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Affinity Binder Knock-Down Initiative 亲和粘合剂击倒倡议
EuPA Open Proteomics Pub Date : 2015-12-01 DOI: 10.1016/j.euprot.2015.07.004
Tove Alm, Emma Lundberg, Mathias Uhlén
{"title":"Affinity Binder Knock-Down Initiative","authors":"Tove Alm, Emma Lundberg, Mathias Uhlén","doi":"10.1016/j.euprot.2015.07.004","DOIUrl":"10.1016/j.euprot.2015.07.004","url":null,"abstract":"","PeriodicalId":38260,"journal":{"name":"EuPA Open Proteomics","volume":"9 ","pages":"Pages 76-77"},"PeriodicalIF":0.0,"publicationDate":"2015-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.euprot.2015.07.004","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"54257283","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
Novel product development and future directions in support of proteomics standardization, biobanking, and binder validation using CRISPR knockout technology 利用CRISPR敲除技术支持蛋白质组学标准化、生物银行和结合剂验证的新产品开发和未来方向
EuPA Open Proteomics Pub Date : 2015-12-01 DOI: 10.1016/j.euprot.2015.07.007
Kevin Ray
{"title":"Novel product development and future directions in support of proteomics standardization, biobanking, and binder validation using CRISPR knockout technology","authors":"Kevin Ray","doi":"10.1016/j.euprot.2015.07.007","DOIUrl":"10.1016/j.euprot.2015.07.007","url":null,"abstract":"","PeriodicalId":38260,"journal":{"name":"EuPA Open Proteomics","volume":"9 ","pages":"Page 77"},"PeriodicalIF":0.0,"publicationDate":"2015-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.euprot.2015.07.007","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"54257324","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
Bottom–up protein identifications from microliter quantities of individual human tear samples. Important steps towards clinical relevance. 从微升个体泪液样品中进行自下而上的蛋白质鉴定。迈向临床相关性的重要步骤。
EuPA Open Proteomics Pub Date : 2015-12-01 DOI: 10.1016/j.euprot.2015.06.005
Peter Raus , Bharath Raghuraman Kumar , Martijn Pinkse , Peter Verhaert
{"title":"Bottom–up protein identifications from microliter quantities of individual human tear samples. Important steps towards clinical relevance.","authors":"Peter Raus ,&nbsp;Bharath Raghuraman Kumar ,&nbsp;Martijn Pinkse ,&nbsp;Peter Verhaert","doi":"10.1016/j.euprot.2015.06.005","DOIUrl":"10.1016/j.euprot.2015.06.005","url":null,"abstract":"<div><p>A relatively simple combination of Schirmer strip sampling with straightforward sensitive nanoLC quadrupole-Orbitrap tandem mass spectrometry after a minimum of sample processing steps allows for replicate proteomic analysis of single human tears, i.e., without the requirement for sample pooling. This opens the way to clinical applications of the analytical workflow, e.g., to monitor disease progression or treatment efficacy within individual patients. Proof of concept is provided by triplicate analyses of a singular sampling of tears of a dry eye patient, before and one and two months after minor salivary gland transplantation. To facilitate comparison with the outcome of previously reported analytical protocols, we also include the data from a typical healthy young adult tear sample as obtained by our streamlined method.</p><p>With 375 confidently identified proteins in the healthy adult tear, the obtained results are comprehensive and in large agreement with previously published observations on pooled samples of multiple patients. We conclude that, to a limited extent, bottom–up tear protein identifications from individual patients may have clinical relevance.</p></div>","PeriodicalId":38260,"journal":{"name":"EuPA Open Proteomics","volume":"9 ","pages":"Pages 8-13"},"PeriodicalIF":0.0,"publicationDate":"2015-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.euprot.2015.06.005","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"54257197","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
Independent validation initiative 独立验证计划
EuPA Open Proteomics Pub Date : 2015-12-01 DOI: 10.1016/j.euprot.2015.07.006
Stefan Pellenz
{"title":"Independent validation initiative","authors":"Stefan Pellenz","doi":"10.1016/j.euprot.2015.07.006","DOIUrl":"10.1016/j.euprot.2015.07.006","url":null,"abstract":"","PeriodicalId":38260,"journal":{"name":"EuPA Open Proteomics","volume":"9 ","pages":"Page 77"},"PeriodicalIF":0.0,"publicationDate":"2015-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.euprot.2015.07.006","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"54257309","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
Comparison of serum fractionation methods by data independent label-free proteomics 数据独立的无标记蛋白质组学血清分离方法的比较
EuPA Open Proteomics Pub Date : 2015-12-01 DOI: 10.1016/j.euprot.2015.07.009
D. Baiwir , G. Mazzucchelli , N. Smargiasso , F. Quesada-Calvo , E. De Pauw , M. Malaise , E. Louis , M.-A. Meuwis
{"title":"Comparison of serum fractionation methods by data independent label-free proteomics","authors":"D. Baiwir ,&nbsp;G. Mazzucchelli ,&nbsp;N. Smargiasso ,&nbsp;F. Quesada-Calvo ,&nbsp;E. De Pauw ,&nbsp;M. Malaise ,&nbsp;E. Louis ,&nbsp;M.-A. Meuwis","doi":"10.1016/j.euprot.2015.07.009","DOIUrl":"10.1016/j.euprot.2015.07.009","url":null,"abstract":"<div><p>Off-line sample prefractionations applied prior to biomarker discovery proteomics are options to enable more protein identifications and detect low-abundance proteins. This work compared five commercial methods efficiency to raw serum analysis using label-free proteomics. The variability of the protein quantities determined for each process was similar to the unprefractionated serum. A 49% increase in protein identifications and 12.2% of reliable quantification were obtained. A 61 times lower limit of protein quantitation was reached compared to protein concentrations observed in raw serum. The concentrations of detected proteins were confronted to estimated reference values.</p></div>","PeriodicalId":38260,"journal":{"name":"EuPA Open Proteomics","volume":"9 ","pages":"Pages 14-22"},"PeriodicalIF":0.0,"publicationDate":"2015-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.euprot.2015.07.009","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"54257396","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: 5
Analysis of the surface, secreted, and intracellular proteome of Propionibacterium acnes 痤疮丙酸杆菌的表面、分泌和细胞内蛋白质组分析
EuPA Open Proteomics Pub Date : 2015-12-01 DOI: 10.1016/j.euprot.2015.06.003
Yang Yu , Jackson Champer , Jenny Kim
{"title":"Analysis of the surface, secreted, and intracellular proteome of Propionibacterium acnes","authors":"Yang Yu ,&nbsp;Jackson Champer ,&nbsp;Jenny Kim","doi":"10.1016/j.euprot.2015.06.003","DOIUrl":"10.1016/j.euprot.2015.06.003","url":null,"abstract":"<div><p><em>Propionibacterium acnes</em>, plays an important role in acne vulgaris and other diseases. However, understanding of the exact mechanisms of <em>P. acnes</em> pathogenesis is limited. Few studies have investigated its proteome, which is essential for vaccine development. Here, we comprehensively investigate the proteome of <em>P. acnes</em> strain ATCC 6919, including secreted, cell wall, membrane, and cytosolic fractions in three types of growth media. A total of 531 proteins were quantified using an Orbitrap mass spectrometer and bioinformatically categorized for localization and function. Several, including PPA1939, a highly expressed surface and secreted protein, were identified as potential vaccine candidates.</p></div>","PeriodicalId":38260,"journal":{"name":"EuPA Open Proteomics","volume":"9 ","pages":"Pages 1-7"},"PeriodicalIF":0.0,"publicationDate":"2015-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.euprot.2015.06.003","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"54257169","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
Enhancing cognate target elution efficiency in gel-free chemical proteomics 提高无凝胶化学蛋白质组学同源目标洗脱效率
EuPA Open Proteomics Pub Date : 2015-12-01 DOI: 10.1016/j.euprot.2015.09.002
Branka Radic-Sarikas , Uwe Rix , Alexey Stukalov , Manuela Gridling , André C. Müller , Jacques Colinge , Giulio Superti-Furga , Keiryn L. Bennett
{"title":"Enhancing cognate target elution efficiency in gel-free chemical proteomics","authors":"Branka Radic-Sarikas ,&nbsp;Uwe Rix ,&nbsp;Alexey Stukalov ,&nbsp;Manuela Gridling ,&nbsp;André C. Müller ,&nbsp;Jacques Colinge ,&nbsp;Giulio Superti-Furga ,&nbsp;Keiryn L. Bennett","doi":"10.1016/j.euprot.2015.09.002","DOIUrl":"10.1016/j.euprot.2015.09.002","url":null,"abstract":"<div><p>Gel-free liquid chromatography mass spectrometry coupled to chemical proteomics is a powerful approach for characterizing cellular target profiles of small molecules. We have previously described a fast and efficient elution protocol; however, altered target profiles were observed. We hypothesised that elution conditions critically impact the effectiveness of disrupting drug-protein interactions. Thus, a number of elution conditions were systematically assessed with the aim of improving the recovery of all classes of proteins whilst maintaining compatibility with immunoblotting procedures. A double elution with formic acid combined with urea emerged as the most efficient and generically applicable elution method for chemical proteomics</p></div>","PeriodicalId":38260,"journal":{"name":"EuPA Open Proteomics","volume":"9 ","pages":"Pages 43-53"},"PeriodicalIF":0.0,"publicationDate":"2015-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.euprot.2015.09.002","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"54257653","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
Assessment of global proteome in LNCaP cells by 2D-RP/RP LC–MS/MS following sulforaphane exposure 利用2D-RP/RP LC-MS /MS评估萝卜硫素暴露后LNCaP细胞的整体蛋白质组
EuPA Open Proteomics Pub Date : 2015-12-01 DOI: 10.1016/j.euprot.2015.08.002
Gregory W. Watson , Samanthi Wickramasekara , Claudia S. Maier , David E. Williams , Roderick H. Dashwood , Emily Ho
{"title":"Assessment of global proteome in LNCaP cells by 2D-RP/RP LC–MS/MS following sulforaphane exposure","authors":"Gregory W. Watson ,&nbsp;Samanthi Wickramasekara ,&nbsp;Claudia S. Maier ,&nbsp;David E. Williams ,&nbsp;Roderick H. Dashwood ,&nbsp;Emily Ho","doi":"10.1016/j.euprot.2015.08.002","DOIUrl":"10.1016/j.euprot.2015.08.002","url":null,"abstract":"<div><p>The phytochemical sulforaphane can induce cell cycle arrest and apoptosis in metastatic prostate cancer cells, though the mechanism of action is not fully known. We conducted a global proteome analysis in LNCaP metastatic prostate cancer cells to characterize how global protein signature responds to sulforaphane. We conducted parallel analyses to evaluate semi-quantitative 1-dimensional versus 2-dimensional liquid chromatography tandem mass spectrometry (LC–MS/MS) and their utility in characterizing whole cell lysate. We show that 2-dimensional LC–MS/MS can be a useful tool for characterizing global protein profiles and identify TRIAP1 as a novel regulator of cell proliferation in LNCaP metastatic prostate cancer cells.</p></div>","PeriodicalId":38260,"journal":{"name":"EuPA Open Proteomics","volume":"9 ","pages":"Pages 34-40"},"PeriodicalIF":0.0,"publicationDate":"2015-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.euprot.2015.08.002","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"54257500","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
Changes in the repertoire of bovine milk proteins during mammary involution 乳蛋白库在乳腺复旧期间的变化
EuPA Open Proteomics Pub Date : 2015-12-01 DOI: 10.1016/j.euprot.2015.09.001
Irina Boggs , Brad Hine , Grant Smolenski , Kasper Hettinga , Lina Zhang , Thomas T. Wheeler
{"title":"Changes in the repertoire of bovine milk proteins during mammary involution","authors":"Irina Boggs ,&nbsp;Brad Hine ,&nbsp;Grant Smolenski ,&nbsp;Kasper Hettinga ,&nbsp;Lina Zhang ,&nbsp;Thomas T. Wheeler","doi":"10.1016/j.euprot.2015.09.001","DOIUrl":"10.1016/j.euprot.2015.09.001","url":null,"abstract":"<div><p>Changes of abundance that occur in the repertoire of low abundance milk proteins after cessation of milk removal have not been characterised. Skimmed milk and whey from cows sampled at day 0 and either day 3 or day 8 after drying off were subjected to three untargeted proteomics techniques; 2-D gel electrophoresis, GeLC-MS, and dimethyl isotopic labelling of tryptic peptides. The changes observed included 45 fragments of abundant milk proteins and 36 host-defence proteins, suggesting activation of proteolysis and inflammation. The findings form a basis for adding value to dairy production.</p></div>","PeriodicalId":38260,"journal":{"name":"EuPA Open Proteomics","volume":"9 ","pages":"Pages 65-75"},"PeriodicalIF":0.0,"publicationDate":"2015-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.euprot.2015.09.001","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"54257527","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: 14
The EuPA Company Club: Emphasis on the synergy with EuPA’s Initiatives beyond education—Towards further integration with EuPA’s goals and objectives EuPA公司俱乐部:强调与EuPA在教育之外的倡议的协同作用-进一步与EuPA的目标和宗旨相结合
EuPA Open Proteomics Pub Date : 2015-12-01 DOI: 10.1016/j.euprot.2015.06.007
Andrea Urbani, Andrey Lisitsa, Peter Verhaert
{"title":"The EuPA Company Club: Emphasis on the synergy with EuPA’s Initiatives beyond education—Towards further integration with EuPA’s goals and objectives","authors":"Andrea Urbani,&nbsp;Andrey Lisitsa,&nbsp;Peter Verhaert","doi":"10.1016/j.euprot.2015.06.007","DOIUrl":"10.1016/j.euprot.2015.06.007","url":null,"abstract":"","PeriodicalId":38260,"journal":{"name":"EuPA Open Proteomics","volume":"9 ","pages":"Pages 41-42"},"PeriodicalIF":0.0,"publicationDate":"2015-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.euprot.2015.06.007","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"54257218","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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