[ { "key": "WVDVQKTX", "version": 119, "library": { "type": "group", "id": 62016, "name": "xavier.robin", "links": { "alternate": { "href": "https://www.zotero.org/groups/xavier.robin", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/62016/items/WVDVQKTX", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/xavier.robin/items/WVDVQKTX", "type": "text/html" } }, "meta": { "createdByUser": { "id": 12953, "username": "Calimo", "name": "Xavier Robin", "links": { "alternate": { "href": "https://www.zotero.org/calimo", "type": "text/html" } } }, "creatorSummary": "Martínez-Bartolomé et al.", "parsedDate": "2014-01-01", "numChildren": 0 }, "data": { "key": "WVDVQKTX", "version": 119, "itemType": "bookSection", "title": "The Minimal Information About a Proteomics Experiment (MIAPE) from the Proteomics Standards Initiative", "creators": [ { "creatorType": "author", "firstName": "Salvador", "lastName": "Martínez-Bartolomé" }, { "creatorType": "author", "firstName": "Pierre-Alain", "lastName": "Binz" }, { "creatorType": "author", "firstName": "Juan P.", "lastName": "Albar" }, { "creatorType": "editor", "firstName": "Jesus V.", "lastName": "Jorrin-Novo" }, { "creatorType": "editor", "firstName": "Setsuko", "lastName": "Komatsu" }, { "creatorType": "editor", "firstName": "Wolfram", "lastName": "Weckwerth" }, { "creatorType": "editor", "firstName": "Stefanie", "lastName": "Wienkoop" } ], "abstractNote": "During the last 10 years, the Proteomics Standards Initiative from the Human Proteome Organization (HUPO-PSI) has worked on defining standards for proteomics data representation as well as guidelines that state the minimum information that should be included when reporting a proteomics experiment (MIAPE). Such minimum information must describe the complete experiment, including both experimental protocols and data processing methods, allowing a critical evaluation of the whole process and the potential recreation of the work. In this chapter we describe the standardization work performed by the HUPO-PSI, and then we concentrate on the MIAPE guidelines, highlighting its importance when publishing proteomics experiments particularly in specialized proteomics journals. Finally, we describe existing bioinformatics resources that generate MIAPE compliant reports or that check proteomics data files for MIAPE compliance.", "bookTitle": "Plant Proteomics", "series": "Methods in Molecular Biology", "seriesNumber": "1072", "volume": "", "numberOfVolumes": "", "edition": "", "date": "2014/01/01", "publisher": "Humana Press", "place": "", "originalDate": "", "originalPublisher": "", "originalPlace": "", "format": "", "pages": "765-780", "ISBN": "978-1-62703-630-6, 978-1-62703-631-3", "DOI": "", "citationKey": "", "url": "http://link.springer.com/protocol/10.1007/978-1-62703-631-3_53", "accessDate": "2013-11-24T10:58:10Z", "ISSN": "", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "en", "libraryCatalog": "link.springer.com", "callNumber": "", "rights": "©2014 Springer Science+Business Media, LLC", "extra": "", "tags": [ { "tag": "Guidelines", "type": 1 }, { "tag": "HUPO-PSI", "type": 1 }, { "tag": "MIAPE", "type": 1 }, { "tag": "Plant Sciences", "type": 1 }, { "tag": "Proteomics", "type": 1 }, { "tag": "Reporting", "type": 1 }, { "tag": "Semantic validator", "type": 1 }, { "tag": "Standards", "type": 1 } ], "collections": [ "J9GQQK9U" ], "relations": {}, "dateAdded": "2013-11-24T10:58:22Z", "dateModified": "2013-11-24T10:58:22Z" } }, { "key": "S6TMNDME", "version": 64, "library": { "type": "group", "id": 62016, "name": "xavier.robin", "links": { "alternate": { "href": "https://www.zotero.org/groups/xavier.robin", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/62016/items/S6TMNDME", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/xavier.robin/items/S6TMNDME", "type": "text/html" } }, "meta": { "createdByUser": { "id": 12953, "username": "Calimo", "name": "Xavier Robin", "links": { "alternate": { "href": "https://www.zotero.org/calimo", "type": "text/html" } } }, "creatorSummary": "Ivanov et al.", "parsedDate": "2013", "numChildren": 0 }, "data": { "key": "S6TMNDME", "version": 64, "itemType": "journalArticle", "title": "Interlaboratory studies and initiatives developing standards for proteomics", "creators": [ { "creatorType": "author", "firstName": "Alexander R.", "lastName": "Ivanov" }, { "creatorType": "author", "firstName": "Christopher M.", "lastName": "Colangelo" }, { "creatorType": "author", "firstName": "Craig P.", "lastName": "Dufresne" }, { "creatorType": "author", "firstName": "David B.", "lastName": "Friedman" }, { "creatorType": "author", "firstName": "Kathryn S.", "lastName": "Lilley" }, { "creatorType": "author", "firstName": "Karl", "lastName": "Mechtler" }, { "creatorType": "author", "firstName": "Brett S.", "lastName": "Phinney" }, { "creatorType": "author", "firstName": "Kristie L.", "lastName": "Rose" }, { "creatorType": "author", "firstName": "Paul A.", "lastName": "Rudnick" }, { "creatorType": "author", "firstName": "Brian C.", "lastName": "Searle" }, { "creatorType": "author", "firstName": "Scott A.", "lastName": "Shaffer" }, { "creatorType": "author", "firstName": "Susan T.", "lastName": "Weintraub" } ], "abstractNote": "Proteomics is a rapidly transforming interdisciplinary field of research that embraces a diverse set of analytical approaches to tackle problems in fundamental and applied biology. This viewpoint article highlights the benefits of interlaboratory studies and standardization initiatives to enable investigators to address many of the challenges found in proteomics research. Among these initiatives, we discuss our efforts on a comprehensive performance standard for characterizing PTMs by MS that was recently developed by the Association of Biomolecular Resource Facilities (ABRF) Proteomics Standards Research Group (sPRG).", "publicationTitle": "PROTEOMICS", "publisher": "", "place": "", "date": "2013", "volume": "13", "issue": "6", "section": "", "partNumber": "", "partTitle": "", "pages": "904–909", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "", "DOI": "10.1002/pmic.201200532", "citationKey": "", "url": "http://onlinelibrary.wiley.com/doi/10.1002/pmic.201200532/abstract", "accessDate": "2013-03-23T13:58:26Z", "PMID": "", "PMCID": "", "ISSN": "1615-9861", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "en", "libraryCatalog": "Wiley Online Library", "callNumber": "", "rights": "© 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim", "extra": "", "tags": [ { "tag": "LC-MS/MS", "type": 1 }, { "tag": "Mass spectrometry-based proteomics", "type": 1 }, { "tag": "Phosphopeptides", "type": 1 }, { "tag": "post-translational modifications", "type": 1 }, { "tag": "protein identification", "type": 1 } ], "collections": [ "J9GQQK9U" ], "relations": {}, "dateAdded": "2013-03-23T13:59:09Z", "dateModified": "2013-03-23T13:59:09Z" } }, { "key": "792TIUC5", "version": 64, "library": { "type": "group", "id": 62016, "name": "xavier.robin", "links": { "alternate": { "href": "https://www.zotero.org/groups/xavier.robin", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/62016/items/792TIUC5", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/xavier.robin/items/792TIUC5", "type": "text/html" }, "up": { "href": "https://api.zotero.org/groups/62016/items/89TWMTTN", "type": "application/json" } }, "meta": { "createdByUser": { "id": 12953, "username": "Calimo", "name": "Xavier Robin", "links": { "alternate": { "href": "https://www.zotero.org/calimo", "type": "text/html" } } } }, "data": { "key": "792TIUC5", "version": 64, "parentItem": "89TWMTTN", "itemType": "attachment", "linkMode": "linked_url", "title": "Full Text PDF", "accessDate": "2013-03-23T13:56:34Z", "url": "http://onlinelibrary.wiley.com/store/10.1002/pmic.201200268/asset/pmic7310.pdf?v=1&t=hemucys6&s=1f3c97dc90ec7d6f14ba5d9a7c4694c276758f4a", "note": "", "contentType": "application/pdf", "charset": "", "tags": [], "relations": {}, "dateAdded": "2013-03-23T13:56:34Z", "dateModified": "2013-03-23T13:56:34Z" } }, { "key": "5RCHQXKK", "version": 64, "library": { "type": "group", "id": 62016, "name": "xavier.robin", "links": { "alternate": { "href": "https://www.zotero.org/groups/xavier.robin", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/62016/items/5RCHQXKK", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/xavier.robin/items/5RCHQXKK", "type": "text/html" }, "up": { "href": "https://api.zotero.org/groups/62016/items/89TWMTTN", "type": "application/json" } }, "meta": { "createdByUser": { "id": 12953, "username": "Calimo", "name": "Xavier Robin", "links": { "alternate": { "href": "https://www.zotero.org/calimo", "type": "text/html" } } } }, "data": { "key": "5RCHQXKK", "version": 64, "parentItem": "89TWMTTN", "itemType": "attachment", "linkMode": "linked_url", "title": "Snapshot", "accessDate": "2013-03-23T13:56:34Z", "url": "http://onlinelibrary.wiley.com/doi/10.1002/pmic.201200268/full", "note": "", "contentType": "text/html", "charset": "", "tags": [], "relations": {}, "dateAdded": "2013-03-23T13:56:34Z", "dateModified": "2013-03-23T13:56:34Z" } }, { "key": "89TWMTTN", "version": 64, "library": { "type": "group", "id": 62016, "name": "xavier.robin", "links": { "alternate": { "href": "https://www.zotero.org/groups/xavier.robin", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/62016/items/89TWMTTN", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/xavier.robin/items/89TWMTTN", "type": "text/html" } }, "meta": { "createdByUser": { "id": 12953, "username": "Calimo", "name": "Xavier Robin", "links": { "alternate": { "href": "https://www.zotero.org/calimo", "type": "text/html" } } }, "creatorSummary": "Medina-Aunon et al.", "parsedDate": "2013", "numChildren": 2 }, "data": { "key": "89TWMTTN", "version": 64, "itemType": "journalArticle", "title": "A guide for integration of proteomic data standards into laboratory workflows", "creators": [ { "creatorType": "author", "firstName": "J. Alberto", "lastName": "Medina-Aunon" }, { "creatorType": "author", "firstName": "Ritesh", "lastName": "Krishna" }, { "creatorType": "author", "firstName": "Fawaz", "lastName": "Ghali" }, { "creatorType": "author", "firstName": "Juan P.", "lastName": "Albar" }, { "creatorType": "author", "firstName": "Andrew J.", "lastName": "Jones" } ], "abstractNote": "The development of the HUPO-Proteomics Standards Initiative standard data formats and Minimum Information About a Proteomics Experiment guidelines facilitate coordination within the scientific community. The data standards provide a framework to exchange and share data regardless of the source instrument or software. Nevertheless there remains a view that Proteomics Standards Initiative standards are challenging to use and integrate into routine laboratory pipelines. In this article, we review the tools available for integrating the different data standards and building compliant software. These tools are focused on a range of different data types and support different scenarios, intended for software developers or end users, allowing the standards to be used in a straightforward manner.", "publicationTitle": "PROTEOMICS", "publisher": "", "place": "", "date": "2013", "volume": "13", "issue": "3-4", "section": "", "partNumber": "", "partTitle": "", "pages": "480–492", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "", "DOI": "10.1002/pmic.201200268", "citationKey": "", "url": "http://onlinelibrary.wiley.com/doi/10.1002/pmic.201200268/abstract", "accessDate": "2013-03-23T13:56:34Z", "PMID": "", "PMCID": "", "ISSN": "1615-9861", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "en", "libraryCatalog": "Wiley Online Library", "callNumber": "", "rights": "© 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim", "extra": "", "tags": [ { "tag": "Bioinformatics", "type": 1 }, { "tag": "Mass spectrometry and review", "type": 1 }, { "tag": "Proteomics Standards Initiative", "type": 1 }, { "tag": "Software evaluation", "type": 1 } ], "collections": [ "J9GQQK9U" ], "relations": {}, "dateAdded": "2013-03-23T13:56:34Z", "dateModified": "2013-03-23T13:56:34Z" } }, { "key": "VZHNPPP7", "version": 1, "library": { "type": "group", "id": 62016, "name": "xavier.robin", "links": { "alternate": { "href": "https://www.zotero.org/groups/xavier.robin", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/62016/items/VZHNPPP7", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/xavier.robin/items/VZHNPPP7", "type": "text/html" } }, "meta": { "createdByUser": { "id": 12953, "username": "Calimo", "name": "Xavier Robin", "links": { "alternate": { "href": "https://www.zotero.org/calimo", "type": "text/html" } } }, "creatorSummary": "Schrattenholz et al.", "parsedDate": "2010", "numChildren": 0 }, "data": { "key": "VZHNPPP7", "version": 1, "itemType": "journalArticle", "title": "Synchronization of posttranslational modifications during aging", "creators": [ { "creatorType": "author", "firstName": "André", "lastName": "Schrattenholz" }, { "creatorType": "author", "firstName": "Vukić", "lastName": "Šoškić" }, { "creatorType": "author", "firstName": "Karlfried", "lastName": "Groebe" } ], "abstractNote": "There is an urgent need for surrogate biomarkers in clinical diagnostics but also preclinical in toxicology of chemicals and efficacy testing of pharmaceuticals. On the background of the emerging fields of systems biology and theranostics, the importance of time scales and the synchronization of complex biological readouts become increasingly obvious. Systemic effects such as responses to stimuli, medical intervention, cellular stress, or toxicity elicit immediate molecular changes on the protein level. Early events include phosphorylation and oxidation of proteins. These posttranslational modifications have a direct impact on enzyme activities and protein2013protein interactions. Only at downstream stages is gene transcription activated. Here we outline the analytical and statistical requirements dealing with complex patterns of protein expression and the extraction of protein surrogate biomarkers defining specific early stages of biological responses. We also present successful examples from research on aging and discuss prerequisites and necessary considerations while moving candidates to validation.", "publicationTitle": "Annals of the New York Academy of Sciences", "publisher": "", "place": "", "date": "2010", "volume": "1197", "issue": "Aging, Cancer, and Age-Related Diseases: Common Mechanisms?", "section": "", "partNumber": "", "partTitle": "", "pages": "118-128", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "", "DOI": "", "citationKey": "", "url": "http://dx.doi.org/10.1111/j.1749-6632.2009.05395.x", "accessDate": "", "PMID": "", "PMCID": "", "ISSN": "", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "", "callNumber": "", "rights": "", "extra": "", "tags": [], "collections": [ "J9GQQK9U" ], "relations": {}, "dateAdded": "2011-12-05T09:45:15Z", "dateModified": "2011-12-05T09:45:15Z" } }, { "key": "TDKAIH95", "version": 1, "library": { "type": "group", "id": 62016, "name": "xavier.robin", "links": { "alternate": { "href": "https://www.zotero.org/groups/xavier.robin", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/62016/items/TDKAIH95", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/xavier.robin/items/TDKAIH95", "type": "text/html" } }, "meta": { "createdByUser": { "id": 12953, "username": "Calimo", "name": "Xavier Robin", "links": { "alternate": { "href": "https://www.zotero.org/calimo", "type": "text/html" } } }, "creatorSummary": "Pottiez et al.", "parsedDate": "2010", "numChildren": 0 }, "data": { "key": "TDKAIH95", "version": 1, "itemType": "journalArticle", "title": "A large-scale electrophoresis- and chromatography-based determination of gene expression profiles in bovine brain capillary endothelial cells after the re-induction of blood-brain barrier properties", "creators": [ { "creatorType": "author", "firstName": "Gwenael", "lastName": "Pottiez" }, { "creatorType": "author", "firstName": "Barbara", "lastName": "Deracinois" }, { "creatorType": "author", "firstName": "Sophie", "lastName": "Duban-Deweer" }, { "creatorType": "author", "firstName": "Romeo", "lastName": "Cecchelli" }, { "creatorType": "author", "firstName": "Laurence", "lastName": "Fenart" }, { "creatorType": "author", "firstName": "Yannis", "lastName": "Karamanos" }, { "creatorType": "author", "firstName": "Christophe", "lastName": "Flahaut" } ], "abstractNote": "BACKGROUND:Brain capillary endothelial cells (BCECs) form the physiological basis of the blood-brain barrier (BBB). The barrier function is (at least in part) due to well-known proteins such as transporters, tight junctions and metabolic barrier proteins (e.g. monoamine oxidase, gamma glutamyltranspeptidase and P-glycoprotein). Our previous 2-dimensional gel proteome analysis had identified a large number of proteins and revealed the major role of dynamic cytoskeletal remodelling in the differentiation of bovine BCECs. The aim of the present study was to elaborate a reference proteome of Triton X-100-soluble species from bovine BCECs cultured in the well-established in vitro BBB model developed in our laboratory.RESULTS:A total of 215 protein spots (corresponding to 130 distinct proteins) were identified by 2-dimensional gel electrophoresis, whereas over 350 proteins were identified by a shotgun approach. We classified around 430 distinct proteins expressed by bovine BCECs. Our large-scale gene expression analysis enabled the correction of mistakes referenced into protein databases (e.g. bovine vinculin) and constitutes valuable evidence for predictions based on genome annotation.CONCLUSIONS:Elaboration of a reference proteome constitutes the first step in creating a gene expression database dedicated to capillary endothelial cells displaying BBB characteristics. It improves of our knowledge of the BBB and the key proteins in cell structures, cytoskeleton organization, metabolism, detoxification and drug resistance. Moreover, our results emphasize the need for both appropriate experimental design and correct interpretation of proteome datasets.", "publicationTitle": "Proteome Science", "publisher": "", "place": "", "date": "2010", "volume": "8", "issue": "1", "section": "", "partNumber": "", "partTitle": "", "pages": "57", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "", "DOI": "10.1186/1477-5956-8-57", "citationKey": "", "url": "http://www.proteomesci.com/content/8/1/57", "accessDate": "2010-12-17T14:11:15Z", "PMID": "", "PMCID": "", "ISSN": "1477-5956", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "BioMed Central and More", "callNumber": "", "rights": "", "extra": "", "tags": [], "collections": [ "J9GQQK9U" ], "relations": {}, "dateAdded": "2011-12-05T09:45:15Z", "dateModified": "2011-12-05T09:45:15Z" } }, { "key": "T3AJQVWU", "version": 1, "library": { "type": "group", "id": 62016, "name": "xavier.robin", "links": { "alternate": { "href": "https://www.zotero.org/groups/xavier.robin", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/62016/items/T3AJQVWU", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/xavier.robin/items/T3AJQVWU", "type": "text/html" } }, "meta": { "createdByUser": { "id": 12953, "username": "Calimo", "name": "Xavier Robin", "links": { "alternate": { "href": "https://www.zotero.org/calimo", "type": "text/html" } } }, "creatorSummary": "Palagi and Lisacek", "parsedDate": "2009-06-03", "numChildren": 0 }, "data": { "key": "T3AJQVWU", "version": 1, "itemType": "bookSection", "title": "Analytical Bioinformatics for Proteomics", "creators": [ { "creatorType": "editor", "firstName": "Ron D.", "lastName": "Appel" }, { "creatorType": "editor", "firstName": "Ernest", "lastName": "Feytmans" }, { "creatorType": "author", "firstName": "Patricia M.", "lastName": "Palagi" }, { "creatorType": "author", "firstName": "Frédérique", "lastName": "Lisacek" } ], "abstractNote": "", "bookTitle": "Bioinformatics: a Swiss perspective", "series": "", "seriesNumber": "", "volume": "", "numberOfVolumes": "", "edition": "", "date": "2009-06-03", "publisher": "World Scientific", "place": "", "originalDate": "", "originalPublisher": "", "originalPlace": "", "format": "", "pages": "169-196", "ISBN": "9789812838773", "DOI": "", "citationKey": "", "url": "", "accessDate": "", "ISSN": "", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "Google Books", "callNumber": "", "rights": "", "extra": "", "tags": [], "collections": [ "J9GQQK9U" ], "relations": {}, "dateAdded": "2011-12-05T09:45:15Z", "dateModified": "2011-12-05T09:45:15Z" } }, { "key": "KGQIR6TU", "version": 1, "library": { "type": "group", "id": 62016, "name": "xavier.robin", "links": { "alternate": { "href": "https://www.zotero.org/groups/xavier.robin", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/62016/items/KGQIR6TU", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/xavier.robin/items/KGQIR6TU", "type": "text/html" } }, "meta": { "createdByUser": { "id": 12953, "username": "Calimo", "name": "Xavier Robin", "links": { "alternate": { "href": "https://www.zotero.org/calimo", "type": "text/html" } } }, "creatorSummary": "Orchard et al.", "parsedDate": "2010", "numChildren": 0 }, "data": { "key": "KGQIR6TU", "version": 1, "itemType": "journalArticle", "title": "Implementing Data Standards: A report on the HUPOPSI Workshop September 2009, Toronto, Canada", "creators": [ { "creatorType": "author", "firstName": "Sandra", "lastName": "Orchard" }, { "creatorType": "author", "firstName": "Juan-Pablo", "lastName": "Albar" }, { "creatorType": "author", "firstName": "Eric W.", "lastName": "Deutsch" }, { "creatorType": "author", "firstName": "Martin", "lastName": "Eisenacher" }, { "creatorType": "author", "firstName": "Pierre-Alain", "lastName": "Binz" }, { "creatorType": "author", "firstName": "Henning", "lastName": "Hermjakob" } ], "abstractNote": "The plenary session of the Proteomics Standards Initiative of the Human Proteome Organisation at the 8th Annual HUPO World Congress updated the delegates on the current status of the ongoing work of this group. The mass spectrometry group reviewed the progress of mzML since its release last year and detailed new work on providing a common format for SRM/MRM transition lists (TraML). The implementation of mzIdentML, for describing the output of proteomics search engines, was outlined and the release of a new web service PSICQUIC, which allows users to simultaneously search multiple interaction databases, was announced. Finally, the audience participated in a lively debate, discussing both the benefits of these standard formats and issues with their adoption and use in a research environment.", "publicationTitle": "PROTEOMICS", "publisher": "", "place": "", "date": "2010", "volume": "10", "issue": "10", "section": "", "partNumber": "", "partTitle": "", "pages": "1895-1898", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "", "DOI": "", "citationKey": "", "url": "http://dx.doi.org/10.1002/pmic.201090034", "accessDate": "", "PMID": "", "PMCID": "", "ISSN": "", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "", "callNumber": "", "rights": "", "extra": "PMID: 20623474", "tags": [], "collections": [ "J9GQQK9U" ], "relations": {}, "dateAdded": "2011-12-05T09:45:15Z", "dateModified": "2011-12-05T09:45:15Z" } }, { "key": "FPV6NWSE", "version": 1, "library": { "type": "group", "id": 62016, "name": "xavier.robin", "links": { "alternate": { "href": "https://www.zotero.org/groups/xavier.robin", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/62016/items/FPV6NWSE", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/xavier.robin/items/FPV6NWSE", "type": "text/html" } }, "meta": { "createdByUser": { "id": 12953, "username": "Calimo", "name": "Xavier Robin", "links": { "alternate": { "href": "https://www.zotero.org/calimo", "type": "text/html" } } }, "creatorSummary": "Montecchi-Palazzi et al.", "parsedDate": "2009", "numChildren": 0 }, "data": { "key": "FPV6NWSE", "version": 1, "itemType": "journalArticle", "title": "The PSI semantic validator: A framework to check MIAPE compliance of proteomics data", "creators": [ { "creatorType": "author", "firstName": "Luisa", "lastName": "Montecchi-Palazzi" }, { "creatorType": "author", "firstName": "Samuel", "lastName": "Kerrien" }, { "creatorType": "author", "firstName": "Florian", "lastName": "Reisinger" }, { "creatorType": "author", "firstName": "Bruno", "lastName": "Aranda" }, { "creatorType": "author", "firstName": "Andrew R.", "lastName": "Jones" }, { "creatorType": "author", "firstName": "Lennart", "lastName": "Martens" }, { "creatorType": "author", "firstName": "Henning", "lastName": "Hermjakob" } ], "abstractNote": "The Human Proteome Organization's Proteomics Standards Initiative (PSI) promotes the development of exchange standards to improve data integration and interoperability. PSI specifies the suitable level of detail required when reporting a proteomics experiment (via the Minimum Information About a Proteomics Experiment), and provides extensible markup language (XML) exchange formats and dedicated controlled vocabularies (CVs) that must be combined to generate a standard compliant document. The framework presented here tackles the issue of checking that experimental data reported using a specific format, CVs and public bio-ontologies (e.g. Gene Ontology, NCBI taxonomy) are compliant with the Minimum Information About a Proteomics Experiment recommendations. The semantic validator not only checks the XML syntax but it also enforces rules regarding the use of an ontology class or CV terms by checking that the terms exist in the resource and that they are used in the correct location of a document. Moreover, this framework is extremely fast, even on sizable data files, and flexible, as it can be adapted to any standard by customizing the parameters it requires: an XML Schema Definition, one or more CVs or ontologies, and a mapping file describing in a formal way how the semantic resources and the format are interrelated. As such, the validator provides a general solution to the common problem in data exchange: how to validate the correct usage of a data standard beyond simple XML Schema Definition validation. The framework source code and its various applications can be found at .", "publicationTitle": "PROTEOMICS", "publisher": "", "place": "", "date": "2009", "volume": "9", "issue": "22", "section": "", "partNumber": "", "partTitle": "", "pages": "5112-5119", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "", "DOI": "", "citationKey": "", "url": "http://dx.doi.org/10.1002/pmic.200900189", "accessDate": "", "PMID": "", "PMCID": "", "ISSN": "", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "", "callNumber": "", "rights": "", "extra": "", "tags": [], "collections": [ "J9GQQK9U" ], "relations": {}, "dateAdded": "2011-12-05T09:45:15Z", "dateModified": "2011-12-05T09:45:15Z" } }, { "key": "G2IFUU8U", "version": 1, "library": { "type": "group", "id": 62016, "name": "xavier.robin", "links": { "alternate": { "href": "https://www.zotero.org/groups/xavier.robin", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/62016/items/G2IFUU8U", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/xavier.robin/items/G2IFUU8U", "type": "text/html" } }, "meta": { "createdByUser": { "id": 12953, "username": "Calimo", "name": "Xavier Robin", "links": { "alternate": { "href": "https://www.zotero.org/calimo", "type": "text/html" } } }, "creatorSummary": "Lull et al.", "parsedDate": "2010-02-01", "numChildren": 0 }, "data": { "key": "G2IFUU8U", "version": 1, "itemType": "journalArticle", "title": "The use of neuroproteomics in drug abuse research", "creators": [ { "creatorType": "author", "firstName": "Melinda E.", "lastName": "Lull" }, { "creatorType": "author", "firstName": "Willard M.", "lastName": "Freeman" }, { "creatorType": "author", "firstName": "Heather D.", "lastName": "VanGuilder" }, { "creatorType": "author", "firstName": "Kent E.", "lastName": "Vrana" } ], "abstractNote": "The number of discovery proteomic studies of drug abuse has begun to increase in recent years, facilitated by the adoption of new techniques such as 2D-DIGE and iTRAQ. For these new tools to provide the greatest insight into the neurobiology of addiction, however, it is important that the addiction field has a clear understanding of the strengths, limitations, and drug abuse-specific research factors of neuroproteomic studies. This review outlines approaches for improving animal models, protein sample quality and stability, proteome fractionation, data analysis, and data sharing to maximize the insights gained from neuroproteomic studies of drug abuse. For both the behavioral researcher interested in what proteomic study results mean, and for biochemists joining the drug abuse research field, a careful consideration of these factors is needed. Similar to genomic, transcriptomic, and epigenetic methods, appropriate use of new proteomic technologies offers the potential to provide a novel and global view of the neurobiological changes underlying drug addiction. Proteomic tools may be an enabling technology to identify key proteins involved in drug abuse behaviors, with the ultimate goal of understanding the etiology of drug abuse and identifying targets for the development of therapeutic agents.", "publicationTitle": "Drug and Alcohol Dependence", "publisher": "", "place": "", "date": "February 1, 2010", "volume": "107", "issue": "1", "section": "", "partNumber": "", "partTitle": "", "pages": "11-22", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "", "DOI": "10.1016/j.drugalcdep.2009.10.001", "citationKey": "", "url": "http://www.sciencedirect.com/science/article/B6T63-4XPXT58-1/2/93814f72fce9f6f29e437d75a9b06af7", "accessDate": "2010-03-26T08:12:30Z", "PMID": "", "PMCID": "", "ISSN": "0376-8716", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "ScienceDirect", "callNumber": "", "rights": "", "extra": "PMID: 19926406", "tags": [], "collections": [ "J9GQQK9U" ], "relations": {}, "dateAdded": "2011-12-05T09:45:15Z", "dateModified": "2011-12-05T09:45:15Z" } }, { "key": "THV264EI", "version": 1, "library": { "type": "group", "id": 62016, "name": "xavier.robin", "links": { "alternate": { "href": "https://www.zotero.org/groups/xavier.robin", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/62016/items/THV264EI", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/xavier.robin/items/THV264EI", "type": "text/html" } }, "meta": { "createdByUser": { "id": 12953, "username": "Calimo", "name": "Xavier Robin", "links": { "alternate": { "href": "https://www.zotero.org/calimo", "type": "text/html" } } }, "creatorSummary": "Gibson et al.", "parsedDate": "2010", "numChildren": 0 }, "data": { "key": "THV264EI", "version": 1, "itemType": "journalArticle", "title": "The Gel Electrophoresis Markup Language (GelML) from the Proteomics Standards Initiative", "creators": [ { "creatorType": "author", "firstName": "Frank", "lastName": "Gibson" }, { "creatorType": "author", "firstName": "Christine", "lastName": "Hoogland" }, { "creatorType": "author", "firstName": "Salvador", "lastName": "Martinez-Bartolomé" }, { "creatorType": "author", "firstName": "J. Alberto", "lastName": "Medina-Aunon" }, { "creatorType": "author", "firstName": "Juan Pablo", "lastName": "Albar" }, { "creatorType": "author", "firstName": "Gyorgy", "lastName": "Babnigg" }, { "creatorType": "author", "firstName": "Anil", "lastName": "Wipat" }, { "creatorType": "author", "firstName": "Henning", "lastName": "Hermjakob" }, { "creatorType": "author", "firstName": "Jonas S.", "lastName": "Almeida" }, { "creatorType": "author", "firstName": "Romesh", "lastName": "Stanislaus" }, { "creatorType": "author", "firstName": "Norman W.", "lastName": "Paton" }, { "creatorType": "author", "firstName": "Andrew R.", "lastName": "Jones" } ], "abstractNote": "The Human Proteome Organisation's Proteomics Standards Initiative has developed the GelML (gel electrophoresis markup language) data exchange format for representing gel electrophoresis experiments performed in proteomics investigations. The format closely follows the reporting guidelines for gel electrophoresis, which are part of the Minimum Information About a Proteomics Experiment (MIAPE) set of modules. GelML supports the capture of metadata (such as experimental protocols) and data (such as gel images) resulting from gel electrophoresis so that laboratories can be compliant with the MIAPE Gel Electrophoresis guidelines, while allowing such data sets to be exchanged or downloaded from public repositories. The format is sufficiently flexible to capture data from a broad range of experimental processes, and complements other PSI formats for MS data and the results of protein and peptide identifications to capture entire gel-based proteome workflows. GelML has resulted from the open standardisation process of PSI consisting of both public consultation and anonymous review of the specifications.", "publicationTitle": "PROTEOMICS", "publisher": "", "place": "", "date": "2010", "volume": "10", "issue": "17", "section": "", "partNumber": "", "partTitle": "", "pages": "3073–3081", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "", "DOI": "10.1002/pmic.201000120", "citationKey": "", "url": "http://dx.doi.org/10.1002/pmic.201000120", "accessDate": "2010-08-06T08:19:35Z", "PMID": "", "PMCID": "", "ISSN": "", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "Wiley InterScience", "callNumber": "", "rights": "", "extra": "", "tags": [], "collections": [ "J9GQQK9U" ], "relations": {}, "dateAdded": "2011-12-05T09:45:15Z", "dateModified": "2011-12-05T09:45:15Z" } }, { "key": "KCE9M32N", "version": 1, "library": { "type": "group", "id": 62016, "name": "xavier.robin", "links": { "alternate": { "href": "https://www.zotero.org/groups/xavier.robin", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/62016/items/KCE9M32N", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/xavier.robin/items/KCE9M32N", "type": "text/html" } }, "meta": { "createdByUser": { "id": 12953, "username": "Calimo", "name": "Xavier Robin", "links": { "alternate": { "href": "https://www.zotero.org/calimo", "type": "text/html" } } }, "creatorSummary": "Stephan et al.", "parsedDate": "2010-03", "numChildren": 0 }, "data": { "key": "KCE9M32N", "version": 1, "itemType": "journalArticle", "title": "Using Laboratory Information Management Systems as central part of a proteomics data workflow", "creators": [ { "creatorType": "author", "firstName": "Christian", "lastName": "Stephan" }, { "creatorType": "author", "firstName": "Michael", "lastName": "Kohl" }, { "creatorType": "author", "firstName": "Michael", "lastName": "Turewicz" }, { "creatorType": "author", "firstName": "Katharina", "lastName": "Podwojski" }, { "creatorType": "author", "firstName": "Helmut E", "lastName": "Meyer" }, { "creatorType": "author", "firstName": "Martin", "lastName": "Eisenacher" } ], "abstractNote": "The organization and storage of proteomics data are challenging issues today and even more for the rising amount of information in the future. This review article describes the advantages of using Laboratory Information Management Systems (LIMS) in proteomics laboratories. Seven typical LIMS are explored in detail to describe their role in an even bigger interrelation. They are a central part of the proteomics data workflow, starting with data generation and ending with the publication in journals and repositories. Therefore, they enable community-wide data utilization and further Systems Biology discoveries.", "publicationTitle": "Proteomics", "publisher": "", "place": "", "date": "Mar 2010", "volume": "10", "issue": "6", "section": "", "partNumber": "", "partTitle": "", "pages": "1230-1249", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "Proteomics", "DOI": "10.1002/pmic.200900420", "citationKey": "", "url": "http://www.ncbi.nlm.nih.gov/pubmed/20077413", "accessDate": "2010-04-16T07:11:58Z", "PMID": "", "PMCID": "", "ISSN": "1615-9861", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "NCBI PubMed", "callNumber": "", "rights": "", "extra": "PMID: 20077413", "tags": [], "collections": [ "J9GQQK9U" ], "relations": {}, "dateAdded": "2011-12-05T09:45:15Z", "dateModified": "2011-12-05T09:45:15Z" } }, { "key": "IXSP69GK", "version": 1, "library": { "type": "group", "id": 62016, "name": "xavier.robin", "links": { "alternate": { "href": "https://www.zotero.org/groups/xavier.robin", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/62016/items/IXSP69GK", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/xavier.robin/items/IXSP69GK", "type": "text/html" } }, "meta": { "createdByUser": { "id": 12953, "username": "Calimo", "name": "Xavier Robin", "links": { "alternate": { "href": "https://www.zotero.org/calimo", "type": "text/html" } } }, "creatorSummary": "Orchard et al.", "parsedDate": "2009", "numChildren": 0 }, "data": { "key": "IXSP69GK", "version": 1, "itemType": "journalArticle", "title": "Managing the Data Explosion A Report on the HUPO-PSI Workshop August 2008, Amsterdam, The Netherlands", "creators": [ { "creatorType": "author", "firstName": "Sandra", "lastName": "Orchard" }, { "creatorType": "author", "firstName": "Christine", "lastName": "Hoogland" }, { "creatorType": "author", "firstName": "Amos", "lastName": "Bairoch" }, { "creatorType": "author", "firstName": "Martin", "lastName": "Eisenacher" }, { "creatorType": "author", "firstName": "Hans-Joachim", "lastName": "Kraus" }, { "creatorType": "author", "firstName": "Pierre-Alain", "lastName": "Binz" } ], "abstractNote": "The plenary session of the Proteomics Standards Initiative (PSI) of the Human Proteome Organisation at the 7th annual HUPO world congress updated the delegates on the current status of the ongoing work of this group. The release of the new MS interchange format, mzML, was formally announced and delegates were also updated on the advances in the area of molecular interactions, protein separations, proteomics informatics and also on PEFF, a common sequence database format currently under review in the PSI documentation process. Community input on this initiative was requested. Finally, the impact these new data standards are having on the data submission process, which increasingly is an integral part of the publication process, was reviewed and discussed.", "publicationTitle": "Proteomics", "publisher": "", "place": "", "date": "2009", "volume": "9", "issue": "3", "section": "", "partNumber": "", "partTitle": "", "pages": "499-501", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "", "DOI": "10.1002/pmic.200800838", "citationKey": "", "url": "http://dx.doi.org/10.1002/pmic.200800838", "accessDate": "2009-05-22T09:04:18Z", "PMID": "", "PMCID": "", "ISSN": "", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "Wiley InterScience", "callNumber": "", "rights": "", "extra": "PMID: 19132688", "tags": [], "collections": [ "J9GQQK9U" ], "relations": {}, "dateAdded": "2011-12-05T09:45:15Z", "dateModified": "2011-12-05T09:45:15Z" } }, { "key": "2I8VMDEB", "version": 1, "library": { "type": "group", "id": 62016, "name": "xavier.robin", "links": { "alternate": { "href": "https://www.zotero.org/groups/xavier.robin", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/62016/items/2I8VMDEB", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/xavier.robin/items/2I8VMDEB", "type": "text/html" } }, "meta": { "createdByUser": { "id": 12953, "username": "Calimo", "name": "Xavier Robin", "links": { "alternate": { "href": "https://www.zotero.org/calimo", "type": "text/html" } } }, "creatorSummary": "Lull et al.", "parsedDate": "2009", "numChildren": 0 }, "data": { "key": "2I8VMDEB", "version": 1, "itemType": "journalArticle", "title": "Persistent proteomic alterations in the medial prefrontal cortex with abstinence from cocaine self-administration", "creators": [ { "creatorType": "author", "firstName": "Melinda E.", "lastName": "Lull" }, { "creatorType": "author", "firstName": "Mandi S.", "lastName": "Erwin" }, { "creatorType": "author", "firstName": "Drake", "lastName": "Morgan" }, { "creatorType": "author", "firstName": "David C. S.", "lastName": "Roberts" }, { "creatorType": "author", "firstName": "Kent E.", "lastName": "Vrana" }, { "creatorType": "author", "firstName": "Willard M.", "lastName": "Freeman" } ], "abstractNote": "Neuroproteomic studies of drug abuse offer the potential for a systems-level understanding of addiction. Understanding cocaine-responsive alterations in brain protein expression that persist even with extended abstinence may provide insight into relapse liability. In the current study, protein changes in the medial prefrontal cortex of cocaine self-administering rats following 1 and 100�days of enforced abstinence were quantified by 2-D DIGE. We have previously reported increased drug-seeking and drug-taking, as well as mRNA and epigenetic changes in this model even after 100�days of enforced abstinence. A number of statistically significant changes in proteins relating to synapse function and neuronal remodeling were evident, including neurofilament medium and Hsp73, which increased at 1�day of abstinence, but returned to normal levels following 100�days of abstinence. Dynamin-1 and synaptosome-associated protein 25�kDa (SNAP-25) were unchanged at 1�day of abstinence, but were significantly decreased after 100�days. These data demonstrate that while some protein changes return to normal levels following enforced cocaine abstinence, a number remain or become altered after long periods, up to 100�days, of cocaine abstinence. Those protein expression changes that do not reset to pre-cocaine exposure levels may contribute to the persistent relapse potential that occurs in response to cocaine abstinence.", "publicationTitle": "Proteomics Clinical Applications", "publisher": "", "place": "", "date": "2009", "volume": "3", "issue": "4", "section": "", "partNumber": "", "partTitle": "", "pages": "462-472", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "Proteomics Clin. Appl.", "DOI": "10.1002/prca.200800055", "citationKey": "", "url": "http://dx.doi.org/10.1002/prca.200800055", "accessDate": "2009-05-22T09:06:17Z", "PMID": "", "PMCID": "", "ISSN": "", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "Wiley InterScience", "callNumber": "", "rights": "", "extra": "PMID: 20161123", "tags": [], "collections": [ "J9GQQK9U" ], "relations": {}, "dateAdded": "2011-12-05T09:45:15Z", "dateModified": "2011-12-05T09:45:15Z" } }, { "key": "R5M4HRBP", "version": 1, "library": { "type": "group", "id": 62016, "name": "xavier.robin", "links": { "alternate": { "href": "https://www.zotero.org/groups/xavier.robin", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/62016/items/R5M4HRBP", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/xavier.robin/items/R5M4HRBP", "type": "text/html" } }, "meta": { "createdByUser": { "id": 12953, "username": "Calimo", "name": "Xavier Robin", "links": { "alternate": { "href": "https://www.zotero.org/calimo", "type": "text/html" } } }, "creatorSummary": "Eisenacher et al.", "parsedDate": "2009", "numChildren": 0 }, "data": { "key": "R5M4HRBP", "version": 1, "itemType": "journalArticle", "title": "Getting a grip on proteomics data - Proteomics Data Collection (ProDaC)", "creators": [ { "creatorType": "author", "firstName": "Martin", "lastName": "Eisenacher" }, { "creatorType": "author", "firstName": "Lennart", "lastName": "Martens" }, { "creatorType": "author", "firstName": "Tanja", "lastName": "Hardt" }, { "creatorType": "author", "firstName": "Michael", "lastName": "Kohl" }, { "creatorType": "author", "firstName": "Harald", "lastName": "Barsnes" }, { "creatorType": "author", "firstName": "Kenny", "lastName": "Helsens" }, { "creatorType": "author", "firstName": "Jari", "lastName": "Häkkinen" }, { "creatorType": "author", "firstName": "Fredrik", "lastName": "Levander" }, { "creatorType": "author", "firstName": "Ruedi", "lastName": "Aebersold" }, { "creatorType": "author", "firstName": "Joël", "lastName": "Vandekerckhove" }, { "creatorType": "author", "firstName": "Michael J.", "lastName": "Dunn" }, { "creatorType": "author", "firstName": "Frederique", "lastName": "Lisacek" }, { "creatorType": "author", "firstName": "Jennifer A.", "lastName": "Siepen" }, { "creatorType": "author", "firstName": "Simon J.", "lastName": "Hubbard" }, { "creatorType": "author", "firstName": "Pierre-Alain", "lastName": "Binz" }, { "creatorType": "author", "firstName": "Martin", "lastName": "Blüggel" }, { "creatorType": "author", "firstName": "Herbert", "lastName": "Thiele" }, { "creatorType": "author", "firstName": "John", "lastName": "Cottrell" }, { "creatorType": "author", "firstName": "Helmut E.", "lastName": "Meyer" }, { "creatorType": "author", "firstName": "Rolf", "lastName": "Apweiler" }, { "creatorType": "author", "firstName": "Christian", "lastName": "Stephan" } ], "abstractNote": "In proteomics, rapid developments in instrumentation led to the acquisition of increasingly large data sets. Correspondingly, ProDaC was founded in 2006 as a Coordination Action project within the 6th European Union Framework Programme to support data sharing and community-wide data collection. The objectives of ProDaC were the development of documentation and storage standards, setup of a standardized data submission pipeline and collection of data. Ending in March 2009, ProDaC has delivered a comprehensive toolbox of standards and computer programs to achieve these goals.", "publicationTitle": "PROTEOMICS", "publisher": "", "place": "", "date": "2009", "volume": "9", "issue": "", "section": "", "partNumber": "", "partTitle": "", "pages": "1-6", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "", "DOI": "10.1002/pmic.200900247", "citationKey": "", "url": "http://dx.doi.org/10.1002/pmic.200900247", "accessDate": "2009-08-03T06:48:36Z", "PMID": "", "PMCID": "", "ISSN": "", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "Wiley InterScience", "callNumber": "", "rights": "", "extra": "PMID: 19637238", "tags": [], "collections": [ "J9GQQK9U" ], "relations": {}, "dateAdded": "2011-12-05T09:45:15Z", "dateModified": "2011-12-05T09:45:15Z" } }, { "key": "K7W24EF7", "version": 1, "library": { "type": "group", "id": 62016, "name": "xavier.robin", "links": { "alternate": { "href": "https://www.zotero.org/groups/xavier.robin", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/62016/items/K7W24EF7", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/xavier.robin/items/K7W24EF7", "type": "text/html" } }, "meta": { "createdByUser": { "id": 12953, "username": "Calimo", "name": "Xavier Robin", "links": { "alternate": { "href": "https://www.zotero.org/calimo", "type": "text/html" } } }, "creatorSummary": "Cilia et al.", "parsedDate": "2011-06-01", "numChildren": 0 }, "data": { "key": "K7W24EF7", "version": 1, "itemType": "journalArticle", "title": "Biomarker discovery from the top down: Protein biomarkers for efficient virus transmission by insects (Homoptera: Aphididae) discovered by coupling genetics and 2‐D DIGE", "creators": [ { "creatorType": "author", "firstName": "Michelle", "lastName": "Cilia" }, { "creatorType": "author", "firstName": "Kevin", "lastName": "Howe" }, { "creatorType": "author", "firstName": "Tara", "lastName": "Fish" }, { "creatorType": "author", "firstName": "Dawn", "lastName": "Smith" }, { "creatorType": "author", "firstName": "Jaclyn", "lastName": "Mahoney" }, { "creatorType": "author", "firstName": "Cecilia", "lastName": "Tamborindeguy" }, { "creatorType": "author", "firstName": "John", "lastName": "Burd" }, { "creatorType": "author", "firstName": "Theodore W", "lastName": "Thannhauser" }, { "creatorType": "author", "firstName": "Stewart", "lastName": "Gray" } ], "abstractNote": "Yellow dwarf viruses cause the most economically important virus diseases of cereal crops worldwide and are vectored by aphids. The identification of vector proteins mediating virus transmission is critical to develop sustainable virus management practices and to understand viral strategies for circulative movement in all insect vectors. Previously, we applied 2-D DIGE to an aphid filial generation 2 population to identify proteins correlated with the transmission phenotype that were stably inherited and expressed in the absence of the virus. In the present study, we examined the expression of the DIGE candidates in previously unstudied, field-collected aphid populations. We hypothesized that the expression of proteins involved in virus transmission could be clinically validated in unrelated, virus transmission-competent, field-collected aphid populations. All putative biomarkers were expressed in the field-collected biotypes, and the expression of nine of these aligned with the virus transmission-competent phenotype. The strong conservation of the expression of the biomarkers in multiple field-collected populations facilitates new and testable hypotheses concerning the genetics and biochemistry of virus transmission. Integration of these biomarkers into current aphid-scouting methodologies will enable rational strategies for vector control aimed at judicious use and development of precision pest control methods that reduce plant virus infection.", "publicationTitle": "PROTEOMICS", "publisher": "", "place": "", "date": "2011/06/01", "volume": "11", "issue": "12", "section": "", "partNumber": "", "partTitle": "", "pages": "2440-2458", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "", "DOI": "10.1002/pmic.201000519", "citationKey": "", "url": "http://onlinelibrary.wiley.com/doi/10.1002/pmic.201000519/abstract", "accessDate": "2011-07-29T06:54:08Z", "PMID": "", "PMCID": "", "ISSN": "1615-9861", "archive": "", "archiveLocation": "", "shortTitle": "Biomarker discovery from the top down", "language": "en", "libraryCatalog": "Wiley Online Library", "callNumber": "", "rights": "", "extra": "", "tags": [], "collections": [ "J9GQQK9U" ], "relations": {}, "dateAdded": "2011-12-05T09:45:15Z", "dateModified": "2011-12-05T09:45:15Z" } }, { "key": "B3Z4TS5S", "version": 1, "library": { "type": "group", "id": 62016, "name": "xavier.robin", "links": { "alternate": { "href": "https://www.zotero.org/groups/xavier.robin", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/62016/items/B3Z4TS5S", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/xavier.robin/items/B3Z4TS5S", "type": "text/html" } }, "meta": { "createdByUser": { "id": 12953, "username": "Calimo", "name": "Xavier Robin", "links": { "alternate": { "href": "https://www.zotero.org/calimo", "type": "text/html" } } }, "creatorSummary": "Hoogland et al.", "parsedDate": "2008", "numChildren": 0 }, "data": { "key": "B3Z4TS5S", "version": 1, "itemType": "journalArticle", "title": "A suite of tools to analyse and publish 2-DE data", "creators": [ { "creatorType": "author", "firstName": "Christine", "lastName": "Hoogland" }, { "creatorType": "author", "firstName": "Daniel", "lastName": "Walther" }, { "creatorType": "author", "firstName": "Patricia M.", "lastName": "Palagi" }, { "creatorType": "author", "firstName": "Gérard", "lastName": "Bouchet" }, { "creatorType": "author", "firstName": "Khaled", "lastName": "Mostaguir" }, { "creatorType": "author", "firstName": "Xavier", "lastName": "Robin" }, { "creatorType": "author", "firstName": "Ron D.", "lastName": "Appel" }, { "creatorType": "author", "firstName": "Frédérique", "lastName": "Lisacek" } ], "abstractNote": "Bioinformatics tools may assist scientists in all steps of a typical 2-DE gel analysis workflow, that is, from the description of the sample preparation protocols, going through the gel image analysis and protein identification, to the publication of Internet-ready 2-DE gel databases. This short communication highlights in a single and summarised view, this workflow and the current bioinformatics solutions developed by the Proteome Informatics Group at the Swiss Institute of Bioinformatics.", "publicationTitle": "Proteomics", "publisher": "", "place": "", "date": "2008", "volume": "8", "issue": "23-24", "section": "", "partNumber": "", "partTitle": "", "pages": "4907-4909", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "Proteomics", "DOI": "10.1002/pmic.200800301", "citationKey": "", "url": "http://dx.doi.org/10.1002/pmic.200800301", "accessDate": "2009-01-09T15:45:46Z", "PMID": "", "PMCID": "", "ISSN": "1615-9853", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "Wiley InterScience", "callNumber": "", "rights": "", "extra": "PMID: 19072735", "tags": [], "collections": [ "75VPBAXC", "J9GQQK9U" ], "relations": {}, "dateAdded": "2011-12-05T09:41:37Z", "dateModified": "2011-12-05T09:41:37Z" } } ]