Proteomes最新文献_第4页

Quantitative Differences in Rumen Epithelium Proteins in Lambs Fed Wheat, Perennial Wheat, or Perennial Wheat plus Lucerne. 饲喂小麦、多年生小麦或多年生小麦加卢塞恩的羔羊瘤胃上皮蛋白质的数量差异。

IF 3.3

Proteomes Pub Date : 2023-09-20 DOI: 10.3390/proteomes11030027

Jude Jessie Bond, Gordon Refshauge, Matthew T Newell, Benjamin W B Holman, David Wheeler, Serey Woodgate, Karthik S Kamath, Richard C Hayes

{"title":"Quantitative Differences in Rumen Epithelium Proteins in Lambs Fed Wheat, Perennial Wheat, or Perennial Wheat plus Lucerne.","authors":"Jude Jessie Bond, Gordon Refshauge, Matthew T Newell, Benjamin W B Holman, David Wheeler, Serey Woodgate, Karthik S Kamath, Richard C Hayes","doi":"10.3390/proteomes11030027","DOIUrl":"https://doi.org/10.3390/proteomes11030027","url":null,"abstract":"The value of crops such as perennial wheat (PW) for grain and grazing compared to conventional wheat (W), or the addition of lucerne to PW (PWL) is still being determined. This research sought to determine if these diets were associated with changes in the membranebound proteins that transport nutrients in the rumen epithelium (RE). Crossbred ewes (Poll Dorset × Merino) were fed W, PW, or PWL (50:50) fresh-cut forage ad libitum for 4 weeks. Average daily gain (ADG; p < 0.001) was highest in the W-fed lambs compared to the PW and PWL. Metabolisable energy intake (MEI) was higher in lambs fed W (p < 0.001) compared to PW and PWL. In pairwise comparisons of the PW and PWL diet group we found protein abundance was significantly (p < 0.05, FDR < 0.05, Benjamini p < 0.05) different in fatty acid metabolism, oxidative phosphorylation, and biosynthesis of cofactors pathways. There were not any differences in protein abundance related to nutrient transport or energy metabolism in the RE between W- vs. PW- and W- vs. PWL-fed lambs. However, in the PW- vs. PWL-fed lambs, there was a difference in the level of proteins regulating the metabolism of fatty acids and energy production in the mitochondria of the rumen epithelium.","PeriodicalId":20877,"journal":{"name":"Proteomes","volume":"11 3","pages":""},"PeriodicalIF":3.3,"publicationDate":"2023-09-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10537991/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41169445","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Algorithmically Reconstructed Molecular Pathways as the New Generation of Prognostic Molecular Biomarkers in Human Solid Cancers. 作为人类实体癌中新一代预测分子生物标志物的算法重建分子通路。

IF 3.3

Proteomes Pub Date : 2023-08-25 DOI: 10.3390/proteomes11030026

Marianna Zolotovskaia, Maks Kovalenko, Polina Pugacheva, Victor Tkachev, Alexander Simonov, Maxim Sorokin, Alexander Seryakov, Andrew Garazha, Nurshat Gaifullin, Marina Sekacheva, Galina Zakharova, Anton A Buzdin

{"title":"Algorithmically Reconstructed Molecular Pathways as the New Generation of Prognostic Molecular Biomarkers in Human Solid Cancers.","authors":"Marianna Zolotovskaia, Maks Kovalenko, Polina Pugacheva, Victor Tkachev, Alexander Simonov, Maxim Sorokin, Alexander Seryakov, Andrew Garazha, Nurshat Gaifullin, Marina Sekacheva, Galina Zakharova, Anton A Buzdin","doi":"10.3390/proteomes11030026","DOIUrl":"https://doi.org/10.3390/proteomes11030026","url":null,"abstract":"Individual gene expression and molecular pathway activation profiles were shown to be effective biomarkers in many cancers. Here, we used the human interactome model to algorithmically build 7470 molecular pathways centered around individual gene products. We assessed their associations with tumor type and survival in comparison with the previous generation of molecular pathway biomarkers (3022 \"classical\" pathways) and with the RNA transcripts or proteomic profiles of individual genes, for 8141 and 1117 samples, respectively. For all analytes in RNA and proteomic data, respectively, we found a total of 7441 and 7343 potential biomarker associations for gene-centric pathways, 3020 and 2950 for classical pathways, and 24,349 and 6742 for individual genes. Overall, the percentage of RNA biomarkers was statistically significantly higher for both types of pathways than for individual genes (p < 0.05). In turn, both types of pathways showed comparable performance. The percentage of cancer-type-specific biomarkers was comparable between proteomic and transcriptomic levels, but the proportion of survival biomarkers was dramatically lower for proteomic data. Thus, we conclude that pathway activation level is the advanced type of biomarker for RNA and proteomic data, and momentary algorithmic computer building of pathways is a new credible alternative to time-consuming hypothesis-driven manual pathway curation and reconstruction.","PeriodicalId":20877,"journal":{"name":"Proteomes","volume":"11 3","pages":""},"PeriodicalIF":3.3,"publicationDate":"2023-08-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10535530/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41161661","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Urine Peptidome Analysis Identifies Common and Stage-Specific Markers in Early Versus Advanced CKD. 尿肽组分析确定早期和晚期CKD的常见和阶段特异性标志物。

IF 3.3

Proteomes Pub Date : 2023-08-23 DOI: 10.3390/proteomes11030025

Sam Hobson, Emmanouil Mavrogeorgis, Tianlin He, Justyna Siwy, Thomas Ebert, Karolina Kublickiene, Peter Stenvinkel, Harald Mischak

{"title":"Urine Peptidome Analysis Identifies Common and Stage-Specific Markers in Early Versus Advanced CKD.","authors":"Sam Hobson, Emmanouil Mavrogeorgis, Tianlin He, Justyna Siwy, Thomas Ebert, Karolina Kublickiene, Peter Stenvinkel, Harald Mischak","doi":"10.3390/proteomes11030025","DOIUrl":"https://doi.org/10.3390/proteomes11030025","url":null,"abstract":"Given the pathophysiological continuum of chronic kidney disease (CKD), different molecular determinants affecting progression may be associated with distinct disease phases; thus, identification of these players are crucial for guiding therapeutic decisions, ideally in a non-invasive, repeatable setting. Analyzing the urinary peptidome has been proven an efficient method for biomarker determination in CKD, among other diseases. In this work, after applying several selection criteria, urine samples from 317 early (stage 2) and advanced (stage 3b-5) CKD patients were analyzed using capillary electrophoresis coupled to mass spectrometry (CE-MS). The entire two groups were initially compared to highlight the respective pathophysiology between initial and late disease phases. Subsequently, slow and fast progressors were compared within each group in an attempt to distinguish phase-specific disease progression molecules. The early vs. late-stage CKD comparison revealed 929 significantly different peptides, most of which were downregulated and 268 with collagen origins. When comparing slow vs. fast progressors in early stage CKD, 42 peptides were significantly altered, 30 of which were collagen peptide fragments. This association suggests the development of structural changes may be reversible at an early stage. The study confirms previous findings, based on its multivariable-matched progression groups derived from a large initial cohort. However, only four peptide fragments differed between slow vs. fast progressors in late-stage CKD, indicating different pathogenic processes occur in fast and slow progressors in different stages of CKD. The defined peptides associated with CKD progression at early stage might potentially constitute a non-invasive approach to improve patient management by guiding (personalized) intervention.","PeriodicalId":20877,"journal":{"name":"Proteomes","volume":"11 3","pages":""},"PeriodicalIF":3.3,"publicationDate":"2023-08-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10534506/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41131859","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Proteomics-Driven Biomarkers in Pancreatic Cancer. 胰腺癌中蛋白质组学驱动的生物标志物。

IF 3.3

Proteomes Pub Date : 2023-08-07 DOI: 10.3390/proteomes11030024

Luís Ramalhete, Emanuel Vigia, Rúben Araújo, Hugo Pinto Marques

{"title":"Proteomics-Driven Biomarkers in Pancreatic Cancer.","authors":"Luís Ramalhete, Emanuel Vigia, Rúben Araújo, Hugo Pinto Marques","doi":"10.3390/proteomes11030024","DOIUrl":"https://doi.org/10.3390/proteomes11030024","url":null,"abstract":"Pancreatic cancer is a devastating disease that has a grim prognosis, highlighting the need for improved screening, diagnosis, and treatment strategies. Currently, the sole biomarker for pancreatic ductal adenocarcinoma (PDAC) authorized by the U.S. Food and Drug Administration is CA 19-9, which proves to be the most beneficial in tracking treatment response rather than in early detection. In recent years, proteomics has emerged as a powerful tool for advancing our understanding of pancreatic cancer biology and identifying potential biomarkers and therapeutic targets. This review aims to offer a comprehensive survey of proteomics' current status in pancreatic cancer research, specifically accentuating its applications and its potential to drastically enhance screening, diagnosis, and treatment response. With respect to screening and diagnostic precision, proteomics carries the capacity to augment the sensitivity and specificity of extant screening and diagnostic methodologies. Nonetheless, more research is imperative for validating potential biomarkers and establishing standard procedures for sample preparation and data analysis. Furthermore, proteomics presents opportunities for unveiling new biomarkers and therapeutic targets, as well as fostering the development of personalized treatment strategies based on protein expression patterns associated with treatment response. In conclusion, proteomics holds great promise for advancing our understanding of pancreatic cancer biology and improving patient outcomes. It is essential to maintain momentum in investment and innovation in this arena to unearth more groundbreaking discoveries and transmute them into practical diagnostic and therapeutic strategies in the clinical context.","PeriodicalId":20877,"journal":{"name":"Proteomes","volume":"11 3","pages":""},"PeriodicalIF":3.3,"publicationDate":"2023-08-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10443269/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10055243","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 1

Comparison of Four Purification Methods on Serum Extracellular Vesicle Recovery, Size Distribution, and Proteomics. 四种纯化方法在血清细胞外囊泡回收、大小分布和蛋白质组学方面的比较。

IF 3.3

Proteomes Pub Date : 2023-07-25 DOI: 10.3390/proteomes11030023

Dianny Elizabeth Jimenez, Muhammad Tahir, Muhammad Faheem, Wellington Bruno Dos Santos Alves, Barbara de Lucena Correa, Gabriel Rocha de Andrade, Martin R Larsen, Getulio Pereira de Oliveira, Rinaldo Wellerson Pereira

{"title":"Comparison of Four Purification Methods on Serum Extracellular Vesicle Recovery, Size Distribution, and Proteomics.","authors":"Dianny Elizabeth Jimenez, Muhammad Tahir, Muhammad Faheem, Wellington Bruno Dos Santos Alves, Barbara de Lucena Correa, Gabriel Rocha de Andrade, Martin R Larsen, Getulio Pereira de Oliveira, Rinaldo Wellerson Pereira","doi":"10.3390/proteomes11030023","DOIUrl":"https://doi.org/10.3390/proteomes11030023","url":null,"abstract":"In recent decades, the role played by extracellular vesicles in physiological and pathological processes has attracted attention. Extracellular vesicles are released by different types of cells and carry molecules that could become biomarkers for the diagnosis of diseases. Extracellular vesicles are also moldable tools for the controlled release of bioactive substances in clinical and therapeutic applications. However, one of the significant challenges when studying these exciting and versatile vesicles is the purification process, which presents significant difficulties in terms of lack of purity, yield, and reproducibility, reflected in unreliable data. Therefore, our objective in the present study was to compare the proteomic profile of serum-derived EVs purified using ExoQuick™ (Systems Biosciences), Total Isolation Kit (Life Technologies), Ultracentrifugation, and Ultrafiltration. Each technique utilized for purification has shown different concentrations and populations of purified particles. The results showed marked differences in distribution, size, and protein content, demonstrating the need to develop reproducible and reliable protocols to isolate extracellular vesicles for their clinical application.","PeriodicalId":20877,"journal":{"name":"Proteomes","volume":"11 3","pages":""},"PeriodicalIF":3.3,"publicationDate":"2023-07-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10443378/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10058798","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Oncogenic Proteomics Approaches for Translational Research and HIV-Associated Malignancy Mechanisms. 用于转化研究的致癌蛋白质组学方法和艾滋病毒相关恶性肿瘤机制。

IF 3.3

Proteomes Pub Date : 2023-07-04 DOI: 10.3390/proteomes11030022

Eduardo Alvarez-Rivera, Emanuel J Ortiz-Hernández, Elyette Lugo, Lorraine M Lozada-Reyes, Nawal M Boukli

{"title":"Oncogenic Proteomics Approaches for Translational Research and HIV-Associated Malignancy Mechanisms.","authors":"Eduardo Alvarez-Rivera, Emanuel J Ortiz-Hernández, Elyette Lugo, Lorraine M Lozada-Reyes, Nawal M Boukli","doi":"10.3390/proteomes11030022","DOIUrl":"10.3390/proteomes11030022","url":null,"abstract":"Recent advances in the field of proteomics have allowed extensive insights into the molecular regulations of the cell proteome. Specifically, this allows researchers to dissect a multitude of signaling arrays while targeting for the discovery of novel protein signatures. These approaches based on data mining are becoming increasingly powerful for identifying both potential disease mechanisms as well as indicators for disease progression and overall survival predictive and prognostic molecular markers for cancer. Furthermore, mass spectrometry (MS) integrations satisfy the ongoing demand for in-depth biomarker validation. For the purpose of this review, we will highlight the current developments based on MS sensitivity, to place quantitative proteomics into clinical settings and provide a perspective to integrate proteomics data for future applications in cancer precision medicine. We will also discuss malignancies associated with oncogenic viruses such as Acquire Immunodeficiency Syndrome (AIDS) and suggest novel mechanisms behind this phenomenon. Human Immunodeficiency Virus type-1 (HIV-1) proteins are known to be oncogenic per se, to induce oxidative and endoplasmic reticulum stresses, and to be released from the infected or expressing cells. HIV-1 proteins can act alone or in collaboration with other known oncoproteins, which cause the bulk of malignancies in people living with HIV-1 on ART.","PeriodicalId":20877,"journal":{"name":"Proteomes","volume":"11 3","pages":""},"PeriodicalIF":3.3,"publicationDate":"2023-07-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10366845/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10233455","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Network-Based Prediction of Side Effects of Repurposed Antihypertensive Sartans against COVID-19 via Proteome and Drug-Target Interactomes. 通过蛋白质组和药物-靶点相互作用组，基于网络预测针对 COVID-19 的重塑用途抗高血压沙坦类药物的副作用

IF 4

Proteomes Pub Date : 2023-06-08 DOI: 10.3390/proteomes11020021

Despoina P Kiouri, Charalampos Ntallis, Konstantinos Kelaidonis, Massimiliano Peana, Sotirios Tsiodras, Thomas Mavromoustakos, Alessandro Giuliani, Harry Ridgway, Graham J Moore, John M Matsoukas, Christos T Chasapis

{"title":"Network-Based Prediction of Side Effects of Repurposed Antihypertensive Sartans against COVID-19 via Proteome and Drug-Target Interactomes.","authors":"Despoina P Kiouri, Charalampos Ntallis, Konstantinos Kelaidonis, Massimiliano Peana, Sotirios Tsiodras, Thomas Mavromoustakos, Alessandro Giuliani, Harry Ridgway, Graham J Moore, John M Matsoukas, Christos T Chasapis","doi":"10.3390/proteomes11020021","DOIUrl":"10.3390/proteomes11020021","url":null,"abstract":"The potential of targeting the Renin-Angiotensin-Aldosterone System (RAAS) as a treatment for the coronavirus disease 2019 (COVID-19) is currently under investigation. One way to combat this disease involves the repurposing of angiotensin receptor blockers (ARBs), which are antihypertensive drugs, because they bind to angiotensin-converting enzyme 2 (ACE2), which in turn interacts with the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein. However, there has been no in silico analysis of the potential toxicity risks associated with the use of these drugs for the treatment of COVID-19. To address this, a network-based bioinformatics methodology was used to investigate the potential side effects of known Food and Drug Administration (FDA)-approved antihypertensive drugs, Sartans. This involved identifying the human proteins targeted by these drugs, their first neighbors, and any drugs that bind to them using publicly available experimentally supported data, and subsequently constructing proteomes and protein-drug interactomes. This methodology was also applied to Pfizer's Paxlovid, an antiviral drug approved by the FDA for emergency use in mild-to-moderate COVID-19 treatment. The study compares the results for both drug categories and examines the potential for off-target effects, undesirable involvement in various biological processes and diseases, possible drug interactions, and the potential reduction in drug efficiency resulting from proteoform identification.","PeriodicalId":20877,"journal":{"name":"Proteomes","volume":"11 2","pages":""},"PeriodicalIF":4.0,"publicationDate":"2023-06-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10305495/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9710831","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Mass Spectrometry and Pharmacological Approaches to Measuring Cooption and Reciprocal Activation of Receptor Tyrosine Kinases. 质谱法和药理学方法测量受体酪氨酸激酶的合作与互作活化。

IF 3.3

Proteomes Pub Date : 2023-06-02 DOI: 10.3390/proteomes11020020

Jason Linzer, Zachary Phelps, Shivasuryan Vummidi, Bo Young Elizabeth Lee, Nicolas Coant, John D Haley

{"title":"Mass Spectrometry and Pharmacological Approaches to Measuring Cooption and Reciprocal Activation of Receptor Tyrosine Kinases.","authors":"Jason Linzer, Zachary Phelps, Shivasuryan Vummidi, Bo Young Elizabeth Lee, Nicolas Coant, John D Haley","doi":"10.3390/proteomes11020020","DOIUrl":"10.3390/proteomes11020020","url":null,"abstract":"Receptor tyrosine kinases (RTKs) can show extensive crosstalk, directly and indirectly. Elucidating RTK crosstalk remains an important goal in the clinical combination of anti-cancer therapies. Here, we present mass spectrometry and pharmacological approaches showing the hepatocyte growth factor receptor (MET)-promoting tyrosine phosphorylation of the epidermal growth factor receptor (EGFR) and other membrane receptors in MET-amplified H1993 NSCLC cells. Conversely, in H292 wt-EGFR NSCLC cells, EGFR promotes the tyrosine phosphorylation of MET. Reciprocal regulation of the EGFR and insulin receptor (IR) was observed in the GEO CRC cells, where inhibition of the EGFR drives tyrosine phosphorylation of the insulin receptor. Similarly, in platelet-derived growth factor receptor (PDGFR)-amplified H1703 NSCLC cells, inhibition of the EGFR promotes the tyrosine phosphorylation of the PDGFR. These RTK interactions are used to illustrate basic principles applicable to other RTK signaling networks. More specifically, we focus on two types of RTK interaction: (1) co-option of one RTK by another and (2) reciprocal activation of one receptor following the inhibition of a distinct receptor.","PeriodicalId":20877,"journal":{"name":"Proteomes","volume":"11 2","pages":""},"PeriodicalIF":3.3,"publicationDate":"2023-06-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10304582/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9719127","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Proteomics Methodologies: The Search of Protein Biomarkers Using Microfluidic Systems Coupled to Mass Spectrometry. 蛋白质组学方法:利用微流体系统耦合质谱法寻找蛋白质生物标志物。

IF 3.3

Proteomes Pub Date : 2023-05-10 DOI: 10.3390/proteomes11020019

Isabel De Figueiredo, Bernard Bartenlian, Guillaume Van der Rest, Antoine Pallandre, Frédéric Halgand

{"title":"Proteomics Methodologies: The Search of Protein Biomarkers Using Microfluidic Systems Coupled to Mass Spectrometry.","authors":"Isabel De Figueiredo, Bernard Bartenlian, Guillaume Van der Rest, Antoine Pallandre, Frédéric Halgand","doi":"10.3390/proteomes11020019","DOIUrl":"https://doi.org/10.3390/proteomes11020019","url":null,"abstract":"Protein biomarkers have been the subject of intensive studies as a target for disease diagnostics and monitoring. Indeed, biomarkers have been extensively used for personalized medicine. In biological samples, these biomarkers are most often present in low concentrations masked by a biologically complex proteome (e.g., blood) making their detection difficult. This complexity is further increased by the needs to detect proteoforms and proteome complexity such as the dynamic range of compound concentrations. The development of techniques that simultaneously pre-concentrate and identify low-abundance biomarkers in these proteomes constitutes an avant-garde approach to the early detection of pathologies. Chromatographic-based methods are widely used for protein separation, but these methods are not adapted for biomarker discovery, as they require complex sample handling due to the low biomarker concentration. Therefore, microfluidics devices have emerged as a technology to overcome these shortcomings. In terms of detection, mass spectrometry (MS) is the standard analytical tool given its high sensitivity and specificity. However, for MS, the biomarker must be introduced as pure as possible in order to avoid chemical noise and improve sensitivity. As a result, microfluidics coupled with MS has become increasingly popular in the field of biomarker discovery. This review will show the different approaches to protein enrichment using miniaturized devices and the importance of their coupling with MS.","PeriodicalId":20877,"journal":{"name":"Proteomes","volume":"11 2","pages":""},"PeriodicalIF":3.3,"publicationDate":"2023-05-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10204491/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9870510","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Proteomic Research of Extracellular Vesicles in Clinical Biofluid. 临床生物体液中细胞外囊泡的蛋白质组学研究。

IF 3.3

Proteomes Pub Date : 2023-05-06 DOI: 10.3390/proteomes11020018

Shipan Fan, Ansgar Poetsch

{"title":"Proteomic Research of Extracellular Vesicles in Clinical Biofluid.","authors":"Shipan Fan, Ansgar Poetsch","doi":"10.3390/proteomes11020018","DOIUrl":"https://doi.org/10.3390/proteomes11020018","url":null,"abstract":"Extracellular vesicles (EVs), the lipid bilayer membranous structures of particles, are produced and released from almost all cells, including eukaryotes and prokaryotes. The versatility of EVs has been investigated in various pathologies, including development, coagulation, inflammation, immune response modulation, and cell-cell communication. Proteomics technologies have revolutionized EV studies by enabling high-throughput analysis of their biomolecules to deliver comprehensive identification and quantification with rich structural information (PTMs, proteoforms). Extensive research has highlighted variations in EV cargo depending on vesicle size, origin, disease, and other features. This fact has sparked activities to use EVs for diagnosis and treatment to ultimately achieve clinical translation with recent endeavors summarized and critically reviewed in this publication. Notably, successful application and translation require a constant improvement of methods for sample preparation and analysis and their standardization, both of which are areas of active research. This review summarizes the characteristics, isolation, and identification approaches for EVs and the recent advances in EVs for clinical biofluid analysis to gain novel knowledge by employing proteomics. In addition, the current and predicted future challenges and technical barriers are also reviewed and discussed.","PeriodicalId":20877,"journal":{"name":"Proteomes","volume":"11 2","pages":""},"PeriodicalIF":3.3,"publicationDate":"2023-05-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10204453/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9568946","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 1