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Comprehensive mass spectrometry based biomarker discovery and validation platform as applied to diabetic kidney disease 基于综合质谱的生物标志物发现和验证平台应用于糖尿病肾病
EuPA Open Proteomics Pub Date : 2017-03-01 DOI: 10.1016/j.euprot.2016.12.001
Scott D. Bringans , Jun Ito , Thomas Stoll , Kaye Winfield , Michael Phillips , Kirsten Peters , Wendy A. Davis , Timothy M.E. Davis , Richard J. Lipscombe
{"title":"Comprehensive mass spectrometry based biomarker discovery and validation platform as applied to diabetic kidney disease","authors":"Scott D. Bringans ,&nbsp;Jun Ito ,&nbsp;Thomas Stoll ,&nbsp;Kaye Winfield ,&nbsp;Michael Phillips ,&nbsp;Kirsten Peters ,&nbsp;Wendy A. Davis ,&nbsp;Timothy M.E. Davis ,&nbsp;Richard J. Lipscombe","doi":"10.1016/j.euprot.2016.12.001","DOIUrl":"10.1016/j.euprot.2016.12.001","url":null,"abstract":"<div><p>A protein biomarker discovery workflow was applied to plasma samples from patients at different stages of diabetic kidney disease. The proteomics platform produced a panel of significant plasma biomarkers that were statistically scrutinised against the current gold standard tests on an analysis of 572 patients. Five proteins were significantly associated with diabetic kidney disease defined by albuminuria, renal impairment (eGFR) and chronic kidney disease staging (CKD Stage ≥1, ROC curve of 0.77). The results prove the suitability and efficacy of the process used, and introduce a biomarker panel with the potential to improve diagnosis of diabetic kidney disease.</p></div>","PeriodicalId":38260,"journal":{"name":"EuPA Open Proteomics","volume":"14 ","pages":"Pages 1-10"},"PeriodicalIF":0.0,"publicationDate":"2017-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.euprot.2016.12.001","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"36221006","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: 28
Prediction of protein-DNA interactions of transcription factors linking proteomics and transcriptomics data 结合蛋白质组学和转录组学数据的转录因子的蛋白质- dna相互作用预测
EuPA Open Proteomics Pub Date : 2016-12-01 DOI: 10.1016/j.euprot.2016.09.001
Yu. Kondrakhin , T. Valeev , R. Sharipov , I. Yevshin , F. Kolpakov , A. Kel
{"title":"Prediction of protein-DNA interactions of transcription factors linking proteomics and transcriptomics data","authors":"Yu. Kondrakhin ,&nbsp;T. Valeev ,&nbsp;R. Sharipov ,&nbsp;I. Yevshin ,&nbsp;F. Kolpakov ,&nbsp;A. Kel","doi":"10.1016/j.euprot.2016.09.001","DOIUrl":"10.1016/j.euprot.2016.09.001","url":null,"abstract":"<div><p>We compared positional weight matrix-based prediction methods for transcription factor (TF) binding sites using selected fraction of ChIP-seq data with the help of partial AUC measure (limited to false positive rate 0.1, that is the most relevant for the application of the TF search in the genome scale). Comparison of three prediction methods—additive, multiplicative and information-vector based (MATCH) showed an advantage of the MATCH method for majority of transcription factors tested. We demonstrated that application of TF site identifying methods can help to connect the proteomics and phosphoproteomics world of signaling networks to gene regulation and transcriptomics world.</p></div>","PeriodicalId":38260,"journal":{"name":"EuPA Open Proteomics","volume":"13 ","pages":"Pages 14-23"},"PeriodicalIF":0.0,"publicationDate":"2016-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.euprot.2016.09.001","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"36220032","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: 4
Multi-omics “upstream analysis” of regulatory genomic regions helps identifying targets against methotrexate resistance of colon cancer 调控基因组区域的多组学“上游分析”有助于确定结肠癌抗甲氨蝶呤耐药的靶标
EuPA Open Proteomics Pub Date : 2016-12-01 DOI: 10.1016/j.euprot.2016.09.002
Alexander E. Kel , Philip Stegmaier , Tagir Valeev , Jeannette Koschmann , Vladimir Poroikov , Olga V. Kel-Margoulis , Edgar Wingender
{"title":"Multi-omics “upstream analysis” of regulatory genomic regions helps identifying targets against methotrexate resistance of colon cancer","authors":"Alexander E. Kel ,&nbsp;Philip Stegmaier ,&nbsp;Tagir Valeev ,&nbsp;Jeannette Koschmann ,&nbsp;Vladimir Poroikov ,&nbsp;Olga V. Kel-Margoulis ,&nbsp;Edgar Wingender","doi":"10.1016/j.euprot.2016.09.002","DOIUrl":"10.1016/j.euprot.2016.09.002","url":null,"abstract":"<div><p>We present an “upstream analysis” strategy for causal analysis of multiple “-omics” data. It analyzes promoters using the TRANSFAC database, combines it with an analysis of the upstream signal transduction pathways and identifies master regulators as potential drug targets for a pathological process. We applied this approach to a complex multi-omics data set that contains transcriptomics, proteomics and epigenomics data. We identified the following potential drug targets against induced resistance of cancer cells towards chemotherapy by methotrexate (MTX): TGFalpha, IGFBP7, alpha9-integrin, and the following chemical compounds: zardaverine and divalproex as well as human metabolites such as nicotinamide N-oxide.</p></div>","PeriodicalId":38260,"journal":{"name":"EuPA Open Proteomics","volume":"13 ","pages":"Pages 1-13"},"PeriodicalIF":0.0,"publicationDate":"2016-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.euprot.2016.09.002","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"36220031","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: 37
Set up of a protocol for rat plasma peptidomics in hemorrhagic shock model in presence of heparin 建立肝素存在下失血性休克模型大鼠血浆肽组学研究方案
EuPA Open Proteomics Pub Date : 2016-09-01 DOI: 10.1016/j.euprot.2016.03.004
Elisa Maffioli , Federico Aletti , Fabiana Santagata , Armando Negri , Marco H. Santamaria , Frank A. De Lano , Erik B. Kistler , Geert W. Schmid-Schönbein , Gabriella Tedeschi
{"title":"Set up of a protocol for rat plasma peptidomics in hemorrhagic shock model in presence of heparin","authors":"Elisa Maffioli ,&nbsp;Federico Aletti ,&nbsp;Fabiana Santagata ,&nbsp;Armando Negri ,&nbsp;Marco H. Santamaria ,&nbsp;Frank A. De Lano ,&nbsp;Erik B. Kistler ,&nbsp;Geert W. Schmid-Schönbein ,&nbsp;Gabriella Tedeschi","doi":"10.1016/j.euprot.2016.03.004","DOIUrl":"10.1016/j.euprot.2016.03.004","url":null,"abstract":"<div><p>A preliminary mass spectrometry based shotgun protocol was set up to compare the peptidome of plasma samples from healthy and hemorrhagic shock rats with the aim of verifying the possible role of uncontrolled proteolytic activity in circulatory shock. Since the hemorrhagic shock model requires heparin as anticoagulant, a preliminary experiment using plasma sample obtained in the presence/absence of heparin from healthy rats was performed to determine whether its presence is fully compatible with the peptidomic protocol proposed. The entire protocol was tested in a pilot experiment to compare the peptidome of healthy or heparin-anticoagulated rats subjected to hemorrhagic shock.</p></div>","PeriodicalId":38260,"journal":{"name":"EuPA Open Proteomics","volume":"12 ","pages":"Pages 1-3"},"PeriodicalIF":0.0,"publicationDate":"2016-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.euprot.2016.03.004","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"36220026","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: 3
Proteomics and its impact on food allergy diagnosis 蛋白质组学及其在食物过敏诊断中的作用
EuPA Open Proteomics Pub Date : 2016-09-01 DOI: 10.1016/j.euprot.2016.03.016
Karin Hoffmann-Sommergruber
{"title":"Proteomics and its impact on food allergy diagnosis","authors":"Karin Hoffmann-Sommergruber","doi":"10.1016/j.euprot.2016.03.016","DOIUrl":"10.1016/j.euprot.2016.03.016","url":null,"abstract":"<div><p>Food allergies are a relevant health problem and symptoms range from mild to severe life-threatening reactions. With the help of up to date proteomics the causative food allergens can be identified from individual food sources. A short overview on the application of proteomics to assess the physicochemical properties of food allergens is presented.</p></div>","PeriodicalId":38260,"journal":{"name":"EuPA Open Proteomics","volume":"12 ","pages":"Pages 10-12"},"PeriodicalIF":0.0,"publicationDate":"2016-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.euprot.2016.03.016","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"36220027","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: 15
Top-down proteomic characterization of DAOY medulloblastoma tumor cell line 自顶向下的成神经管细胞瘤细胞系的蛋白质组学特征
EuPA Open Proteomics Pub Date : 2016-09-01 DOI: 10.1016/j.euprot.2016.03.015
Claudia Martelli , Luca D’Angelo , Marta Barba , Mirko Baranzini , Ilaria Inserra , Federica Iavarone , Federica Vincenzoni , Gianpiero Tamburrini , Luca Massimi , Concezio Di Rocco , Massimo Caldarelli , Irene Messana , Fabrizio Michetti , Massimo Castagnola , Wanda Lattanzi , Claudia Desiderio
{"title":"Top-down proteomic characterization of DAOY medulloblastoma tumor cell line","authors":"Claudia Martelli ,&nbsp;Luca D’Angelo ,&nbsp;Marta Barba ,&nbsp;Mirko Baranzini ,&nbsp;Ilaria Inserra ,&nbsp;Federica Iavarone ,&nbsp;Federica Vincenzoni ,&nbsp;Gianpiero Tamburrini ,&nbsp;Luca Massimi ,&nbsp;Concezio Di Rocco ,&nbsp;Massimo Caldarelli ,&nbsp;Irene Messana ,&nbsp;Fabrizio Michetti ,&nbsp;Massimo Castagnola ,&nbsp;Wanda Lattanzi ,&nbsp;Claudia Desiderio","doi":"10.1016/j.euprot.2016.03.015","DOIUrl":"10.1016/j.euprot.2016.03.015","url":null,"abstract":"<div><p>The proteome of the DAOY medulloblastoma cell line has been investigated by an LC–MS top-down platform. This approach, unlike bottom-up ones, allows identifying proteins and peptides in their intact/native forms, disclosing post-translational modifications, proteoforms and naturally occurring peptides. Indeed, 25 out of the 53 proteins identified, were not previously characterized in DAOY cells. Most of them were functionally interconnected, being mainly involved in binding, catalytic and structural activities, and metabolic processes. The top-down approach, applied in this preliminary study, disclosed the presence of several naturally occurring peptide fragments that characterize DAOY cells.</p></div>","PeriodicalId":38260,"journal":{"name":"EuPA Open Proteomics","volume":"12 ","pages":"Pages 13-21"},"PeriodicalIF":0.0,"publicationDate":"2016-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.euprot.2016.03.015","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"36220029","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: 3
Sprague Dawley rats: A model of successful heart aging Sprague Dawley大鼠:成功的心脏衰老模型
EuPA Open Proteomics Pub Date : 2016-09-01 DOI: 10.1016/j.euprot.2016.03.017
Daniele Capitanio , Roberta Leone , Chiara Fania , Enrica Torretta , Cecilia Gelfi
{"title":"Sprague Dawley rats: A model of successful heart aging","authors":"Daniele Capitanio ,&nbsp;Roberta Leone ,&nbsp;Chiara Fania ,&nbsp;Enrica Torretta ,&nbsp;Cecilia Gelfi","doi":"10.1016/j.euprot.2016.03.017","DOIUrl":"10.1016/j.euprot.2016.03.017","url":null,"abstract":"<div><p>Aging is a universal phenomenon involving the whole body and is characterized by metabolic and physiological decline, leading to cardiovascular defects and heart failure.</p><p>To characterize the molecular basis of physiological cardiac aging, the proteomic profiles of Sprague Dawley rat hearts of 6, 22 and 30 months were analysed by DIGE and immunoblotting.</p><p>Results indicate changes in myosin binding protein C, aldehyde dehydrogenase, serpins and sirtuin-3 which protects from the opening of the mitochondrial permeability transition pore induced by cyclophilin D increment.</p><p>Conversely, an increase of fusion, a decrease of mitochondrial fission and the activation of the non-canonical autophagy pathway were observed. These results support the hypothesis of successful aging in this rat model.</p></div>","PeriodicalId":38260,"journal":{"name":"EuPA Open Proteomics","volume":"12 ","pages":"Pages 22-30"},"PeriodicalIF":0.0,"publicationDate":"2016-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.euprot.2016.03.017","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"36220030","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: 7
Metabolite extraction for high-throughput FTICR-MS-based metabolomics of grapevine leaves 基于fticr - ms的葡萄叶片代谢组学的高通量代谢产物提取
EuPA Open Proteomics Pub Date : 2016-09-01 DOI: 10.1016/j.euprot.2016.03.002
Marisa Maia , Filipa Monteiro , Mónica Sebastiana , Ana Patrícia Marques , António E.N. Ferreira , Ana Ponces Freire , Carlos Cordeiro , Andreia Figueiredo , Marta Sousa Silva
{"title":"Metabolite extraction for high-throughput FTICR-MS-based metabolomics of grapevine leaves","authors":"Marisa Maia ,&nbsp;Filipa Monteiro ,&nbsp;Mónica Sebastiana ,&nbsp;Ana Patrícia Marques ,&nbsp;António E.N. Ferreira ,&nbsp;Ana Ponces Freire ,&nbsp;Carlos Cordeiro ,&nbsp;Andreia Figueiredo ,&nbsp;Marta Sousa Silva","doi":"10.1016/j.euprot.2016.03.002","DOIUrl":"10.1016/j.euprot.2016.03.002","url":null,"abstract":"<div><p>In metabolomics there is an ever-growing need for faster and more comprehensive analysis methods to cope with the increase of biological studies. Direct infusion Fourier-transform ion cyclotron-resonance mass spectrometry (DI-FTICR-MS) is used in non-targeted metabolomics to obtain high-resolution snapshots of the metabolic state of a system. In any metabolic profiling study, the establishment of an effective metabolite extraction protocol is paramount. We developed an improved metabolite extraction method, compatible with DI-FTICR-MS-based metabolomics, using grapevine leaves. This extraction protocol allowed the extraction of polar and non-polar compounds, covering all major classes found in plants and increasing metabolome coverage.</p></div>","PeriodicalId":38260,"journal":{"name":"EuPA Open Proteomics","volume":"12 ","pages":"Pages 4-9"},"PeriodicalIF":0.0,"publicationDate":"2016-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.euprot.2016.03.002","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"36220028","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: 34
Use of a charge reducing agent to enable intact mass analysis of cysteine-linked antibody-drug-conjugates by native mass spectrometry 使用电荷还原剂，使半胱氨酸连接抗体-药物偶联物的天然质谱完整的质量分析
EuPA Open Proteomics Pub Date : 2016-06-01 DOI: 10.1016/j.euprot.2016.02.004
Kamila J. Pacholarz , Perdita E. Barran
{"title":"Use of a charge reducing agent to enable intact mass analysis of cysteine-linked antibody-drug-conjugates by native mass spectrometry","authors":"Kamila J. Pacholarz ,&nbsp;Perdita E. Barran","doi":"10.1016/j.euprot.2016.02.004","DOIUrl":"10.1016/j.euprot.2016.02.004","url":null,"abstract":"<div><p>Antibody-drug-conjugates (ADC) are a growing class of anticancer biopharmaceuticals. Conjugation of cysteine linked ADCs, requires initial reduction of mAb inter-chain disulfide bonds, as the drugs a<em>r</em>e attached <em>via</em> thiol chemistry. This results in the active mAb moiety being transformed from a covalently linked tetramer to non-covalently linked complexes, which hinders precise determination of drug load with LC–MS. Here, we show how the addition of the charge reducing agent triethylammonium acetate (TEAA) preserves the intact mAb structure, is well suited to the study of cysteine linked conjugates and facilitates easy drug load determination by direct infusion native MS.</p></div>","PeriodicalId":38260,"journal":{"name":"EuPA Open Proteomics","volume":"11 ","pages":"Pages 23-27"},"PeriodicalIF":0.0,"publicationDate":"2016-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.euprot.2016.02.004","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"36220635","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: 36
EuPA News from the EuPA Conference and Communication Committee (CCC) 来自EuPA会议与传播委员会(CCC)的EuPA新闻
EuPA Open Proteomics Pub Date : 2016-06-01 DOI: 10.1016/j.euprot.2016.03.006
Concha Gil , Martina Marchetti-Deschmann , Deborah Penque , Paola Roncada , Natacha Turck , Fernando J. Corrales (Coordinator)
{"title":"EuPA News from the EuPA Conference and Communication Committee (CCC)","authors":"Concha Gil ,&nbsp;Martina Marchetti-Deschmann ,&nbsp;Deborah Penque ,&nbsp;Paola Roncada ,&nbsp;Natacha Turck ,&nbsp;Fernando J. Corrales (Coordinator)","doi":"10.1016/j.euprot.2016.03.006","DOIUrl":"10.1016/j.euprot.2016.03.006","url":null,"abstract":"","PeriodicalId":38260,"journal":{"name":"EuPA Open Proteomics","volume":"11 ","pages":"Page 30"},"PeriodicalIF":0.0,"publicationDate":"2016-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.euprot.2016.03.006","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"54257662","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
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