Expert Review of Proteomics最新文献_第9页

Biochemical and proteomic insights into sarcoplasmic reticulum Ca²⁺-ATPase complexes in skeletal muscles. 骨骼肌肌浆网Ca2+-ATP酶复合物的生化和蛋白质组学研究。

IF 3.4 3区生物学

Expert Review of Proteomics Pub Date : 2023-07-01 Epub Date: 2023-09-07 DOI: 10.1080/14789450.2023.2255743

Paul Dowling, Dieter Swandulla, Kay Ohlendieck

{"title":"Biochemical and proteomic insights into sarcoplasmic reticulum Ca2+-ATPase complexes in skeletal muscles.","authors":"Paul Dowling, Dieter Swandulla, Kay Ohlendieck","doi":"10.1080/14789450.2023.2255743","DOIUrl":"10.1080/14789450.2023.2255743","url":null,"abstract":"Introduction: Skeletal muscles contain large numbers of high-molecular-mass protein complexes in elaborate membrane systems. Integral membrane proteins are involved in diverse cellular functions including the regulation of ion handling, membrane homeostasis, energy metabolism and force transmission.Areas covered: The proteomic profiling of membrane proteins and large protein assemblies in skeletal muscles are outlined in this article. This includes a critical overview of the main biochemical separation techniques and the mass spectrometric approaches taken to study membrane proteins. As an illustrative example of an analytically challenging large protein complex, the proteomic detection and characterization of the Ca2+-ATPase of the sarcoplasmic reticulum is discussed. The biological role of this large protein complex during normal muscle functioning, in the context of fiber type diversity and in relation to mechanisms of physiological adaptations and pathophysiological abnormalities is evaluated from a proteomics perspective.Expert opinion: Mass spectrometry-based muscle proteomics has decisively advanced the field of basic and applied myology. Although it is technically challenging to study membrane proteins, innovations in protein separation methodology in combination with sensitive mass spectrometry and improved systems bioinformatics has allowed the detailed proteomic detection and characterization of skeletal muscle membrane protein complexes, such as Ca2+-pump proteins of the sarcoplasmic reticulum.","PeriodicalId":50463,"journal":{"name":"Expert Review of Proteomics","volume":" ","pages":"125-142"},"PeriodicalIF":3.4,"publicationDate":"2023-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10166439","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: 1

Improving single cell proteomics experiments: how can we best utilize latest-generation data acquisition and MS instrument architecture? 改进单细胞蛋白质组学实验：我们如何最好地利用最新一代的数据采集和MS仪器架构？

IF 3.4 3区生物学

Expert Review of Proteomics Pub Date : 2023-07-01 Epub Date: 2023-09-16 DOI: 10.1080/14789450.2023.2260954

Manuel Matzinger, Karl Mechtler

引用次数: 0

Utilizing databases for astrocyte secretome research. 利用数据库进行星形胶质细胞分泌组研究。

IF 3.4 3区生物学

Expert Review of Proteomics Pub Date : 2023-07-01 Epub Date: 2023-12-30 DOI: 10.1080/14789450.2023.2285311

Ruqayya Afridi, Won-Ha Lee, Jong-Heon Kim, Kyoungho Suk

{"title":"Utilizing databases for astrocyte secretome research.","authors":"Ruqayya Afridi, Won-Ha Lee, Jong-Heon Kim, Kyoungho Suk","doi":"10.1080/14789450.2023.2285311","DOIUrl":"10.1080/14789450.2023.2285311","url":null,"abstract":"Introduction: Astrocytes are the most abundant cell type in the central nervous system (CNS). They play a pivotal role in supporting neuronal function and maintaining homeostasis by releasing a variety of bioactive proteins, collectively known as the astrocyte secretome. Investigating secretome provides insights into the molecular mechanisms underlying astrocyte function and dysfunction, as well as novel strategies to prevent and treat diseases affecting the CNS.Areas covered: Proteomics databases are a valuable resource for studying the role of astrocytes in healthy and diseased brain function, as they provide information about gene expression, protein expression, and cellular function. In this review, we discuss existing databases that are useful for astrocyte secretome research.Expert opinion: Astrocyte secretomics is a field that is rapidly progressing, yet the availability of dedicated databases is currently limited. To meet the increasing demand for comprehensive omics data in glia research, developing databases specifically focused on astrocyte secretome is crucial. Such databases would allow researchers to investigate the intricate molecular landscape of astrocytes and comprehend their involvement in diverse physiological and pathological processes. Expanding resources through the development of databases dedicated to the astrocyte secretome may facilitate further advancements in this field.","PeriodicalId":50463,"journal":{"name":"Expert Review of Proteomics","volume":" ","pages":"371-379"},"PeriodicalIF":3.4,"publicationDate":"2023-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"136400121","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

Understanding the age-related alterations in the testis-specific proteome. 了解睾丸特异性蛋白质组中与年龄相关的变化。

IF 3.4 3区生物学

Expert Review of Proteomics Pub Date : 2023-07-01 Epub Date: 2023-12-30 DOI: 10.1080/14789450.2023.2274857

Ana D Martins, João C Ribeiro, Rita Ferreira, Marco G Alves, Pedro F Oliveira

{"title":"Understanding the age-related alterations in the testis-specific proteome.","authors":"Ana D Martins, João C Ribeiro, Rita Ferreira, Marco G Alves, Pedro F Oliveira","doi":"10.1080/14789450.2023.2274857","DOIUrl":"10.1080/14789450.2023.2274857","url":null,"abstract":"Introduction: Fertility rates in developing countries have declined over the past decades, and the trend of delayed fatherhood is rising as societies develop. The reasons behind the decline in male fertility with advancing age remain mysterious, making it a compelling and crucial area for further research. However, the limited number of studies dedicated to unraveling this enigma poses a challenge. Thus, our objective is to illuminate some of the upregulated and downregulated mechanisms in the male testis during the aging process.Areas covered: Herein, we present a critical overview of the studies addressing the alterations of testicular proteome through the aging process, starting from sexually matured young males to end-of-life-expectancy aged males. The comparative studies of the proteomic testicular profile of men with and without spermatogenic impairment are also discussed and key proteins and pathways involved are highlighted.Expert opinion: The difficulty of making age-comparative studies, especially of advanced-age study subjects, makes this topic of study quite challenging. Another topic worth mentioning is the heterogeneous nature and vast cellular composition of testicular tissue, which makes proteome data interpretation tricky. The cell type sorting and comorbidities testing in the testicular tissue of the studied subjects would help mitigate these problems.","PeriodicalId":50463,"journal":{"name":"Expert Review of Proteomics","volume":" ","pages":"331-343"},"PeriodicalIF":3.4,"publicationDate":"2023-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"50163506","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 advances in proteomic-based diagnostics of cystic fibrosis. 囊性纤维化基于蛋白质组学诊断的最新进展。

IF 3.4 3区生物学

Expert Review of Proteomics Pub Date : 2023-07-01 Epub Date: 2023-10-16 DOI: 10.1080/14789450.2023.2258282

Refat M Nimer, Anas M Abdel Rahman

{"title":"Recent advances in proteomic-based diagnostics of cystic fibrosis.","authors":"Refat M Nimer, Anas M Abdel Rahman","doi":"10.1080/14789450.2023.2258282","DOIUrl":"10.1080/14789450.2023.2258282","url":null,"abstract":"Introduction: Cystic fibrosis (CF) is a genetic disease characterized by thick and sticky mucus accumulation, which may harm numerous internal organs. Various variables such as gene modifiers, environmental factors, age of diagnosis, and CF transmembrane conductance regulator (CFTR) gene mutations influence phenotypic disease diversity. Biomarkers that are based on genomic information may not accurately represent the underlying mechanism of the disease as well as its lethal complications. Therefore, recent advancements in mass spectrometry (MS)-based proteomics may provide deep insights into CF mechanisms and cellular functions by examining alterations in the protein expression patterns from various samples of individuals with CF.Areas covered: We present current developments in MS-based proteomics, its application, and findings in CF. In addition, the future roles of proteomics in finding diagnostic and prognostic novel biomarkers.Expert opinion: Despite significant advances in MS-based proteomics, extensive research in a large cohort for identifying and validating diagnostic, prognostic, predictive, and therapeutic biomarkers for CF disease is highly needed.","PeriodicalId":50463,"journal":{"name":"Expert Review of Proteomics","volume":" ","pages":"151-169"},"PeriodicalIF":3.4,"publicationDate":"2023-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41138729","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

Integrating analysis of proteome profile and drug screening identifies therapeutic potential of MET pathway for the treatment of malignant peripheral nerve sheath tumor. 结合蛋白质组谱分析和药物筛选，确定MET通路治疗恶性周围神经鞘肿瘤的治疗潜力。

IF 3.4 3区生物学

Expert Review of Proteomics Pub Date : 2023-04-01 DOI: 10.1080/14789450.2023.2218035

Ryuto Tsuchiya, Yuki Yoshimatsu, Rei Noguchi, Yooksil Sin, Takuya Ono, Taro Akiyama, Hidetaka Kosako, Akihiko Yoshida, Seiji Ohtori, Akira Kawai, Tadashi Kondo

{"title":"Integrating analysis of proteome profile and drug screening identifies therapeutic potential of MET pathway for the treatment of malignant peripheral nerve sheath tumor.","authors":"Ryuto Tsuchiya, Yuki Yoshimatsu, Rei Noguchi, Yooksil Sin, Takuya Ono, Taro Akiyama, Hidetaka Kosako, Akihiko Yoshida, Seiji Ohtori, Akira Kawai, Tadashi Kondo","doi":"10.1080/14789450.2023.2218035","DOIUrl":"https://doi.org/10.1080/14789450.2023.2218035","url":null,"abstract":"Background: Malignant peripheral nerve sheath tumor (MPNST) is an aggressive sarcoma with a poor prognosis that requires novel therapeutic agents. Proteome information is useful for identifying new therapeutic candidates because it directly reflects the biological phenotype. Additionally, in vitro drug screening is an effective tool to identify candidate drugs for common cancers. Hence, we attempted to identify novel therapeutic candidates for MPNST by integrating proteomic analysis and drug screening.Methods: We performed comprehensive proteomic analysis on 23 MPNST tumor samples using liquid chromatography - tandem mass spectrometry to identify therapeutic targets. We also conducted drug screening of six MPNST cell lines using 214 drugs.Results: Proteomic analysis revealed that the MET and IGF pathways were significantly enriched in the local recurrence/distant metastasis group of MPNST, whereas drug screening revealed that 24 drugs showed remarkable antitumor effects on the MPNST cell lines. By integrating the results of these two approaches, MET inhibitors, crizotinib and foretinib, were identified as novel therapeutic candidates for the treatment of MPNST.Conclusions: We successfully identified novel therapeutic candidates for the treatment of MPNST, namely crizotinib and foretinib, which target the MET pathway. We hope that these candidate drugs will contribute to the treatment of MPNST.","PeriodicalId":50463,"journal":{"name":"Expert Review of Proteomics","volume":"20 4-6","pages":"109-119"},"PeriodicalIF":3.4,"publicationDate":"2023-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9740793","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

Evaluation of a 'plug and play' nanoflow liquid chromatography system for MS-based proteomic characterization of clinical FFPE specimens. 评价“即插即用”纳米流液相色谱系统用于临床FFPE标本的MS-based蛋白质组学表征。

IF 3.4 3区生物学

Expert Review of Proteomics Pub Date : 2023-04-01 DOI: 10.1080/14789450.2023.2219844

Georgia Mitsa, Vincent R Richard, Yasamin Majedi, Josiane Lafleur, Adriana Aguilar-Mahecha, Mark Basik, Christoph H Borchers

{"title":"Evaluation of a 'plug and play' nanoflow liquid chromatography system for MS-based proteomic characterization of clinical FFPE specimens.","authors":"Georgia Mitsa, Vincent R Richard, Yasamin Majedi, Josiane Lafleur, Adriana Aguilar-Mahecha, Mark Basik, Christoph H Borchers","doi":"10.1080/14789450.2023.2219844","DOIUrl":"https://doi.org/10.1080/14789450.2023.2219844","url":null,"abstract":"Introduction: Proteomic analysis of formalin-fixed paraffin-embedded (FFPE) tumor tissue specimens has gained interest in the last 5 years due to technological advances and improved sample collection, as well as biobanking for clinical trials. The real-world implementation of clinical proteomics to these specimens, however, is hampered by tedious sample preparation steps and long instrument acquisition times.Areas covered: To advance the translation of quantitative proteomics into the clinic, we are comparing the performance of the leading commercial nanoflow liquid chromatography (nLC) system (based on literature reviews), the Easy-nLC 1200 (Thermo Fisher Scientific, Waltham, MA, U.S.A.), to the Evosep One HPLC (Evosep Biosystems, Odense, Denmark). We measured FFPE-tissue digests from 21 biological replicates with a similar gradient on both of the LC systems while keeping the on-column amount (1 µg total protein) and the single-shot data-dependent acquisition-based MS/MS method constant.Expert opinion: Overall, the Evosep One facilitates robust and sensitive high-throughput sample acquisition, making it suitable for clinical MS. We found the Evosep One to be a useful platform for positioning mass spectrometry-based proteomics in the clinical setting. The clinical application of nLC/MS will inform clinical decision-making in oncology and other diseases.","PeriodicalId":50463,"journal":{"name":"Expert Review of Proteomics","volume":"20 4-6","pages":"87-92"},"PeriodicalIF":3.4,"publicationDate":"2023-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9752610","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 tools to study phosphorylation of intrinsically disordered proteins. 蛋白质组学工具用于研究内在无序蛋白的磷酸化。

IF 3.4 3区生物学

Expert Review of Proteomics Pub Date : 2023-04-01 DOI: 10.1080/14789450.2023.2217359

Barbara Spolaore, Luca Secco, Giulia Rocca, Guidalberto Manfioletti, Giorgio Arrigoni, Riccardo Sgarra

{"title":"Proteomic tools to study phosphorylation of intrinsically disordered proteins.","authors":"Barbara Spolaore, Luca Secco, Giulia Rocca, Guidalberto Manfioletti, Giorgio Arrigoni, Riccardo Sgarra","doi":"10.1080/14789450.2023.2217359","DOIUrl":"https://doi.org/10.1080/14789450.2023.2217359","url":null,"abstract":"Introduction: Intrinsically disordered proteins (IDPs) represent a family of proteins that lack secondary or tertiary structure. IDPs are hubs in interaction networks, participate in liquid-liquid phase separation processes, and drive the formation of proteinaceous membrane-less organelles. Their unfolded structure makes them particularly prone to post-translational modifications (PTMs) that play key functional modulatory roles.Areas covered: We discuss different analytical approaches to study phosphorylation of IDPs starting from methods for IDP enrichment (strong acid extractions and heat-based pre-fractionation), strategies to enrich and map phosphopeptides/proteins, and mass spectrometry-based tools to study the phosphorylation-dependent conformational alterations of IDPs (limited proteolysis, HDX, chemical cross-linking, covalent labeling, and ion mobility).Expert opinion: There is a growing interest in IDPs and their PTMs since they are involved in several diseases. The intrinsic disorder could be exploited to facilitate purification and synthetic production of IDPs taking full advantage of those structural mass-spectrometry-based methods that can be used to investigate IDPs and their phospho-dependent conformational alterations. The diffusion and implementation of mass spectrometers with ion mobility devices and electron transfer dissociation capabilities could be key-elements for increasing information on IDP biology.","PeriodicalId":50463,"journal":{"name":"Expert Review of Proteomics","volume":"20 4-6","pages":"93-107"},"PeriodicalIF":3.4,"publicationDate":"2023-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10108674","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

Advances in the clinical use of metaproteomics. 元蛋白质组学的临床应用进展。

IF 3.4 3区生物学

Expert Review of Proteomics Pub Date : 2023-04-01 DOI: 10.1080/14789450.2023.2215440

Maximilian Wolf, Kay Schallert, Luca Knipper, Albert Sickmann, Alexander Sczyrba, Dirk Benndorf, Robert Heyer

引用次数: 1

Data-independent acquisition mass spectrometry reveals comprehensive plasma protein profiles in the natural history of patients with hereditary transthyretin amyloidosis (ATTRv). 数据独立采集质谱揭示了遗传性甲状腺转蛋白淀粉样变性(ATTRv)患者自然史中的全面血浆蛋白谱。

IF 3.4 3区生物学

Expert Review of Proteomics Pub Date : 2023-01-01 DOI: 10.1080/14789450.2023.2195096

Shan He, XinYue He, RuoKai Pan, LuRong Pan, Xiaoying Lv, YuTong Jin, Yue Fan, YuTong Wang, Zhuang Tian, ShuYang Zhang

{"title":"Data-independent acquisition mass spectrometry reveals comprehensive plasma protein profiles in the natural history of patients with hereditary transthyretin amyloidosis (ATTRv).","authors":"Shan He, XinYue He, RuoKai Pan, LuRong Pan, Xiaoying Lv, YuTong Jin, Yue Fan, YuTong Wang, Zhuang Tian, ShuYang Zhang","doi":"10.1080/14789450.2023.2195096","DOIUrl":"https://doi.org/10.1080/14789450.2023.2195096","url":null,"abstract":"Objectives: Hereditary transthyretin amyloidosis (ATTRv) is a rare, fatal, autosomal dominant disease with more than 140 mutations discovered. Three phenotypes of amyloid infiltration are neuropathy (ATTRv-PN), cardiopathy (ATTRv-CM), and neuropathy + cardiopathy (ATTRv-MIX). The lack of ATTR-specific biomarkers, difficulties in biopsy evidence, and limited known pathogenic mechanisms have made diagnosis difficult. Newly emerging noninvasive measures for monitoring progression and disease-modifying therapies have improved early diagnosis and patient management.Methods: Our research applies the latest technology, Data-Independent Acquisition-Based Quantitative Proteomics (DIA), to reveal comprehensive plasma protein profiles in the natural history of Chinese patients with hereditary transthyretin amyloidosis (ATTRv). We analyzed differentially expressed proteins (DEPs) in three phenotypes (ATTRv-PN, ATTRv-CM, and ATTRv-MIX).Results: Serum samples were collected from a total of 18 patients (6 ATTRv-PN, 5 ATTRv-CM, and 7 ATTRv-MIX patients) and 20 healthy participants as a control group. Combined with the results of the proteomic and bioinformatic analyses, we found 30 DEPs and protein interaction networks clustered in KRT family proteins and DSC3 between ATTRv-PN and the control, which were rich in the estrogen signaling pathway and the cell adhesion molecule (CAM) pathway.Conclusion: This study demonstrates a global and significant proteomic profile in different stages of ATTRv.","PeriodicalId":50463,"journal":{"name":"Expert Review of Proteomics","volume":"20 1-3","pages":"57-69"},"PeriodicalIF":3.4,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9536233","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