Expert Review of Proteomics最新文献_第7页

How glycomic studies can impact on prostate cancer. 糖组学研究如何影响前列腺癌症。

IF 3.4 3区生物学

Expert Review of Proteomics Pub Date : 2023-07-01 Epub Date: 2023-10-27 DOI: 10.1080/14789450.2023.2265061

Jan Tkac, Tomas Bertok

引用次数: 0

A computational method for the prediction and functional analysis of potential Mycobacterium tuberculosis adhesin-related proteins. 一种用于预测和功能分析潜在结核分枝杆菌粘附素相关蛋白的计算方法。

IF 3.4 3区生物学

Expert Review of Proteomics Pub Date : 2023-07-01 Epub Date: 2023-12-30 DOI: 10.1080/14789450.2023.2275678

Rivesh Maharajh, Manormoney Pillay, Sibusiso Senzani

{"title":"A computational method for the prediction and functional analysis of potential Mycobacterium tuberculosis adhesin-related proteins.","authors":"Rivesh Maharajh, Manormoney Pillay, Sibusiso Senzani","doi":"10.1080/14789450.2023.2275678","DOIUrl":"10.1080/14789450.2023.2275678","url":null,"abstract":"Objectives: Mycobacterial adherence plays a major role in the establishment of infection within the host. Adhesin-related proteins attach to host receptors and cell-surface components. The current study aimed to utilize in-silico strategies to determine the adhesin potential of conserved hypothetical (CH) proteins.Methods: Computational analysis was performed on the whole Mycobacterium tuberculosis H37Rv proteome using a software program for the prediction of adhesin and adhesin-like proteins using neural networks (SPAAN) to determine the adhesin potential of CH proteins. A robust pipeline of computational analysis tools: Phyre2 and pFam for homology prediction; Mycosub, PsortB, and Loctree3 for subcellular localization; SignalP-5.0 and SecretomeP-2.0 for secretory prediction, were utilized to identify adhesin candidates.Results: SPAAN revealed 776 potential adhesins within the whole MTB H37Rv proteome. Comprehensive analysis of the literature was cross-tabulated with SPAAN to verify the adhesin prediction potential of known adhesin (n = 34). However, approximately a third of known adhesins were below the probability of adhesin (Pad) threshold (Pad ≥0.51). Subsequently, 167 CH proteins of interest were categorized using essential in-silico tools.Conclusion: The use of SPAAN with supporting in-silico tools should be fundamental when identifying novel adhesins. This study provides a pipeline to identify CH proteins as functional adhesin molecules.","PeriodicalId":50463,"journal":{"name":"Expert Review of Proteomics","volume":" ","pages":"483-493"},"PeriodicalIF":3.4,"publicationDate":"2023-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49693533","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 use of urine peptidomics to define dietary gluten peptides from patients with celiac disease and the clinical relevance. 尿肽组学用于确定乳糜泻患者的膳食谷蛋白肽及其临床相关性。

IF 3.4 3区生物学

Expert Review of Proteomics Pub Date : 2023-07-01 Epub Date: 2023-10-30 DOI: 10.1080/14789450.2023.2270775

Chiara Monachesi, Giulia Catassi, Carlo Catassi

{"title":"The use of urine peptidomics to define dietary gluten peptides from patients with celiac disease and the clinical relevance.","authors":"Chiara Monachesi, Giulia Catassi, Carlo Catassi","doi":"10.1080/14789450.2023.2270775","DOIUrl":"10.1080/14789450.2023.2270775","url":null,"abstract":"Introduction: Determination of urinary gluten immunogenic peptides (GIP) has emerged as one of the most attractive test to monitor the adherence to the gluten-free diet (GFD) of patients with celiac disease (CD), being a simple, noninvasive and direct method to detect gluten contamination of the GFD.Areas covered: We conducted a scoping review in Medline (PubMed) of articles published up to April 2023 that analyzed any aspect of the clinical relevance of the use of urinary GIP measurement in patients with CD. A total of 17 articles reporting the clinical use of urinary peptidomics for the follow-up of CD patients were finally included.Expert opinion: Available data suggest that a negative urinary GIP result is a reliable noninvasive predictor of intestinal mucosa healing in CD patients treated with the GFD, especially if testing three urine samples on different days including the weekend. Due to conflicting results about the sensitivity and the specificity of the urinary GIP determination, additional in-depth information is needed, particularly related to (1) the relationship between the amount of ingested gluten and the quantity of urinary GIP excreted in treated CD patients, (2) the GIP kinetics and best timing for sample collection.","PeriodicalId":50463,"journal":{"name":"Expert Review of Proteomics","volume":" ","pages":"281-290"},"PeriodicalIF":3.4,"publicationDate":"2023-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49684452","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

A Galaxy of informatics resources for MS-based proteomics. 基于MS的蛋白质组学的信息学资源星系。

IF 3.4 3区生物学

Expert Review of Proteomics Pub Date : 2023-07-01 Epub Date: 2023-10-30 DOI: 10.1080/14789450.2023.2265062

Subina Mehta, Matthias Bernt, Matthew Chambers, Matthias Fahrner, Melanie Christine Föll, Bjoern Gruening, Carlos Horro, James E Johnson, Valentin Loux, Andrew T Rajczewski, Oliver Schilling, Yves Vandenbrouck, Ove Johan Ragnar Gustafsson, W C Mike Thang, Cameron Hyde, Gareth Price, Pratik D Jagtap, Timothy J Griffin

{"title":"A Galaxy of informatics resources for MS-based proteomics.","authors":"Subina Mehta, Matthias Bernt, Matthew Chambers, Matthias Fahrner, Melanie Christine Föll, Bjoern Gruening, Carlos Horro, James E Johnson, Valentin Loux, Andrew T Rajczewski, Oliver Schilling, Yves Vandenbrouck, Ove Johan Ragnar Gustafsson, W C Mike Thang, Cameron Hyde, Gareth Price, Pratik D Jagtap, Timothy J Griffin","doi":"10.1080/14789450.2023.2265062","DOIUrl":"10.1080/14789450.2023.2265062","url":null,"abstract":"Introduction: Continuous advances in mass spectrometry (MS) technologies have enabled deeper and more reproducible proteome characterization and a better understanding of biological systems when integrated with other 'omics data. Bioinformatic resources meeting the analysis requirements of increasingly complex MS-based proteomic data and associated multi-omic data are critically needed. These requirements included availability of software that would span diverse types of analyses, scalability for large-scale, compute-intensive applications, and mechanisms to ease adoption of the software.Areas covered: The Galaxy ecosystem meets these requirements by offering a multitude of open-source tools for MS-based proteomics analyses and applications, all in an adaptable, scalable, and accessible computing environment. A thriving global community maintains these software and associated training resources to empower researcher-driven analyses.Expert opinion: The community-supported Galaxy ecosystem remains a crucial contributor to basic biological and clinical studies using MS-based proteomics. In addition to the current status of Galaxy-based resources, we describe ongoing developments for meeting emerging challenges in MS-based proteomic informatics. We hope this review will catalyze increased use of Galaxy by researchers employing MS-based proteomics and inspire software developers to join the community and implement new tools, workflows, and associated training content that will add further value to this already rich ecosystem.","PeriodicalId":50463,"journal":{"name":"Expert Review of Proteomics","volume":" ","pages":"251-266"},"PeriodicalIF":3.4,"publicationDate":"2023-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41118584","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: 2

Glycobiology and proteomics: has mass spectrometry moved the field forward? 糖生物学和蛋白质组学：质谱技术是否推动了该领域的发展？

IF 3.8 3区生物学

Expert Review of Proteomics Pub Date : 2023-07-01 Epub Date: 2023-09-05 DOI: 10.1080/14789450.2023.2255748

Senhan Xu, Ronghu Wu

引用次数: 0

A proteome-level view of brain tumors for a better understanding of novel diagnosis, prognosis, and therapy. 脑肿瘤的蛋白质组水平的观点，以更好地了解新的诊断，预后和治疗。

IF 3.4 3区生物学

Expert Review of Proteomics Pub Date : 2023-07-01 Epub Date: 2023-12-30 DOI: 10.1080/14789450.2023.2283498

Medha Gayathri J Pai, Deeptarup Biswas, Ayushi Verma, Sanjeeva Srivastava

{"title":"A proteome-level view of brain tumors for a better understanding of novel diagnosis, prognosis, and therapy.","authors":"Medha Gayathri J Pai, Deeptarup Biswas, Ayushi Verma, Sanjeeva Srivastava","doi":"10.1080/14789450.2023.2283498","DOIUrl":"10.1080/14789450.2023.2283498","url":null,"abstract":"Introduction: Brain tumors are complex and heterogeneous malignancies with significant challenges in diagnosis, prognosis, and therapy. Proteomics, the large-scale study of proteins and their functions, has emerged as a powerful tool to comprehensively investigate the molecular mechanisms underlying brain tumor regulation.Areas covered: This review explores brain tumors from a proteomic standpoint, highlighting recent progress and insights gained through proteomic methods. It delves into the proteomic techniques employed and underscores potential biomarkers for early detection, prognosis, and treatment planning. Recent PubMed Central proteomic studies (2017-present) are discussed, summarizing findings on altered protein expression, post-translational changes, and protein interactions. This sheds light on brain tumor signaling pathways and their significance in innovative therapeutic approaches.Expert opinion: Proteomics offers immense potential for revolutionizing brain tumor diagnosis and therapy. To unlock its full benefits, further translational research is crucial. Combining proteomics with other omics data enhances our grasp of brain tumors. Validating and translating proteomic biomarkers are vital for better patient results. Challenges include tumor complexity, lack of curated proteomic databases, and the need for collaboration between researchers and clinicians. Overcoming these challenges requires investment in technology, data sharing, and translational research.","PeriodicalId":50463,"journal":{"name":"Expert Review of Proteomics","volume":" ","pages":"381-395"},"PeriodicalIF":3.4,"publicationDate":"2023-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"134650412","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 in diabetes mellitus: clinical insight. 糖尿病的代谢组学：临床见解。

IF 3.4 3区生物学

Expert Review of Proteomics Pub Date : 2023-07-01 Epub Date: 2023-12-30 DOI: 10.1080/14789450.2023.2295866

Shereen M Aleidi, Hiba Al Fahmawi, Afshan Masoud, Anas Abdel Rahman

{"title":"Metabolomics in diabetes mellitus: clinical insight.","authors":"Shereen M Aleidi, Hiba Al Fahmawi, Afshan Masoud, Anas Abdel Rahman","doi":"10.1080/14789450.2023.2295866","DOIUrl":"10.1080/14789450.2023.2295866","url":null,"abstract":"Introduction: Diabetes Mellitus (DM) is a chronic heterogeneous metabolic disorder characterized by hyperglycemia due to the destruction of insulin-producing pancreatic β cells and/or insulin resistance. It is now considered a global epidemic disease associated with serious threats to a patient's life. Understanding the metabolic pathways involved in disease pathogenesis and progression is important and would improve prevention and management strategies. Metabolomics is an emerging field of research that offers valuable insights into the metabolic perturbation associated with metabolic diseases, including DM.Area covered: Herein, we discussed the metabolomics in type 1 and 2 DM research, including its contribution to understanding disease pathogenesis and identifying potential novel biomarkers clinically useful for disease screening, monitoring, and prognosis. In addition, we highlighted the metabolic changes associated with treatment effects, including insulin and different anti-diabetic medications.Expert opinion: By analyzing the metabolome, the metabolic disturbances involved in T1DM and T2DM can be explored, enhancing our understanding of the disease progression and potentially leading to novel clinical diagnostic and effective new therapeutic approaches. In addition, identifying specific metabolites would be potential clinical biomarkers for predicting the disease and thus preventing and managing hyperglycemia and its complications.","PeriodicalId":50463,"journal":{"name":"Expert Review of Proteomics","volume":" ","pages":"451-467"},"PeriodicalIF":3.4,"publicationDate":"2023-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138812702","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

How can proteomics help solve the lack of biomarkers to aid in the early diagnosis of motor neuron disease (MND)? 蛋白质组学如何帮助解决运动神经元疾病（MND）早期诊断缺乏生物标志物的问题？

IF 3.4 3区生物学

Expert Review of Proteomics Pub Date : 2023-07-01 Epub Date: 2023-07-24 DOI: 10.1080/14789450.2023.2240513

Hannah Jane Suddull, Livia Rosa-Fernandes, Albert Lee

引用次数: 0

Next-generation proteomics technologies in Alzheimer's disease: from clinical research to routine diagnostics. 阿尔茨海默病的下一代蛋白质组学技术：从临床研究到常规诊断。

IF 3.4 3区生物学

Expert Review of Proteomics Pub Date : 2023-07-01 Epub Date: 2023-09-13 DOI: 10.1080/14789450.2023.2255752

Sophia Weiner, Kaj Blennow, Henrik Zetterberg, Johan Gobom

{"title":"Next-generation proteomics technologies in Alzheimer's disease: from clinical research to routine diagnostics.","authors":"Sophia Weiner, Kaj Blennow, Henrik Zetterberg, Johan Gobom","doi":"10.1080/14789450.2023.2255752","DOIUrl":"10.1080/14789450.2023.2255752","url":null,"abstract":"Introduction: Clinical proteomics studies of Alzheimer's disease (AD) research aim to identify biomarkers useful for clinical research, diagnostics, and improve our understanding of the pathological processes involved in the disease. The rapidly increasing performance of proteomics technologies is likely to have great impact on AD research.Areas covered: We review recent proteomics approaches that have advanced the field of clinical AD research. Specifically, we discuss the application of targeted mass spectrometry (MS), labeling-based and label-free MS-based as well as affinity-based proteomics to AD biomarker development, underpinning their importance with the latest impactful clinical studies. We evaluate how proteomics technologies have been adapted to meet current challenges. Finally, we discuss the limitations and potential of proteomics techniques and whether their scope might extend beyond current research-based applications.Expert opinion: To date, proteomics technologies in the AD field have been largely limited to AD biomarker discovery. The recent development of the first successful disease-modifying treatments of AD will further increase the need for blood biomarkers for early, accurate diagnosis, and CSF biomarkers that reflect specific pathological processes. Proteomics has the potential to meet these requirements and to progress into clinical routine practice, provided that current limitations are overcome.","PeriodicalId":50463,"journal":{"name":"Expert Review of Proteomics","volume":" ","pages":"143-150"},"PeriodicalIF":3.4,"publicationDate":"2023-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10278636","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

Positional proteomics: is the technology ready to study clinical cohorts? 位置蛋白质组学：这项技术准备好研究临床队列了吗？

IF 3.4 3区生物学

Expert Review of Proteomics Pub Date : 2023-07-01 Epub Date: 2023-12-30 DOI: 10.1080/14789450.2023.2272046

Philipp F Lange, Oliver Schilling, Pitter F Huesgen

{"title":"Positional proteomics: is the technology ready to study clinical cohorts?","authors":"Philipp F Lange, Oliver Schilling, Pitter F Huesgen","doi":"10.1080/14789450.2023.2272046","DOIUrl":"10.1080/14789450.2023.2272046","url":null,"abstract":"Introduction: Positional proteomics provides proteome-wide information on protein termini and their modifications, uniquely enabling unambiguous identification of site-specific, limited proteolysis. Such proteolytic cleavage irreversibly modifies protein sequences resulting in new proteoforms with distinct protease-generated neo-N and C-termini and altered localization and activity. Misregulated proteolysis is implicated in a wide variety of human diseases. Protein termini, therefore, constitute a huge, largely unexplored source of specific analytes that provides a deep view into the functional proteome and a treasure trove for biomarkers.Areas covered: We briefly review principal approaches to define protein termini and discuss recent advances in method development. We further highlight the potential of positional proteomics to identify and trace specific proteoforms, with a focus on proteolytic processes altered in disease. Lastly, we discuss current challenges and potential for applying positional proteomics in biomarker and pre-clinical research.Expert opinion: Recent developments in positional proteomics have provided significant advances in sensitivity and throughput. In-depth analysis of proteolytic processes in clinical cohorts thus appears feasible in the near future. We argue that this will provide insights into the functional state of the proteome and offer new opportunities to utilize proteolytic processes altered or targeted in disease as specific diagnostic, prognostic and companion biomarkers.","PeriodicalId":50463,"journal":{"name":"Expert Review of Proteomics","volume":" ","pages":"309-318"},"PeriodicalIF":3.4,"publicationDate":"2023-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49693534","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