Proteomics最新文献

{"title":"Recent Advances in Labeling-Based Quantitative Glycomics: From High-Throughput Quantification to Structural Elucidation.","authors":"Zicong Wang, Jingwei Zhang, Lingjun Li","doi":"10.1002/pmic.202400057","DOIUrl":"10.1002/pmic.202400057","url":null,"abstract":"<p><p>Glycosylation, a crucial posttranslational modification (PTM), plays important roles in numerous biological processes and is linked to various diseases. Despite its significance, the structural complexity and diversity of glycans present significant challenges for mass spectrometry (MS)-based quantitative analysis. This review aims to provide an in-depth overview of recent advancements in labeling strategies for N-glycomics and O-glycomics, with a specific focus on enhancing the sensitivity, specificity, and throughput of MS analyses. We categorize these advancements into three major areas: (1) the development of isotopic/isobaric labeling techniques that significantly improve multiplexing capacity and throughput for glycan quantification; (2) novel methods that aid in the structural elucidation of complex glycans, particularly sialylated and fucosylated glycans; and (3) labeling techniques that enhance detection ionization efficiency, separation, and sensitivity for matrix-assisted laser desorption/ionization (MALDI)-MS and capillary electrophoresis (CE)-based glycan analysis. In addition, we highlight emerging trends in single-cell glycomics and bioinformatics tools that have the potential to revolutionize glycan quantification. These developments not only expand our understanding of glycan structures and functions but also open new avenues for biomarker discovery and therapeutic applications. Through detailed discussions of methodological advancements, this review underscores the critical role of derivatization methods in advancing glycan identification and quantification.</p>","PeriodicalId":224,"journal":{"name":"Proteomics","volume":" ","pages":"e202400057"},"PeriodicalIF":3.4,"publicationDate":"2024-11-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142708787","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Urinary Proteomics and Systems Biology Link Eight Proteins to the Higher Risk of Hypertension and Related Complications in Blacks Versus Whites.","authors":"De-Wei An, Dries S Martens, Gontse G Mokwatsi, Yu-Ling Yu, Babangida S Chori, Agnieszka Latosinska, Godsent Isiguzo, Susanne Eder, Dong-Yan Zhang, Gert Mayer, Ruan Kruger, Jana Brguljan-Hitij, Christian Delles, Catharina M C Mels, Katarzyna Stolarz-Skrzypek, Marek Rajzer, Peter Verhamme, Aletta E Schutte, Tim S Nawrot, Yan Li, Harald Mischak, Augustine N Odili, Jan A Staessen","doi":"10.1002/pmic.202400207","DOIUrl":"https://doi.org/10.1002/pmic.202400207","url":null,"abstract":"<p><p>Blacks are more prone to salt-sensitive hypertension than Whites. This cross-sectional analysis of a multi-ethnic cohort aimed to search for proteins potentially involved in the susceptibility to salt sensitivity, hypertension, and hypertension-related complications. The study included individuals enrolled in African Prospective Study on the Early Detection and Identification of Cardiovascular Disease and Hypertension (African-PREDICT), Flemish Study of the Environment, Genes and Health Outcomes (FLEMENGHO), Prospective Cohort Study in Patients with Type 2 Diabetes Mellitus for Validation of Biomarkers (PROVALID)-Austria, and Urinary Proteomics Combined with Home Blood Pressure Telemonitoring for Health Care Reform Trial (UPRIGHT-HTM). Sequenced urinary peptides detectable in 70% of participants allowed the identification of parental proteins and were compared between Blacks and Whites. Of 513 urinary peptides, 300 had significantly different levels among healthy Black (n = 476) and White (n = 483) South Africans sharing the same environment. Analyses contrasting 582 Blacks versus 1731 Whites, and Sub-Saharan Blacks versus European Whites replicated the findings. COL4A1, COL4A2, FGA, PROC, MGP, MYOCD, FYXD2, and UMOD were identified as the most likely candidates underlying the racially different susceptibility to salt sensitivity, hypertension, and related complications. Enriched pathways included hemostasis, platelet activity, collagens, biology of the extracellular matrix, and protein digestion and absorption. Our study suggests that MGP and MYOCD being involved in cardiovascular function, FGA and PROC in coagulation, FYXD2 and UMOD in salt homeostasis, and COL4A1 and COL4A2 as major components of the glomerular basement membrane are among the many proteins potentially incriminated in the higher susceptibility of Blacks compared to Whites to salt sensitivity, hypertension, and its complication. Nevertheless, these eight proteins and their associated pathways deserve further exploration in molecular and human studies as potential targets for intervention to reduce the excess risk of hypertension and cardiovascular complications in Blacks versus Whites.</p>","PeriodicalId":224,"journal":{"name":"Proteomics","volume":" ","pages":"e202400207"},"PeriodicalIF":3.4,"publicationDate":"2024-11-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142708789","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"(Prote)omics for Superior Management of Kidney and Cardiovascular Disease-A Thought-Provoking Impulse From Nephrology.","authors":"Joachim Beige, Michael Masanneck","doi":"10.1002/pmic.202400143","DOIUrl":"https://doi.org/10.1002/pmic.202400143","url":null,"abstract":"<p><p>Chronic kidney disease (CKD) and cardiovascular disease (CVD) are complex conditions often managed by nephrologists. This viewpoint paper advocates for a multi-omics approach, integrating clinical symptom patterns, non-invasive biomarkers, imaging and invasive diagnostics to enhance diagnosis and treatment. Early detection of molecular changes, particularly in collagen turnover, is crucial for preventing disease progression. For instance, urinary proteomics can detect early molecular changes in diabetic kidney disease (DKD), heart failure (HF) and coronary artery disease (CAD), enabling proactive interventions and reducing the need for invasive procedures like renal biopsies. For example, urinary proteomic patterns can differentiate between glomerular and extraglomerular pathologies, aiding in the diagnosis of specific kidney diseases. Additionally, urinary peptides can predict CKD progression and HF development, offering a non-invasive alternative to traditional biomarkers like eGFR and NT-proBNP. The integration of multi-omics data with artificial intelligence (AI) holds promise for personalised treatment strategies, optimizing patient outcomes. This approach can also reduce healthcare costs by minimizing unnecessary invasive procedures and hospitalizations. In conclusion, the adoption of multi-omics and non-invasive biomarkers in nephrology and cardiology can revolutionize disease management, enabling early detection, personalised treatment and improved patient outcomes.</p>","PeriodicalId":224,"journal":{"name":"Proteomics","volume":" ","pages":"e202400143"},"PeriodicalIF":3.4,"publicationDate":"2024-11-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142708779","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Editorial Board: Proteomics 21–22'24","authors":"","doi":"10.1002/pmic.202470172","DOIUrl":"https://doi.org/10.1002/pmic.202470172","url":null,"abstract":"","PeriodicalId":224,"journal":{"name":"Proteomics","volume":"24 21-22","pages":""},"PeriodicalIF":3.4,"publicationDate":"2024-11-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/pmic.202470172","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142685336","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Contents: Proteomics 21–22'24","authors":"","doi":"10.1002/pmic.202470173","DOIUrl":"https://doi.org/10.1002/pmic.202470173","url":null,"abstract":"","PeriodicalId":224,"journal":{"name":"Proteomics","volume":"24 21-22","pages":""},"PeriodicalIF":3.4,"publicationDate":"2024-11-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/pmic.202470173","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142692073","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Standard abbreviations","authors":"","doi":"10.1002/pmic.202470174","DOIUrl":"10.1002/pmic.202470174","url":null,"abstract":"","PeriodicalId":224,"journal":{"name":"Proteomics","volume":"24 21-22","pages":""},"PeriodicalIF":3.4,"publicationDate":"2024-11-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142674591","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Special Issue on “Metaproteomics and meta-omics perspectives to decrypt Microbiome Functionality”","authors":"Lucia Grenga,&nbsp;Magnus Øverlie Arntzen,&nbsp;Jean Armengaud","doi":"10.1002/pmic.202400072","DOIUrl":"10.1002/pmic.202400072","url":null,"abstract":"&lt;p&gt;&lt;i&gt;Proteomics&lt;/i&gt; is inviting submissions to a special issue dedicated to microbiome research, emphasizing the integration of omics to uncover the functionality of microbiomes. This special issue is tentatively scheduled for publication for mid-2025. It provides an ideal platform for showcasing cutting-edge research on microbiomes, proposing new strategies to make the most of acquired molecular data, and fostering discussions on the future prospects of metaproteomics in the field and the synergies with other omics. The objective of this special issue is to cover the full spectrum of technologies aimed at enhancing our understanding of microbiome and holobionts' function and illustrate their practical applications. We encourage submissions from all areas of microbiome research focusing on functionality. We are open to considering different types of papers, including research articles, review articles, technical briefs, dataset briefs, and viewpoint articles.&lt;/p&gt;&lt;p&gt;Microorganisms contribute to crucial biological processes within vast and intricate ecosystems like soils and oceans [&lt;span&gt;1&lt;/span&gt;]. Typically operating within complex communities known as microbiota, microorganisms employ an ingenious mixture of task specialization, cooperation, and competition as a winning strategy to navigate environmental conditions [&lt;span&gt;2&lt;/span&gt;] and ensure the stability of ecosystems [&lt;span&gt;3&lt;/span&gt;]. Establishing symbiotic relationships with their hosts if any, they often provide mutual benefits, although in some instances, they may contribute to host diseases. The significance of ecosystem services rendered by microbiota is increasingly recognized, underscoring the growing importance of characterizing these ecosystems. Enhanced understanding holds promise for diverse fields, including medicine, well-being, food industry, agriculture, animal breeding and fish farming, biotechnology, remediation and protection of the environment.&lt;/p&gt;&lt;p&gt;It's time to face the music and admit that exploring microbial communities will entail an extra layer of challenging hurdles due to their extensive taxonomic diversity, genomic heterogeneity, dynamic nature, and our limited understanding of their components, which primarily focuses on cultivable species [&lt;span&gt;4&lt;/span&gt;]. Beyond mere taxonomic catalogue of microorganisms within a microbiota and their enumeration to determine their abundance, it is crucial to discern who the active contributors are and what the ongoing molecular processes are to grasp these biological systems fully. The functionality of microbiomes involves a complex interplay of numerous interconnected variables, ranging from genetic makeup and mRNA transcripts to proteins and their potential post-translational modifications, inherent protein catalytic properties, subcellular localization, and the resultant enzymatic products that can retroact on catalysis levels. Omics technologies have become indispensable in unravelling the intricacies of these molecular pro","PeriodicalId":224,"journal":{"name":"Proteomics","volume":"24 23-24","pages":""},"PeriodicalIF":3.4,"publicationDate":"2024-11-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/pmic.202400072","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142646460","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"In-Depth Proteome Profiling of the Hippocampus of LDLR Knockout Mice Reveals Alternation in Synaptic Signaling Pathway.","authors":"Hong-Beom Park, Hyeyoon Kim, Dohyun Han","doi":"10.1002/pmic.202400152","DOIUrl":"https://doi.org/10.1002/pmic.202400152","url":null,"abstract":"<p><p>The low-density lipoprotein receptor (LDLR) is a major apolipoprotein receptor that regulates cholesterol homeostasis. LDLR deficiency is associated with cognitive impairment by the induction of synaptopathy in the hippocampus. Despite the close relationship between LDLR and neurodegenerative disorders, proteomics research for protein profiling in the LDLR knockout (KO) model remains insufficient. Therefore, understanding LDLR KO-mediated differential protein expression within the hippocampus is crucial for elucidating a role of LDLR in neurodegenerative disorders. In this study, we conducted first-time proteomic profiling of hippocampus tissue from LDLR KO mice using tandem mass tag (TMT)-based MS analysis. LDLR deficiency induces changes in proteins associated with the transport of diverse molecules, and activity of kinase and catalyst within the hippocampus. Additionally, significant alterations in the expression of components in the major synaptic pathways were found. Furthermore, these synaptic effects were verified using a data-independent acquisition (DIA)-based proteomic method. Our data will serve as a valuable resource for further studies to discover the molecular function of LDLR in neurodegenerative disorders.</p>","PeriodicalId":224,"journal":{"name":"Proteomics","volume":" ","pages":"e202400152"},"PeriodicalIF":3.4,"publicationDate":"2024-11-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142643571","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Review and Practical Guide for Getting Started With Single-Cell Proteomics.","authors":"Hsien-Jung L Lin, Kei G I Webber, Andikan J Nwosu, Ryan T Kelly","doi":"10.1002/pmic.202400021","DOIUrl":"https://doi.org/10.1002/pmic.202400021","url":null,"abstract":"<p><p>Single-cell proteomics (SCP) has advanced significantly in recent years, with new tools specifically designed for the preparation and analysis of single cells now commercially available to researchers. The field is sufficiently mature to be broadly accessible to any lab capable of isolating single cells and performing bulk-scale proteomic analyses. In this review, we highlight recent work in the SCP field that has significantly lowered the barrier to entry, thus providing a practical guide for those who are newly entering the SCP field. We outline the fundamental principles and report multiple paths to accomplish the key steps of a successful SCP experiment including sample preparation, separation, and mass spectrometry data acquisition and analysis. We recommend that researchers start with a label-free SCP workflow, as achieving high-quality and quantitatively accurate results is more straightforward than label-based multiplexed strategies. By leveraging these accessible means, researchers can confidently perform SCP experiments and make meaningful discoveries at the single-cell level.</p>","PeriodicalId":224,"journal":{"name":"Proteomics","volume":" ","pages":"e202400021"},"PeriodicalIF":3.4,"publicationDate":"2024-11-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142643573","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Parallel Analyses by Mass Spectrometry (MS) and Reverse Phase Protein Array (RPPA) Reveal Complementary Proteomic Profiles in Triple-Negative Breast Cancer (TNBC) Patient Tissues and Cell Cultures.","authors":"Nan Wang, Yiying Zhu, Lianshui Wang, Wenshuang Dai, Taobo Hu, Zhentao Song, Xia Li, Qi Zhang, Jianfei Ma, Qianghua Xia, Jin Li, Yiqiang Liu, Mengping Long, Zhiyong Ding","doi":"10.1002/pmic.202400107","DOIUrl":"https://doi.org/10.1002/pmic.202400107","url":null,"abstract":"<p><p>High-plex proteomic technologies have made substantial contributions to mechanism studies and biomarker discovery in complex diseases, particularly cancer. Despite technological advancements, inherent limitations in individual proteomic approaches persist, impeding the achievement of comprehensive quantitative insights into the proteome. In this study, we employed two widely used proteomic technologies, mass spectrometry (MS) and reverse phase protein array (RPPA) to analyze identical samples, aiming to systematically assess the outcomes and performance of the different technologies. Additionally, we sought to establish an integrated workflow by combining these two proteomic approaches to augment the coverage of protein targets for discovery purposes. We used 14 fresh frozen tissue samples from triple-negative breast cancer (TNBC: seven tumors versus seven adjacent non-cancerous tissues) and cell line samples to evaluate both technologies and implement this dual-proteomic strategy. Using a single-step protein denaturation and extraction protocol, protein samples were subjected to reverse-phase liquid chromatography (LC) followed by electrospray ionization (ESI)-mediated MS/MS for proteomic profiling. Concurrently, identical sample aliquots were analyzed by RPPA for profiling of over 300 proteins and phosphoproteins that are in key signaling pathways or druggable targets in cancer. Both proteomic methods demonstrated the expected ability to differentiate samples by groups, revealing distinct proteomic patterns under various experimental conditions, albeit with minimal overlap in identified targets. Mechanism-based analysis uncovered divergent biological processes identified with the two proteomic technologies, capitalizing on their complementary exploratory potential.</p>","PeriodicalId":224,"journal":{"name":"Proteomics","volume":" ","pages":"e202400107"},"PeriodicalIF":3.4,"publicationDate":"2024-11-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142643572","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}