proteomics Pub Date : 2025-01-01 Epub Date: 2025-01-19 DOI: 10.1080/14789450.2025.2451715

Jiangning Song, Lukasz Kurgan

{"title":"Two decades of advances in sequence-based prediction of MoRFs, disorder-to-order transitioning binding regions.","authors":"Jiangning Song, Lukasz Kurgan","doi":"10.1080/14789450.2025.2451715","DOIUrl":"10.1080/14789450.2025.2451715","url":null,"abstract":"Introduction: Molecular recognition features (MoRFs) are regions in protein sequences that undergo induced folding upon binding partner molecules. MoRFs are common in nature and can be predicted from sequences based on their distinctive sequence signatures.Areas covered: We overview 20 years of progress in the sequence-based prediction of MoRFs which resulted in the development of 25 predictors of MoRFs that interact with proteins, peptides, and lipids. These methods range from simple discriminant analysis to sophisticated deep transformer networks that use protein language models. They generate relatively accurate predictions as evidenced by the results of a recently published community-driven assessment.Expert opinion: MoRFs prediction is a mature field of research that is poised to continue at a steady pace in the foreseeable future. We anticipate further expansion of the scope of MoRF predictions to additional partner molecules, such as nucleic acids, and continued use of recent machine learning advances. Other future efforts should concentrate on improving availability of MoRF predictions by releasing, maintaining, and popularizing web servers and by depositing MoRF predictions to large databases of protein structure and function predictions. Furthermore, accurate MoRF predictions should be coupled with the equally accurate prediction and modeling of the resulting structures of complexes.","PeriodicalId":50463,"journal":{"name":"Expert Review of Proteomics","volume":" ","pages":"1-9"},"PeriodicalIF":3.8,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142958276","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

Interaction and regulation of the mitochondrial proteome - in health and disease. 线粒体蛋白质组在健康和疾病中的相互作用和调节。

IF 3.8 3区生物学

Expert Review of Proteomics Pub Date : 2025-01-01 Epub Date: 2025-01-15 DOI: 10.1080/14789450.2025.2451704

Johan Palmfeldt

{"title":"Interaction and regulation of the mitochondrial proteome - in health and disease.","authors":"Johan Palmfeldt","doi":"10.1080/14789450.2025.2451704","DOIUrl":"10.1080/14789450.2025.2451704","url":null,"abstract":"Introduction: Mitochondria contain multiple pathways including energy metabolism and several signaling and synthetic pathways. Mitochondrial proteomics is highly valuable for studying diseases including inherited metabolic disorders, complex and common disorders like neurodegeneration, diabetes, and cancer, since they all to some degree have mitochondrial underpinnings.Areas covered: The main mitochondrial functions and pathways are outlined, and systematic protein lists are presented. The main energy metabolic pathways are as follows: iron-sulfur cluster synthesis, one carbon metabolism, catabolism of hydrogen sulfide, kynurenines and reactive oxygen species (ROS), and others, described with the aim of laying a foundation for systematic mitochondrial pathway analysis based on proteomics data. The links of the proteins and pathways to functional effects and diseases are discussed. The disease examples are focussed on inherited metabolic disorders, cancer, neurological, and cardiovascular disorders.Expert opinion: To elucidate the role of mitochondria in health and disease, there is a need for comprehensive proteomics analyses with stringent, systematic data treatment for proper interpretation of mitochondrial pathway data. In that way, comprehensive hypothesis-based research can be performed based on proteomics data.","PeriodicalId":50463,"journal":{"name":"Expert Review of Proteomics","volume":" ","pages":"19-33"},"PeriodicalIF":3.8,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142980559","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

Spatial Proteomics towards cellular Resolution. 面向细胞分辨率的空间蛋白质组学。

IF 3.8 3区生物学

Expert Review of Proteomics Pub Date : 2024-12-25 DOI: 10.1080/14789450.2024.2445809

Yumi Kwon, James M Fulcher, Ljiljana Paša-Tolić, Wei-Jun Qian

{"title":"Spatial Proteomics towards cellular Resolution.","authors":"Yumi Kwon, James M Fulcher, Ljiljana Paša-Tolić, Wei-Jun Qian","doi":"10.1080/14789450.2024.2445809","DOIUrl":"10.1080/14789450.2024.2445809","url":null,"abstract":"Introduction: Spatial biology is an emerging interdisciplinary field facilitating biological discoveries through the use of spatial omics technologies. Recent advancements in spatial transcriptomics, spatial genomics (e.g. genetic mutations and epigenetic marks), multiplexed immunofluorescence, and spatial metabolomics/lipidomics have enabled high-resolution spatial profiling of gene expression, genetic variation, protein expression, and metabolites/lipids profiles in tissue. These developments contribute to a deeper understanding of the spatial organization within tissue microenvironments at the molecular level.Areas covered: This report provides an overview of the untargeted, bottom-up mass spectrometry (MS)-based spatial proteomics workflow. It highlights recent progress in tissue dissection, sample processing, bioinformatics, and liquid chromatography (LC)-MS technologies that are advancing spatial proteomics toward cellular resolution.Expert opinion: The field of untargeted MS-based spatial proteomics is rapidly evolving and holds great promise. To fully realize the potential of spatial proteomics, it is critical to advance data analysis and develop automated and intelligent tissue dissection at the cellular or subcellular level, along with high-throughput LC-MS analyses of thousands of samples. Achieving these goals will necessitate significant advancements in tissue dissection technologies, LC-MS instrumentation, and computational tools.","PeriodicalId":50463,"journal":{"name":"Expert Review of Proteomics","volume":" ","pages":"1-10"},"PeriodicalIF":3.8,"publicationDate":"2024-12-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142878616","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

Can we use proteomics to predict cardiovascular events? 我们能用蛋白质组学预测心血管事件吗？

IF 3.8 3区生物学

Expert Review of Proteomics Pub Date : 2024-12-22 DOI: 10.1080/14789450.2024.2445248

Zachery R Gregorich

引用次数: 0

Patient-responsive protein biomarkers for cartilage degeneration and repair identified in the infrapatellar fat pad. 髌下脂肪垫中软骨退变和修复的患者反应性蛋白生物标志物。

IF 3.8 3区生物学

Expert Review of Proteomics Pub Date : 2024-12-12 DOI: 10.1080/14789450.2024.2438774

Kaj S Emanuel, Luojiao Huang, Mirella J J Haartmans, Javier Sanmartin Martinez, Frank Zijta, Ron M A Heeren, Gino M M J Kerkhoffs, Pieter J Emans, Berta Cillero-Pastor

{"title":"Patient-responsive protein biomarkers for cartilage degeneration and repair identified in the infrapatellar fat pad.","authors":"Kaj S Emanuel, Luojiao Huang, Mirella J J Haartmans, Javier Sanmartin Martinez, Frank Zijta, Ron M A Heeren, Gino M M J Kerkhoffs, Pieter J Emans, Berta Cillero-Pastor","doi":"10.1080/14789450.2024.2438774","DOIUrl":"10.1080/14789450.2024.2438774","url":null,"abstract":"Objectives: Cartilage defects (CDs) are regarded as early manifestation of osteoarthritis (OA). The infrapatellar fat pad (IPFP) is an important mediator in maintaining joint homeostasis, disease progression and tissue repair, with a crucial role of its secreted proteins. Here, we investigate the proteome of the IPFP in relation to clinical status and response to surgical treatment of CDs.Methods: In order to characterize the proteome of the IPFP, samples from a cohort of 53 patients who received surgical treatment for knee CDs were analyzed with label-free proteomics. Patients were divided based on validated outcome scores for pain and knee function, preoperatively and at 1-year postoperatively, and on MRI assessment of the defect severity, fibrosis and synovitis.Results: Specific proteins were differentially abundant in patients with MRI features and better clinical outcome after CD surgery, including a downregulation of cartilage intermediate layer protein 2 (CILP-2) and microsomal glutathione s-transferase 1 (MGST1), and an upregulation of aggrecan (ACAN), and proteoglycan 4 (PRG4). Pathways related to cell interaction, oxidation and matrix remodeling were altered.Conclusion: Proteins in the IPFP that have a function in extracellular matrix, inflammation and immunomodulation were identified as potentially relevant markers for cartilage repair monitoring.","PeriodicalId":50463,"journal":{"name":"Expert Review of Proteomics","volume":" ","pages":"1-11"},"PeriodicalIF":3.8,"publicationDate":"2024-12-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142787624","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 path to anti-vector vaccines: current advances and limitations in proteomics and bioinformatics. 抗载体疫苗之路：蛋白质组学和生物信息学的当前进展和限制。

IF 3.8 3区生物学

Expert Review of Proteomics Pub Date : 2024-12-09 DOI: 10.1080/14789450.2024.2438792

Isidro Sobrino, Margarita Villar, José de la Fuente

引用次数: 0

Urine proteomics in cardiovascular disease: advances in biomarker discovery and clinical applications. 尿蛋白质组学在心血管疾病中的应用：生物标志物的发现和临床应用进展。

IF 3.8 3区生物学

Expert Review of Proteomics Pub Date : 2024-12-03 DOI: 10.1080/14789450.2024.2436401

Xiaohong Song, Zhaoran Chen, Yuehong Zheng, Jianqiang Wu

{"title":"Urine proteomics in cardiovascular disease: advances in biomarker discovery and clinical applications.","authors":"Xiaohong Song, Zhaoran Chen, Yuehong Zheng, Jianqiang Wu","doi":"10.1080/14789450.2024.2436401","DOIUrl":"10.1080/14789450.2024.2436401","url":null,"abstract":"Introduction: Cardiovascular diseases (CVDs) are the leading causes of mortality and morbidity worldwide, making early diagnosis and effective treatment essential. As a promising and noninvasive research method, urine proteomics shows excellent potential to identify reliable urinary biomarkers that could enhance prediction, prevention, and prognosis in patients with CVD.Areas covered: This review summarizes recent advancements in urinary protein biomarker profiling using urine proteomic techniques to identify potential CVD biomarkers. Additionally, it highlights potential disease biomarkers for the early detection, risk stratification, and monitoring of CVD, including hypertension, atherosclerosis, coronary artery disease, angina, myocardial infarction, heart failure, preeclampsia, and vasculitis. A literature search was conducted through Pubmed, Scopus, Google Scholar, and Web of Science. The period is January 2009 to February 2024.Expert opinion: Over the past decade, urinary proteomics has been employed in CVD research, with the potential to facilitate the discovery of novel disease biomarkers and the exploration of prospective therapeutic targets. Proteomics-based multicenter cohort studies should be conducted in the future to gain deeper insights into the pathophysiological mechanisms of CVD, accelerate the identification of potential biomarkers for disease prediction, diagnosis, and treatment, and facilitate their clinical translation.","PeriodicalId":50463,"journal":{"name":"Expert Review of Proteomics","volume":" ","pages":"1-15"},"PeriodicalIF":3.8,"publicationDate":"2024-12-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142751605","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

Identifying therapeutic strategies for triple-negative breast cancer via phosphoproteomics. 通过磷蛋白组学确定三阴性乳腺癌的治疗策略。

IF 3.8 3区生物学

Expert Review of Proteomics Pub Date : 2024-11-26 DOI: 10.1080/14789450.2024.2432477

Yuhan Sheng, Gordon Mills, Xuejiao Zhao

{"title":"Identifying therapeutic strategies for triple-negative breast cancer via phosphoproteomics.","authors":"Yuhan Sheng, Gordon Mills, Xuejiao Zhao","doi":"10.1080/14789450.2024.2432477","DOIUrl":"https://doi.org/10.1080/14789450.2024.2432477","url":null,"abstract":"Introduction: Given the poor prognosis of patients with TNBC, it is urgent to identify new biomarkers and therapeutic targets to enable personalized treatment strategies and improve patient survival. Comprehensive insights beyond genomic and transcriptomic analysis are crucial to improved outcomes for patients. As proteins are the workhorses of cellular function with their activity primarily regulated by phosphorylation, advanced phosphoproteomics techniques, such as mass spectrometry and antibody arrays, are essential for elucidating kinase signaling pathways that drive TNBC progression and contribute to therapy resistance.Area covered: This review discusses the critical need to integrate phosphoproteomics into TNBC research, evaluates commonly used technologies and their applications, and explores their advantages and limitations. We highlight significant findings from phosphoproteomic analyses in TNBC and address the challenges of implementing these technologies into clinical practice.Expert opinion: Rapid advances in phosphoproteomics analysis facilitate subtype stratification, adaptive response monitoring, and identification of biomarkers and therapeutic targets in TNBC. However, challenges in analyzing protein phosphorylation, especially in deep spatially resolved analysis of malignant cells and the tumor ecosystem, hinder the translation of phosphoproteomics to the CLIA setting. Nonetheless, phosphoproteomics offers a powerful tool that, when integrated into routine clinical practice, has the potential to revolutionize patient care.","PeriodicalId":50463,"journal":{"name":"Expert Review of Proteomics","volume":" ","pages":"1-17"},"PeriodicalIF":3.8,"publicationDate":"2024-11-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142717651","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

Proteogenomic profiling of acute myeloid leukemia to identify therapeutic targets. 对急性髓性白血病进行蛋白质基因组分析，以确定治疗目标。

IF 3.8 3区生物学

Expert Review of Proteomics Pub Date : 2024-11-22 DOI: 10.1080/14789450.2024.2431272

Heather C Murray, Jonathan Sillar, Maddison Chambers, Nicole M Verrills

{"title":"Proteogenomic profiling of acute myeloid leukemia to identify therapeutic targets.","authors":"Heather C Murray, Jonathan Sillar, Maddison Chambers, Nicole M Verrills","doi":"10.1080/14789450.2024.2431272","DOIUrl":"https://doi.org/10.1080/14789450.2024.2431272","url":null,"abstract":"Introduction: Acute myeloid leukemia (AML) is an aggressive and poor-prognosis blood cancer. Despite a low mutation burden compared to other cancers, AML is heterogenous and identifying robust therapeutic targets has been difficult. Genomic profiling has greatly advanced our understanding of AML, and has revealed targets for AML therapy. However, only 50% of AML patients have gene mutations that are currently druggable, and relapse rates remain high. The addition of proteomic profiling is emerging to address these challenges.Areas covered: Using references collected through Pubmed, we review recent studies that have combined genomic and proteomic profiling (i.e. proteogenomic profiling), as well as studies that have additionally integrated other omics approaches, such as phosphoproteomics. We highlight how proteogenomic profiling promises to deconvolve the cellular pathways driving leukemogenesis, uncover novel therapeutic targets, and identify biomarkers of response to novel and existing therapies.Expert opinion: Proteogenomic profiling is providing unparalleled insight into AML, and is beginning to identify robust biomarkers. Standardization of workflows will be required before mass spectrometry-based proteomic assays can be integrated into routine clinical use. However, the demonstrated ability to adapt signatures into biomarker panels that can be assayed by existing clinical workflows is enabling current clinical translation.","PeriodicalId":50463,"journal":{"name":"Expert Review of Proteomics","volume":" ","pages":"1-14"},"PeriodicalIF":3.8,"publicationDate":"2024-11-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142689424","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 insights into the extracellular matrix: a focus on proteoforms and their implications in health and disease. 细胞外基质的蛋白质组学研究：关注蛋白质形式及其对健康和疾病的影响。

IF 3.8 3区生物学

Expert Review of Proteomics Pub Date : 2024-11-01 Epub Date: 2024-11-15 DOI: 10.1080/14789450.2024.2427136

Amanpreet Kaur Bains, Alexandra Naba

{"title":"Proteomic insights into the extracellular matrix: a focus on proteoforms and their implications in health and disease.","authors":"Amanpreet Kaur Bains, Alexandra Naba","doi":"10.1080/14789450.2024.2427136","DOIUrl":"10.1080/14789450.2024.2427136","url":null,"abstract":"Introduction: The extracellular matrix (ECM) is a highly organized and dynamic network of proteins and glycosaminoglycans that provides critical structural, mechanical, and biochemical support to cells. The functions of the ECM are directly influenced by the conformation of the proteins that compose it. ECM proteoforms, which can result from genetic, transcriptional, and/or post-translational modifications, adopt different conformations and, consequently, confer different structural properties and functionalities to the ECM in both physiological and pathological contexts.Areas covered: In this review, we discuss how bottom-up proteomics has been applied to identify, map, and quantify post-translational modifications (e.g. additions of chemical groups, proteolytic cleavage, or cross-links) and ECM proteoforms arising from alternative splicing or genetic variants. We further illustrate how proteoform-level information can be leveraged to gain novel insights into ECM protein structure and ECM functions in health and disease.Expert opinion: In the Expert opinion section, we discuss remaining challenges and opportunities with an emphasis on the importance of devising experimental and computational methods tailored to account for the unique biochemical properties of ECM proteins with the goal of increasing sequence coverage and, hence, accurate ECM proteoform identification.","PeriodicalId":50463,"journal":{"name":"Expert Review of Proteomics","volume":" ","pages":"463-481"},"PeriodicalIF":3.8,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11602344/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142607406","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0