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Profiling the tumor microenvironment proteome in prostate cancer using laser capture microdissection coupled to LC⿿MS⿿A technical report 利用激光捕获显微解剖结合LC、MS、A技术报告分析前列腺癌肿瘤微环境蛋白质组
EuPA Open Proteomics Pub Date : 2016-03-01 DOI: 10.1016/j.euprot.2015.11.001
L. Staunton , C. Tonry , R. Lis , S. Finn , J. O⿿Leary , M. Loda , M. Bowden , S.R. Pennington
{"title":"Profiling the tumor microenvironment proteome in prostate cancer using laser capture microdissection coupled to LC⿿MS⿿A technical report","authors":"L. Staunton ,&nbsp;C. Tonry ,&nbsp;R. Lis ,&nbsp;S. Finn ,&nbsp;J. O⿿Leary ,&nbsp;M. Loda ,&nbsp;M. Bowden ,&nbsp;S.R. Pennington","doi":"10.1016/j.euprot.2015.11.001","DOIUrl":"10.1016/j.euprot.2015.11.001","url":null,"abstract":"<div><p>Laser capture microdissection (LCM) allows microscopic procurement of specific cell types from tissue sections. Here, we present an optimized workflow for coupling LCM to LC⿿MS/MS including: sectioning of tissue, a standard LCM workflow, protein digestion and advanced LC⿿MS/MS. Soluble proteins extracted from benign epithelial cells, their associated stroma, tumor epithelial cells and their associated stromal cells from a single patient tissue sample were digested and profiled using advanced LC⿿MS/MS. The correlation between technical replicates was R<sup>2</sup> <!-->=<!--> <!-->0.99 with a mean % CV of 9.55%<!--> <!-->±<!--> <!-->8.73. The correlation between sample replicates was R<sup>2</sup> <!-->=<!--> <!-->0.97 with a mean % CV of 13.83%<!--> <!-->±<!--> <!-->10.17. This represents a robust, systematic approach for profiling of the tumor microenvironment using LCM coupled to label-free LC⿿MS/MS.</p></div>","PeriodicalId":38260,"journal":{"name":"EuPA Open Proteomics","volume":"10 ","pages":"Pages 19-23"},"PeriodicalIF":0.0,"publicationDate":"2016-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.euprot.2015.11.001","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"36221183","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: 12
Towards a functional definition of the mitochondrial human proteome 迈向人类线粒体蛋白质组的功能定义
EuPA Open Proteomics Pub Date : 2016-03-01 DOI: 10.1016/j.euprot.2016.01.004
Mauro Fasano , Tiziana Alberio , Mohan Babu , Emma Lundberg , Andrea Urbani
{"title":"Towards a functional definition of the mitochondrial human proteome","authors":"Mauro Fasano ,&nbsp;Tiziana Alberio ,&nbsp;Mohan Babu ,&nbsp;Emma Lundberg ,&nbsp;Andrea Urbani","doi":"10.1016/j.euprot.2016.01.004","DOIUrl":"10.1016/j.euprot.2016.01.004","url":null,"abstract":"<div><p>The mitochondrial human proteome project (mt-HPP) was initiated by the Italian HPP group as a part of both the chromosome-centric initiative (C-HPP) and the ⿿biology and disease driven⿿ initiative (B/D-HPP). In recent years several reports highlighted how mitochondrial biology and disease are regulated by specific interactions with non-mitochondrial proteins. Thus, it is of great relevance to extend our present view of the mitochondrial proteome not only to those proteins that are encoded by or transported to mitochondria, but also to their interactors that take part in mitochondria functionality. Here, we propose a graphical representation of the functional mitochondrial proteome by retrieving mitochondrial proteins from the NeXtProt database and adding to the network their interactors as annotated in the IntAct database. Notably, the network may represent a reference to map all the proteins that are currently being identified in mitochondrial proteomics studies.</p></div>","PeriodicalId":38260,"journal":{"name":"EuPA Open Proteomics","volume":"10 ","pages":"Pages 24-27"},"PeriodicalIF":0.0,"publicationDate":"2016-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.euprot.2016.01.004","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"36221184","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: 6
Comparative proteomic analysis of malignant pleural mesothelioma: Focusing on the biphasic subtype 恶性胸膜间皮瘤的比较蛋白质组学分析:以双期亚型为重点
EuPA Open Proteomics Pub Date : 2016-03-01 DOI: 10.1016/j.euprot.2016.01.006
Laura Giusti , Federica Ciregia , Alessandra Bonotti , Ylenia Da Valle , Elena Donadio , Claudia Boldrini , Rudy Foddis , Gino Giannaccini , Maria R. Mazzoni , Pier Aldo Canessa , Alfonso Cristaudo , Antonio Lucacchini
{"title":"Comparative proteomic analysis of malignant pleural mesothelioma: Focusing on the biphasic subtype","authors":"Laura Giusti ,&nbsp;Federica Ciregia ,&nbsp;Alessandra Bonotti ,&nbsp;Ylenia Da Valle ,&nbsp;Elena Donadio ,&nbsp;Claudia Boldrini ,&nbsp;Rudy Foddis ,&nbsp;Gino Giannaccini ,&nbsp;Maria R. Mazzoni ,&nbsp;Pier Aldo Canessa ,&nbsp;Alfonso Cristaudo ,&nbsp;Antonio Lucacchini","doi":"10.1016/j.euprot.2016.01.006","DOIUrl":"10.1016/j.euprot.2016.01.006","url":null,"abstract":"<div><p>Malignant pleural mesothelioma (MPM) is a rare cancer originated from pleural mesothelial cells. MPM has been associated with long-term exposure to asbestos. In this work we performed a comparative proteomic analysis of biphasic pleural mesothelioma (B-PM).</p><p>Tissue biopsies were obtained from 61 patients who were subjected to a diagnostic thoracoscopy. 2D/MS based approach was used for proteomic analysis. The 22 proteins found differentially expressed in B-PM, with respect to benign, were analyzed by Ingenuity Pathways Analysis and compared with those obtained for epitheliod pleural mesothelioma (E-PM). A different activation of transcription factors, proteins and cytokines were observed between two subtypes.</p></div>","PeriodicalId":38260,"journal":{"name":"EuPA Open Proteomics","volume":"10 ","pages":"Pages 42-49"},"PeriodicalIF":0.0,"publicationDate":"2016-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.euprot.2016.01.006","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"36221187","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
Developmental origins of metabolic disorders: The need for biomarker candidates and therapeutic targets from adequate preclinical models 代谢性疾病的发育起源:从足够的临床前模型中寻找生物标志物候选物和治疗靶点的需求
EuPA Open Proteomics Pub Date : 2016-03-01 DOI: 10.1016/j.euprot.2016.01.001
Antonio Gonzalez-Bulnes , Susana Astiz , Marta Vazquez-Gomez , Consolación Garcia-Contreras
{"title":"Developmental origins of metabolic disorders: The need for biomarker candidates and therapeutic targets from adequate preclinical models","authors":"Antonio Gonzalez-Bulnes ,&nbsp;Susana Astiz ,&nbsp;Marta Vazquez-Gomez ,&nbsp;Consolación Garcia-Contreras","doi":"10.1016/j.euprot.2016.01.001","DOIUrl":"10.1016/j.euprot.2016.01.001","url":null,"abstract":"<div><p>The investigation on obesity and associated disorders have changed from an scenario in which genome drove the phenotype to a dynamic setup in which prenatal and early-postnatal conditions are determinant. However, research in human beings is difficult due to confounding factors (lifestyle and socioeconomic heterogeneity) plus ethical issues. Hence, there is currently an intensive effort for developing adequate preclinical models, aiming for an adequate combination of basic studies in rodent models and specific preclinical studies in large animals. The results of these research strategies may increase the identification and development of contrasted biomarkers and therapeutic targets.</p></div>","PeriodicalId":38260,"journal":{"name":"EuPA Open Proteomics","volume":"10 ","pages":"Pages 50-55"},"PeriodicalIF":0.0,"publicationDate":"2016-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.euprot.2016.01.001","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"36221188","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: 8
Introducing the Affinity Binder Knockdown Initiative⿿A public⿿private partnership for validation of affinity reagents 引入亲和结合物敲低倡议(Affinity Binder Knockdown Initiative)，这是一种用于验证亲和试剂的公私合作伙伴关系
EuPA Open Proteomics Pub Date : 2016-03-01 DOI: 10.1016/j.euprot.2016.01.002
Tove Alm, Emma Lundberg, Mathias Uhlén
{"title":"Introducing the Affinity Binder Knockdown Initiative⿿A public⿿private partnership for validation of affinity reagents","authors":"Tove Alm,&nbsp;Emma Lundberg,&nbsp;Mathias Uhlén","doi":"10.1016/j.euprot.2016.01.002","DOIUrl":"10.1016/j.euprot.2016.01.002","url":null,"abstract":"<div><p>The newly launched Affinity Binder Knockdown Initiative encourages antibody suppliers and users to join this public⿿private partnership, which uses crowdsourcing to collect characterization data on antibodies. Researchers are asked to share validation data from experiments where gene-editing techniques (such as siRNA or CRISPR) have been used to verify antibody binding. The initiative is launched under the aegis of Antibodypedia, a database designed to allow comparisons and scoring of publicly available antibodies towards human protein targets. What is known about an antibody is the foundation of the scoring and ranking system in Antibodypedia.</p></div>","PeriodicalId":38260,"journal":{"name":"EuPA Open Proteomics","volume":"10 ","pages":"Pages 56-58"},"PeriodicalIF":0.0,"publicationDate":"2016-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.euprot.2016.01.002","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"36221189","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: 2
Effect of fetal bovine serum in culture media on MS analysis of mesenchymal stromal cells secretome 培养基中胎牛血清对间充质间质细胞分泌组质谱分析的影响
EuPA Open Proteomics Pub Date : 2016-03-01 DOI: 10.1016/j.euprot.2016.01.005
Simona Nonnis , Elisa Maffioli , Lucia Zanotti , Fabiana Santagata , Armando Negri , Antonella Viola , Stephen Elliman , Gabriella Tedeschi
{"title":"Effect of fetal bovine serum in culture media on MS analysis of mesenchymal stromal cells secretome","authors":"Simona Nonnis ,&nbsp;Elisa Maffioli ,&nbsp;Lucia Zanotti ,&nbsp;Fabiana Santagata ,&nbsp;Armando Negri ,&nbsp;Antonella Viola ,&nbsp;Stephen Elliman ,&nbsp;Gabriella Tedeschi","doi":"10.1016/j.euprot.2016.01.005","DOIUrl":"10.1016/j.euprot.2016.01.005","url":null,"abstract":"<div><p>The analysis of mesenchymal stromal cells secretome is fundamental to identify key players of processes involving these cells. Truly secreted proteins may be difficult to detect in MS based analysis of conditioned media (CM) due to proteins supplemented with fetal bovine serum (FBS). We compared different growth conditions to determine the effect of varying FBS concentration on the number and quantity of truly secreted human proteins <em>vs</em> contaminating bovine proteins. The results suggest that to minimize interference cells should be grown in presence of FBS until confluence and transferred into a serum-free medium prior to secretome collection.</p></div>","PeriodicalId":38260,"journal":{"name":"EuPA Open Proteomics","volume":"10 ","pages":"Pages 28-30"},"PeriodicalIF":0.0,"publicationDate":"2016-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.euprot.2016.01.005","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"36221185","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: 23
⿿Comparing the proteome of snap frozen, RNAlater preserved, and formalin-fixed paraffin-embedded human tissue samples 并比较速冻、RNAlater保存和福尔马林固定石蜡包埋人体组织样本的蛋白质组
EuPA Open Proteomics Pub Date : 2016-03-01 DOI: 10.1016/j.euprot.2015.10.001
Tue Bjerg Bennike , Kenneth Kastaniegaard , Simona Padurariu , Michael Gaihede , Svend Birkelund , Vibeke Andersen , Allan Stensballe
{"title":"⿿Comparing the proteome of snap frozen, RNAlater preserved, and formalin-fixed paraffin-embedded human tissue samples","authors":"Tue Bjerg Bennike ,&nbsp;Kenneth Kastaniegaard ,&nbsp;Simona Padurariu ,&nbsp;Michael Gaihede ,&nbsp;Svend Birkelund ,&nbsp;Vibeke Andersen ,&nbsp;Allan Stensballe","doi":"10.1016/j.euprot.2015.10.001","DOIUrl":"https://doi.org/10.1016/j.euprot.2015.10.001","url":null,"abstract":"<div><p>Large biobanks exist worldwide containing formalin-fixed, paraffin-embedded samples and samples stored in RNAlater. However, the impact of tissue preservation on the result of a quantative proteome analysis remains poorly described.</p><p>Human colon mucosal biopsies were extracted from the sigmoideum and either immediately frozen, stabilized in RNAlater, or stabilized by formalin-fixation. In one set of biopsies, formalin stabilization was delayed for 30<!--> <!-->min. The protein content of the samples was characterized by high throughput quantitative proteomics.</p><p>We were able to identify a similar high number of proteins in the samples regardless of preservation method, with only minor differences in protein quantitation.</p></div>","PeriodicalId":38260,"journal":{"name":"EuPA Open Proteomics","volume":"10 ","pages":"Pages 9-18"},"PeriodicalIF":0.0,"publicationDate":"2016-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.euprot.2015.10.001","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"91711507","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: 40
Standardization initiative. Integrating proteomic strengths across Europe 标准化的倡议。整合整个欧洲的蛋白质组学优势
EuPA Open Proteomics Pub Date : 2015-12-01 DOI: 10.1016/j.euprot.2015.07.003
Fernando J. Corrales
{"title":"Standardization initiative. Integrating proteomic strengths across Europe","authors":"Fernando J. Corrales","doi":"10.1016/j.euprot.2015.07.003","DOIUrl":"10.1016/j.euprot.2015.07.003","url":null,"abstract":"","PeriodicalId":38260,"journal":{"name":"EuPA Open Proteomics","volume":"9 ","pages":"Page 76"},"PeriodicalIF":0.0,"publicationDate":"2015-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.euprot.2015.07.003","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"54257272","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
Bayesian methods for proteomic biomarker development 蛋白质组学生物标志物开发的贝叶斯方法
EuPA Open Proteomics Pub Date : 2015-12-01 DOI: 10.1016/j.euprot.2015.08.001
Belinda Hernández , Stephen R Pennington , Andrew C Parnell
{"title":"Bayesian methods for proteomic biomarker development","authors":"Belinda Hernández ,&nbsp;Stephen R Pennington ,&nbsp;Andrew C Parnell","doi":"10.1016/j.euprot.2015.08.001","DOIUrl":"10.1016/j.euprot.2015.08.001","url":null,"abstract":"<div><p>The advent of liquid chromatography mass spectrometry has seen a dramatic increase in the amount of data derived from proteomic biomarker discovery. These experiments have seemingly identified many potential candidate biomarkers. Frustratingly, very few of these candidates have been evaluated and validated sufficiently such that that they have progressed to the stage of routine clinical use. It is becoming apparent that the statistical methods used to evaluate the performance of new candidate biomarkers are a major limitation in their development. Bayesian methods offer some advantages over traditional statistical and machine learning methods. In particular they can incorporate external information into current experiments so as to guide biomarker selection. Further, they can be more robust to over-fitting than other approaches, especially when the number of samples used for discovery is relatively small.</p><p>In this review we provide an introduction to Bayesian inference and demonstrate some of the advantages of using a Bayesian framework. We summarize how Bayesian methods have been used previously in proteomics and other areas of bioinformatics. Finally, we describe some popular and emerging Bayesian models from the statistical literature and provide a worked tutorial including code snippets to show how these methods may be applied for the evaluation of proteomic biomarkers.</p></div>","PeriodicalId":38260,"journal":{"name":"EuPA Open Proteomics","volume":"9 ","pages":"Pages 54-64"},"PeriodicalIF":0.0,"publicationDate":"2015-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.euprot.2015.08.001","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"54257491","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: 18
Flagship program for EuPA Initiatives: Opportunities for the EuPA Company Club EuPA计划的旗舰项目:EuPA公司俱乐部的机会
EuPA Open Proteomics Pub Date : 2015-12-01 DOI: 10.1016/j.euprot.2015.07.002
Andrey Lisitsa
{"title":"Flagship program for EuPA Initiatives: Opportunities for the EuPA Company Club","authors":"Andrey Lisitsa","doi":"10.1016/j.euprot.2015.07.002","DOIUrl":"10.1016/j.euprot.2015.07.002","url":null,"abstract":"","PeriodicalId":38260,"journal":{"name":"EuPA Open Proteomics","volume":"9 ","pages":"Page 76"},"PeriodicalIF":0.0,"publicationDate":"2015-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.euprot.2015.07.002","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"54257261","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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