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Math, science, history, unraveling the mystery—That all started with de novo! 数学、科学、历史、揭开神秘——这一切都是从从头开始的!
EuPA Open Proteomics Pub Date : 2019-03-01 DOI: 10.1016/j.euprot.2019.07.011
Ekaterina Ilgisonis, Olga Kiseleva, Ksenia Kuznetsova Dr.
{"title":"Math, science, history, unraveling the mystery—That all started with de novo!","authors":"Ekaterina Ilgisonis,&nbsp;Olga Kiseleva,&nbsp;Ksenia Kuznetsova Dr.","doi":"10.1016/j.euprot.2019.07.011","DOIUrl":"10.1016/j.euprot.2019.07.011","url":null,"abstract":"<div><p>This work on solving the mystery of words encoded by amino acids in peptides was derived by the YPIC-EuPA Challenge. We received a dry synthetic peptide sample and performed a mass spectrometric analysis followed by <em>de novo</em> peptide sequencing. As a result, a part of “Rays of positive electricity and their application to chemical analyses” by J.J.Tomson was found to be encoded in the peptides of the sample. The words were first revealed from the peptides, that matched by Google search to find the answer. After that, the answer was validated using a standard proteomic search against a database constructed from the quotation found.</p></div>","PeriodicalId":38260,"journal":{"name":"EuPA Open Proteomics","volume":"22 ","pages":"Pages 25-27"},"PeriodicalIF":0.0,"publicationDate":"2019-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.euprot.2019.07.011","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37502638","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
Team COUNCIL OF RICKS submission for EUPA YPIC 2017 瑞克斯团队委员会提交的2017年EUPA YPIC
EuPA Open Proteomics Pub Date : 2019-03-01 DOI: 10.1016/j.euprot.2019.07.009
Lindsay K. Pino, Brian C Searle, Han-Yin Yang
{"title":"Team COUNCIL OF RICKS submission for EUPA YPIC 2017","authors":"Lindsay K. Pino,&nbsp;Brian C Searle,&nbsp;Han-Yin Yang","doi":"10.1016/j.euprot.2019.07.009","DOIUrl":"10.1016/j.euprot.2019.07.009","url":null,"abstract":"<div><p>Using primarily LC-MS/MS <em>de novo</em> sequencing techniques, we concluded that the peptides form the following sentence from Sir JJ Thomson’s preface to Rays of Positive Electricity and Their Application to Chemical Analyses:</p><p><em>“I feel sure that there are many problems in chemistry which could be solved with far greater ease by this than by any other method. The method is surprisingly sensitive, more so even than that of spectrum</em> analysis<em>, requires an infinitesimal amount of material, and does not require this to be specially purified.”</em></p><p>Here, we detail our process for deciphering the peptide mixture composition and finding the sentence they form and from what book the sentence comes from.</p></div>","PeriodicalId":38260,"journal":{"name":"EuPA Open Proteomics","volume":"22 ","pages":"Pages 22-24"},"PeriodicalIF":0.0,"publicationDate":"2019-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.euprot.2019.07.009","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37502637","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
The Young Proteomics Investigator Club turns three! 青年蛋白质组学研究者俱乐部三岁了！
EuPA Open Proteomics Pub Date : 2019-03-01 DOI: 10.1016/j.euprot.2019.07.003
{"title":"The Young Proteomics Investigator Club turns three!","authors":"","doi":"10.1016/j.euprot.2019.07.003","DOIUrl":"10.1016/j.euprot.2019.07.003","url":null,"abstract":"","PeriodicalId":38260,"journal":{"name":"EuPA Open Proteomics","volume":"22 ","pages":"Pages 8-9"},"PeriodicalIF":0.0,"publicationDate":"2019-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.euprot.2019.07.003","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"46320386","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
The author identified by his method: EuPA YPIC challenge solved 作者通过他的方法确定:EuPA解决了YPIC挑战
EuPA Open Proteomics Pub Date : 2018-12-01 DOI: 10.1016/j.euprot.2018.10.001
M.I. Indeykina , D.A. Podgrudkov , A.S. Kononikhin
{"title":"The author identified by his method: EuPA YPIC challenge solved","authors":"M.I. Indeykina ,&nbsp;D.A. Podgrudkov ,&nbsp;A.S. Kononikhin","doi":"10.1016/j.euprot.2018.10.001","DOIUrl":"10.1016/j.euprot.2018.10.001","url":null,"abstract":"<div><p>Here we present the results of our attempt on the EuPA YPIC challenge. The task was to sequence the provided synthetic peptides, build the sentence encrypted in them and determine from which book the sentence originated.</p><p>The task itself, while holding no direct scientific value, offers an insight in less formal terms (for participants at least) on how the overall process of a scientific study of a “new protein” looks like. Hence, we decided to look at the challenge as if it was a general task of sequencing an unknown protein from an unusual proteome database. To solve the task we used LC–MS/MS, MALDI-MS and de novo sequencing. A combination of two MS instruments and de novo MS/MS data analysis make it possible to sequence new peptides and proteins not yet present in proteomic databases.</p></div>","PeriodicalId":38260,"journal":{"name":"EuPA Open Proteomics","volume":"20 ","pages":"Pages 1-8"},"PeriodicalIF":0.0,"publicationDate":"2018-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.euprot.2018.10.001","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"36779383","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
Proteomics—An unexpected journey into the complexity of protein structures and functions 蛋白质组学——一个意想不到的旅程，进入蛋白质结构和功能的复杂性
EuPA Open Proteomics Pub Date : 2018-12-01 DOI: 10.1016/j.euprot.2018.11.001
Friedrich Lottspeich
{"title":"Proteomics—An unexpected journey into the complexity of protein structures and functions","authors":"Friedrich Lottspeich","doi":"10.1016/j.euprot.2018.11.001","DOIUrl":"10.1016/j.euprot.2018.11.001","url":null,"abstract":"","PeriodicalId":38260,"journal":{"name":"EuPA Open Proteomics","volume":"21 ","pages":"Pages 1-2"},"PeriodicalIF":0.0,"publicationDate":"2018-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.euprot.2018.11.001","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"36779384","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
Expression, characterization and one step purification of heterologous glucose oxidase gene from Aspergillus niger ATCC 9029 in Pichia pastoris 毕赤酵母中黑曲霉ATCC 9029异源葡萄糖氧化酶基因的表达、鉴定及一步纯化
EuPA Open Proteomics Pub Date : 2018-09-01 DOI: 10.1016/j.euprot.2018.09.001
Fakhry Belyad , Ali Asghar Karkhanei , Jamshid Raheb
{"title":"Expression, characterization and one step purification of heterologous glucose oxidase gene from Aspergillus niger ATCC 9029 in Pichia pastoris","authors":"Fakhry Belyad ,&nbsp;Ali Asghar Karkhanei ,&nbsp;Jamshid Raheb","doi":"10.1016/j.euprot.2018.09.001","DOIUrl":"10.1016/j.euprot.2018.09.001","url":null,"abstract":"<div><p>Glucose Oxidase (GOD), is a common flavoprotein from <em>Aspergillus niger</em> ATCC 9029 with a broad application in biotechnology, food and medical industries. In this study, GOD gene was cloned into the expression vector, pPIC9 and screened by the alcohol oxidase promoter. The enzyme production increased at 28 °C. GOD activity induced by 1.0% methanol and the highest level of GOD production was the result of shaking rate at 225 rpm. The highest enzyme activity obtained at a pH value ranged from 5 to 7 at 50 °C. The enzyme was stable at a broad pH range and temperature.</p></div>","PeriodicalId":38260,"journal":{"name":"EuPA Open Proteomics","volume":"19 ","pages":"Pages 1-5"},"PeriodicalIF":0.0,"publicationDate":"2018-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.euprot.2018.09.001","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"36476624","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: 13
Proteomic analysis of a Candida albicans pga1 Null Strain 一株白色念珠菌pga1零株的蛋白质组学分析
EuPA Open Proteomics Pub Date : 2018-06-01 DOI: 10.1016/j.euprot.2018.02.001
Andy Awad , Pamela El Khoury , Brigitte Wex, Roy A. Khalaf
{"title":"Proteomic analysis of a Candida albicans pga1 Null Strain","authors":"Andy Awad ,&nbsp;Pamela El Khoury ,&nbsp;Brigitte Wex,&nbsp;Roy A. Khalaf","doi":"10.1016/j.euprot.2018.02.001","DOIUrl":"https://doi.org/10.1016/j.euprot.2018.02.001","url":null,"abstract":"<div><p>We previously characterized Pga1, a <em>Candida albicans</em> (<em>C. albicans</em>) cell wall protein necessary for proper virulence, adhesion, and resistance to oxidative stress. By utilizing tandem mass spectrometry coupled with bioinformatics to investigate cell wall proteome expression in a <em>pga1</em> null fourteen and 36 proteins were identified in the wild type grown under filamentous and non-filamentous conditions respectively, but were not detected in the mutant, including members of the PGA GPI anchored family. Virulence and adhesion proteins such as Hsp 90, Sap10, Cdc11, Int 3 and members of the lipase family were also identified exclusively in the wild type.</p></div>","PeriodicalId":38260,"journal":{"name":"EuPA Open Proteomics","volume":"18 ","pages":"Pages 1-6"},"PeriodicalIF":0.0,"publicationDate":"2018-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.euprot.2018.02.001","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"91992594","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: 10
Proteomic analysis reveals differential protein expression in variants of papillary thyroid carcinoma 蛋白质组学分析揭示了甲状腺乳头状癌变体中的差异蛋白表达
EuPA Open Proteomics Pub Date : 2017-12-01 DOI: 10.1016/j.euprot.2017.09.001
Yasemin Ucal , Murat Eravci , Fatma Tokat , Mete Duren , Umit Ince , Aysel Ozpinar
{"title":"Proteomic analysis reveals differential protein expression in variants of papillary thyroid carcinoma","authors":"Yasemin Ucal ,&nbsp;Murat Eravci ,&nbsp;Fatma Tokat ,&nbsp;Mete Duren ,&nbsp;Umit Ince ,&nbsp;Aysel Ozpinar","doi":"10.1016/j.euprot.2017.09.001","DOIUrl":"10.1016/j.euprot.2017.09.001","url":null,"abstract":"<div><h3>Introduction</h3><p>Fine Needle Aspiration Biopsy (FNAB) allows the cytological differentiation of benign and malignant thyroid nodules. However, the method itself is not adequate in determining some cases. For example, the diagnosis of Follicular Variant Papillary Thyroid Carcinoma (FV-PTC) can be challenging. In the current study we investigate the protein profiles of FV-PTC and classical variant PTC (CV-PTC) with no lymph node metastasis and compare it with benign thyroid tissue.</p></div><div><h3>Method</h3><p>We used CV-PTC (n<!--> <!-->=<!--> <!-->6), FV-PTC (n<!--> <!-->=<!--> <!-->6) and benign thyroid tissues (n<!--> <!-->=<!--> <!-->6) to prepare tissue lysates. Proteins from each group were trypsin and lys-C digested. The samples were analyzed on a Q Exactive Orbitrap mass spectrometer.</p></div><div><h3>Results</h3><p>We identified 2560 proteins across all 18 specimens. Protein profiles revealed that there was no clear distinction between benign and FV-PTC samples. However, further examination of our data showed that proteins in energy metabolism have altered in FV-PTC. Proteomic pathway analysis showed marked alteration of the actin cytoskeleton proteins, especially several members of Arp2/3 complex were significantly increased in CV-PTC. We made the novel observation that IQGAP1 protein was significantly increased in CV-PTC, whereas IQGAP2 protein was highly expressed in FV-PTC lesions, suggesting differential roles of IQGAP proteins in thyroid pathology.</p></div><div><h3>Conclusion</h3><p>In the present study, mass spectrometry based label free quantification approach was applied to investigate the protein profiles of FV-PTC, CV-PTC and benign thyroid tissues. This study pointed out that actin cytoskeleton proteins, IQGAP proteins and changes in energy metabolism play predominant roles in thyroid pathology.</p></div>","PeriodicalId":38260,"journal":{"name":"EuPA Open Proteomics","volume":"17 ","pages":"Pages 1-6"},"PeriodicalIF":0.0,"publicationDate":"2017-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.euprot.2017.09.001","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"36221009","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: 11
Quantitative proteomic analysis identifies proteins and pathways related to neuronal development in differentiated SH-SY5Y neuroblastoma cells 定量蛋白质组学分析鉴定分化的SH-SY5Y神经母细胞瘤细胞中与神经元发育相关的蛋白质和通路
EuPA Open Proteomics Pub Date : 2017-09-01 DOI: 10.1016/j.euprot.2017.06.001
Jimmy Rodriguez Murillo , Livia Goto-Silva , Aniel Sánchez , Fábio C.S. Nogueira , Gilberto B. Domont , Magno Junqueira
{"title":"Quantitative proteomic analysis identifies proteins and pathways related to neuronal development in differentiated SH-SY5Y neuroblastoma cells","authors":"Jimmy Rodriguez Murillo ,&nbsp;Livia Goto-Silva ,&nbsp;Aniel Sánchez ,&nbsp;Fábio C.S. Nogueira ,&nbsp;Gilberto B. Domont ,&nbsp;Magno Junqueira","doi":"10.1016/j.euprot.2017.06.001","DOIUrl":"10.1016/j.euprot.2017.06.001","url":null,"abstract":"<div><p>SH-SY5Y neuroblastoma cells are susceptible to differentiation using retinoic acid (RA) and brain-derived neurotrophic factor (BDNF), providing a model of neuronal differentiation. We compared SH-SY5Y cells proteome before and after RA/BDNF treatment using iTRAQ and phosphopeptide enrichment strategies. We identified 5587 proteins, 366 of them with differential abundance. Differentiated cells expressed proteins related to neuronal development, and, undifferentiated cells expressed proteins involved in cell proliferation. Interactive network covered focal adhesion, cytoskeleton dynamics and neurodegenerative diseases processes and regulation of mitogen-activated protein kinase-related signaling pathways; key proteins involved in those processes might be explored as markers for neuronal differentiation.</p></div>","PeriodicalId":38260,"journal":{"name":"EuPA Open Proteomics","volume":"16 ","pages":"Pages 1-11"},"PeriodicalIF":0.0,"publicationDate":"2017-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.euprot.2017.06.001","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"36221008","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: 39
Novel Kazal-type proteinase inhibitors from the skin secretion of the Splendid leaf frog, Cruziohyla calcarifer 从金叶蛙皮肤分泌物中提取新的卡扎尔型蛋白酶抑制剂
EuPA Open Proteomics Pub Date : 2017-06-01 DOI: 10.1016/j.euprot.2017.02.001
Carolina Proaño-Bolaños , Renjie Li , Mei Zhou , Lei Wang , Xinping Xi , Elicio E. Tapia , Luis A. Coloma , Tianbao Chen , Chris Shaw
{"title":"Novel Kazal-type proteinase inhibitors from the skin secretion of the Splendid leaf frog, Cruziohyla calcarifer","authors":"Carolina Proaño-Bolaños ,&nbsp;Renjie Li ,&nbsp;Mei Zhou ,&nbsp;Lei Wang ,&nbsp;Xinping Xi ,&nbsp;Elicio E. Tapia ,&nbsp;Luis A. Coloma ,&nbsp;Tianbao Chen ,&nbsp;Chris Shaw","doi":"10.1016/j.euprot.2017.02.001","DOIUrl":"10.1016/j.euprot.2017.02.001","url":null,"abstract":"<div><p>Peptidase inhibitors have an important role controlling a variety of biological processes. Here, we employed a peptidomic approach including molecular cloning, tandem mass spectrometry and enzymatic assays to reveal 7 Kazal-type proteinase inhibitors (CCKPs) (18 variants) in the skin secretion of the unexplored frog, <em>Cruziohyla calcarifer</em>. All 18 proteins shared the Kazal pattern C-X<sub>(7)</sub>-C-X<sub>(6,7)</sub>-C-X<sub>(6,7)</sub>-Y-X<sub>(3)</sub>-C-X<sub>(2)</sub>-C-X<sub>(15-21)</sub>-C and 3 disulphide bridges. Based on structural comparative analysis, we deemed trypsin and chymotrypsin inhibitory activity in CCKP-1, 4 and CCKP 2, 5, 7, respectively. These peptidase inhibitors presumably play a role to control the balance between other functional peptides produced in the amphibian skin secretions.</p></div>","PeriodicalId":38260,"journal":{"name":"EuPA Open Proteomics","volume":"15 ","pages":"Pages 1-13"},"PeriodicalIF":0.0,"publicationDate":"2017-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.euprot.2017.02.001","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"36221007","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
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