[ { "key": "9KPICZMJ", "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/9KPICZMJ", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/xavier.robin/items/9KPICZMJ", "type": "text/html" } }, "meta": { "createdByUser": { "id": 12953, "username": "Calimo", "name": "Xavier Robin", "links": { "alternate": { "href": "https://www.zotero.org/calimo", "type": "text/html" } } }, "creatorSummary": "Taylor", "parsedDate": "2006", "numChildren": 0 }, "data": { "key": "9KPICZMJ", "version": 1, "itemType": "journalArticle", "title": "Minimum Reporting Requirements for Proteomics: A MIAPE Primer", "creators": [ { "creatorType": "author", "firstName": "Chris F.", "lastName": "Taylor" } ], "abstractNote": "Amongst other functions, the Human Proteome Organization's Proteomics Standards Initiative (HUPO PSI) facilitates the generation by the proteomics community of guidelines that specify the appropriate level of detail to provide when describing the various components of a proteomics experiment. These guidelines are codified as the MIAPE (Minimum Information About a Proteomics Experiment) specification, the first modules of which are now finalized. This primer describes the structure and scope of MIAPE, places it in context amongst reporting specifications for other domains, briefly discusses related informatics resources and closes by considering the ramifications for the proteomics community.", "publicationTitle": "Proteomics", "publisher": "", "place": "", "date": "2006", "volume": "6", "issue": "S2", "section": "", "partNumber": "", "partTitle": "", "pages": "39-44", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "", "DOI": "10.1002/pmic.200600549", "citationKey": "", "url": "http://dx.doi.org/10.1002/pmic.200600549", "accessDate": "2009-11-11T16:58:16Z", "PMID": "", "PMCID": "", "ISSN": "", "archive": "", "archiveLocation": "", "shortTitle": "Minimum Reporting Requirements for Proteomics", "language": "", "libraryCatalog": "Wiley InterScience", "callNumber": "", "rights": "", "extra": "", "tags": [], "collections": [ "3EF9VTPK", "QN36N5W7" ], "relations": {}, "dateAdded": "2011-12-05T09:52:32Z", "dateModified": "2011-12-05T09:52:32Z" } }, { "key": "N7D633QX", "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/N7D633QX", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/xavier.robin/items/N7D633QX", "type": "text/html" } }, "meta": { "createdByUser": { "id": 12953, "username": "Calimo", "name": "Xavier Robin", "links": { "alternate": { "href": "https://www.zotero.org/calimo", "type": "text/html" } } }, "creatorSummary": "Taylor et al.", "parsedDate": "2007", "numChildren": 0 }, "data": { "key": "N7D633QX", "version": 1, "itemType": "journalArticle", "title": "The minimum information about a proteomics experiment (MIAPE)", "creators": [ { "creatorType": "author", "firstName": "Chris F", "lastName": "Taylor" }, { "creatorType": "author", "firstName": "Norman W", "lastName": "Paton" }, { "creatorType": "author", "firstName": "Kathryn S", "lastName": "Lilley" }, { "creatorType": "author", "firstName": "Pierre-Alain", "lastName": "Binz" }, { "creatorType": "author", "firstName": "Randall K", "lastName": "Julian" }, { "creatorType": "author", "firstName": "Andrew R", "lastName": "Jones" }, { "creatorType": "author", "firstName": "Weimin", "lastName": "Zhu" }, { "creatorType": "author", "firstName": "Rolf", "lastName": "Apweiler" }, { "creatorType": "author", "firstName": "Ruedi", "lastName": "Aebersold" }, { "creatorType": "author", "firstName": "Eric W", "lastName": "Deutsch" }, { "creatorType": "author", "firstName": "Michael J", "lastName": "Dunn" }, { "creatorType": "author", "firstName": "Albert J R", "lastName": "Heck" }, { "creatorType": "author", "firstName": "Alexander", "lastName": "Leitner" }, { "creatorType": "author", "firstName": "Marcus", "lastName": "Macht" }, { "creatorType": "author", "firstName": "Matthias", "lastName": "Mann" }, { "creatorType": "author", "firstName": "Lennart", "lastName": "Martens" }, { "creatorType": "author", "firstName": "Thomas A", "lastName": "Neubert" }, { "creatorType": "author", "firstName": "Scott D", "lastName": "Patterson" }, { "creatorType": "author", "firstName": "Peipei", "lastName": "Ping" }, { "creatorType": "author", "firstName": "Sean L", "lastName": "Seymour" }, { "creatorType": "author", "firstName": "Puneet", "lastName": "Souda" }, { "creatorType": "author", "firstName": "Akira", "lastName": "Tsugita" }, { "creatorType": "author", "firstName": "Joel", "lastName": "Vandekerckhove" }, { "creatorType": "author", "firstName": "Thomas M", "lastName": "Vondriska" }, { "creatorType": "author", "firstName": "Julian P", "lastName": "Whitelegge" }, { "creatorType": "author", "firstName": "Marc R", "lastName": "Wilkins" }, { "creatorType": "author", "firstName": "Ioannnis", "lastName": "Xenarios" }, { "creatorType": "author", "firstName": "John R", "lastName": "Yates" }, { "creatorType": "author", "firstName": "Henning", "lastName": "Hermjakob" } ], "abstractNote": "", "publicationTitle": "Nature Biotechnology", "publisher": "", "place": "", "date": "2007", "volume": "25", "issue": "8", "section": "", "partNumber": "", "partTitle": "", "pages": "887-893", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "Nat Biotech", "DOI": "10.1038/nbt1329", "citationKey": "", "url": "http://dx.doi.org/10.1038/nbt1329", "accessDate": "2009-11-11T16:51:18Z", "PMID": "", "PMCID": "", "ISSN": "1087-0156", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "Nature", "callNumber": "", "rights": "", "extra": "", "tags": [], "collections": [ "3EF9VTPK" ], "relations": {}, "dateAdded": "2011-12-05T09:52:32Z", "dateModified": "2011-12-05T09:52:32Z" } }, { "key": "WHPJTG23", "version": 1, "library": { "type": "group", "id": 62016, "name": "xavier.robin", "links": { "alternate": { "href": 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"lastName": "Baker" }, { "creatorType": "author", "firstName": "Matthias", "lastName": "Berth" }, { "creatorType": "author", "firstName": "Pierre-Alain", "lastName": "Binz" }, { "creatorType": "author", "firstName": "Andy", "lastName": "Borthwick" }, { "creatorType": "author", "firstName": "Phil", "lastName": "Cash" }, { "creatorType": "author", "firstName": "Billy W", "lastName": "Day" }, { "creatorType": "author", "firstName": "David B", "lastName": "Friedman" }, { "creatorType": "author", "firstName": "Donita", "lastName": "Garland" }, { "creatorType": "author", "firstName": "Howard B", "lastName": "Gutstein" }, { "creatorType": "author", "firstName": "Christine", "lastName": "Hoogland" }, { "creatorType": "author", "firstName": "Neil A", "lastName": "Jones" }, { "creatorType": "author", "firstName": "Alamgir", "lastName": "Khan" }, { "creatorType": "author", "firstName": "Joachim", "lastName": "Klose" }, { "creatorType": "author", "firstName": "Angus I", "lastName": "Lamond" }, { "creatorType": "author", "firstName": "Peter F", "lastName": "Lemkin" }, { "creatorType": "author", "firstName": "Kathryn S", "lastName": "Lilley" }, { "creatorType": "author", "firstName": "Jonathan", "lastName": "Minden" }, { "creatorType": "author", "firstName": "Nicholas J", "lastName": "Morris" }, { "creatorType": "author", "firstName": "Norman W", "lastName": "Paton" }, { "creatorType": "author", "firstName": "Michael R", "lastName": "Pisano" }, { "creatorType": "author", "firstName": "John E", "lastName": "Prime" }, { "creatorType": "author", "firstName": "Thierry", "lastName": "Rabilloud" }, { "creatorType": "author", "firstName": "David A", "lastName": "Stead" }, { "creatorType": "author", "firstName": "Chris F", "lastName": "Taylor" }, { "creatorType": "author", "firstName": "Hans", "lastName": "Voshol" }, { "creatorType": "author", "firstName": "Anil", "lastName": "Wipat" }, { "creatorType": "author", "firstName": "Andrew R", "lastName": "Jones" } ], "abstractNote": "", "publicationTitle": "Nature Biotechnology", "publisher": "", "place": "", "date": "2008", "volume": "26", "issue": "8", "section": "", "partNumber": "", "partTitle": "", "pages": "863-864", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "Nat Biotech", "DOI": "10.1038/nbt0808-863", "citationKey": "", "url": "http://dx.doi.org/10.1038/nbt0808-863", "accessDate": "2009-11-11T16:57:11Z", "PMID": "", "PMCID": "", "ISSN": "1087-0156", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "Nature", "callNumber": "", "rights": "", "extra": "", "tags": [], "collections": [ "3EF9VTPK" ], "relations": {}, "dateAdded": "2011-12-05T09:52:32Z", "dateModified": "2011-12-05T09:52:32Z" } }, { "key": "8AGFENRI", "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/8AGFENRI", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/xavier.robin/items/8AGFENRI", "type": "text/html" } }, "meta": { "createdByUser": { "id": 12953, "username": "Calimo", "name": "Xavier Robin", "links": { "alternate": { "href": "https://www.zotero.org/calimo", "type": "text/html" } } }, "creatorSummary": "Brazma et al.", "parsedDate": "2001-12", "numChildren": 0 }, "data": { "key": "8AGFENRI", "version": 1, "itemType": "journalArticle", "title": "Minimum information about a microarray experiment (MIAME)—toward standards for microarray data", "creators": [ { "creatorType": "author", "firstName": "Alvis", "lastName": "Brazma" }, { "creatorType": "author", "firstName": "Pascal", "lastName": "Hingamp" }, { "creatorType": "author", "firstName": "John", "lastName": "Quackenbush" }, { "creatorType": "author", "firstName": "Gavin", "lastName": "Sherlock" }, { "creatorType": "author", "firstName": "Paul", "lastName": "Spellman" }, { "creatorType": "author", "firstName": "Chris", "lastName": "Stoeckert" }, { "creatorType": "author", "firstName": "John", "lastName": "Aach" }, { "creatorType": "author", "firstName": "Wilhelm", "lastName": "Ansorge" }, { "creatorType": "author", "firstName": "Catherine A.", "lastName": "Ball" }, { "creatorType": "author", "firstName": "Helen C.", "lastName": "Causton" }, { "creatorType": "author", "firstName": "Terry", "lastName": "Gaasterland" }, { "creatorType": "author", "firstName": "Patrick", "lastName": "Glenisson" }, { "creatorType": "author", "firstName": "Frank C.P.", "lastName": "Holstege" }, { "creatorType": "author", "firstName": "Irene F.", "lastName": "Kim" }, { "creatorType": "author", "firstName": "Victor", "lastName": "Markowitz" }, { "creatorType": "author", "firstName": "John C.", "lastName": "Matese" }, { "creatorType": "author", "firstName": "Helen", "lastName": "Parkinson" }, { "creatorType": "author", "firstName": "Alan", "lastName": "Robinson" }, { "creatorType": "author", "firstName": "Ugis", "lastName": "Sarkans" }, { "creatorType": "author", "firstName": "Steffen", "lastName": "Schulze-Kremer" }, { "creatorType": "author", "firstName": "Jason", "lastName": "Stewart" }, { "creatorType": "author", "firstName": "Ronald", "lastName": "Taylor" }, { "creatorType": "author", "firstName": "Jaak", "lastName": "Vilo" }, { "creatorType": "author", "firstName": "Martin", "lastName": "Vingron" } ], "abstractNote": "", "publicationTitle": "Nat Genet", "publisher": "", "place": "", "date": "December 2001", "volume": "29", "issue": "4", "section": "", "partNumber": "", "partTitle": "", "pages": "365-371", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "Nat Genet", "DOI": "10.1038/ng1201-365", "citationKey": "", "url": "http://dx.doi.org/10.1038/ng1201-365", "accessDate": "2009-04-23T13:58:59Z", "PMID": "", "PMCID": "", "ISSN": "1061-4036", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "Nature", "callNumber": "", "rights": "", "extra": "", "tags": [], "collections": [ "3EF9VTPK" ], "relations": {}, "dateAdded": "2011-12-05T09:52:32Z", "dateModified": "2011-12-05T09:52:32Z" } }, { "key": "TH2ZDAPW", "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/TH2ZDAPW", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/xavier.robin/items/TH2ZDAPW", "type": "text/html" } }, "meta": { "createdByUser": { "id": 12953, "username": "Calimo", "name": "Xavier Robin", "links": { "alternate": { "href": "https://www.zotero.org/calimo", "type": "text/html" } } }, "creatorSummary": "Wilkins et al.", "parsedDate": "2006", "numChildren": 0 }, "data": { "key": "TH2ZDAPW", "version": 1, "itemType": "journalArticle", "title": "Guidelines for the next 10 years of proteomics", "creators": [ { "creatorType": "author", "firstName": "Marc R.", "lastName": "Wilkins" }, { "creatorType": "author", "firstName": "Ron D.", "lastName": "Appel" }, { "creatorType": "author", "firstName": "Jennifer E. Van", "lastName": "Eyk" }, { "creatorType": "author", "firstName": "Maxey C. M.", "lastName": "Chung" }, { "creatorType": "author", "firstName": "Angelika", "lastName": "Görg" }, { "creatorType": "author", "firstName": "Michael", "lastName": "Hecker" }, { "creatorType": "author", "firstName": "Lukas A.", "lastName": "Huber" }, { "creatorType": "author", "firstName": "Hanno", "lastName": "Langen" }, { "creatorType": "author", "firstName": "Andrew J.", "lastName": "Link" }, { "creatorType": "author", "firstName": "Young-Ki", "lastName": "Paik" }, { "creatorType": "author", "firstName": "Scott D.", "lastName": "Patterson" }, { "creatorType": "author", "firstName": "Stephen R.", "lastName": "Pennington" }, { "creatorType": "author", "firstName": "Thierry", "lastName": "Rabilloud" }, { "creatorType": "author", "firstName": "Richard J.", "lastName": "Simpson" }, { "creatorType": "author", "firstName": "Walter", "lastName": "Weiss" }, { "creatorType": "author", "firstName": "Michael J.", "lastName": "Dunn" } ], "abstractNote": "In the last ten years, the field of proteomics has expanded at a rapid rate. A range of exciting new technology has been developed and enthusiastically applied to an enormous variety of biological questions. However, the degree of stringency required in proteomic data generation and analysis appears to have been underestimated. As a result, there are likely to be numerous published findings that are of questionable quality, requiring further confirmation and/or validation. This manuscript outlines a number of key issues in proteomic research, including those associated with experimental design, differential display and biomarker discovery, protein identification and analytical incompleteness. In an effort to set a standard that reflects current thinking on the necessary and desirable characteristics of publishable manuscripts in the field, a minimal set of guidelines for proteomics research is then described. These guidelines will serve as a set of criteria which editors of PROTEOMICS will use for assessment of future submissions to the Journal.", "publicationTitle": "Proteomics", "publisher": "", "place": "", "date": "2006", "volume": "6", "issue": "1", "section": "", "partNumber": "", "partTitle": "", "pages": "4-8", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "", "DOI": "10.1002/pmic.200500856", "citationKey": "", "url": "http://dx.doi.org/10.1002/pmic.200500856", "accessDate": "2009-11-11T16:52:25Z", "PMID": "", "PMCID": "", "ISSN": "", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "Wiley InterScience", "callNumber": "", "rights": "", "extra": "", "tags": [], "collections": [ "3EF9VTPK" ], "relations": {}, "dateAdded": "2011-12-05T09:52:32Z", "dateModified": "2011-12-05T09:52:32Z" } }, { "key": "NR5SXQ8C", "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/NR5SXQ8C", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/xavier.robin/items/NR5SXQ8C", "type": "text/html" } }, "meta": { "createdByUser": { "id": 12953, "username": "Calimo", "name": "Xavier Robin", "links": { "alternate": { "href": "https://www.zotero.org/calimo", "type": "text/html" } } }, "creatorSummary": "Taylor et al.", "parsedDate": "2006", "numChildren": 0 }, "data": { "key": "NR5SXQ8C", "version": 1, "itemType": "journalArticle", "title": "The work of the Human Proteome Organisation's Proteomics Standards Initiative (HUPO PSI)", "creators": [ { "creatorType": "author", "firstName": "Chris F", "lastName": "Taylor" }, { "creatorType": "author", "firstName": "Henning", "lastName": "Hermjakob" }, { "creatorType": "author", "firstName": "Randall K", "lastName": "Julian" }, { "creatorType": "author", "firstName": "John S", "lastName": "Garavelli" }, { "creatorType": "author", "firstName": "Ruedi", "lastName": "Aebersold" }, { "creatorType": "author", "firstName": "Rolf", "lastName": "Apweiler" } ], "abstractNote": "This article describes the origins, working practices and various development projects of the HUman Proteome Organisation's Proteomics Standards Initiative (HUPO PSI), specifically, our work on reporting requirements, data exchange formats and controlled vocabulary terms. We also offer our view of the two functional genomics projects in which the PSI plays a role (FuGE and FuGO), discussing their impact on our process and laying out the benefits we see as accruing, both to the PSI and to biomedical science as a whole as a result of their widespread acceptance.", "publicationTitle": "OMICS", "publisher": "", "place": "", "date": "2006", "volume": "10", "issue": "2", "section": "", "partNumber": "", "partTitle": "", "pages": "145-151", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "OMICS", "DOI": "10.1089/omi.2006.10.145", "citationKey": "", "url": "http://www.ncbi.nlm.nih.gov/pubmed/16901219", "accessDate": "2009-11-11T16:52:47Z", "PMID": "", "PMCID": "", "ISSN": "1536-2310", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "NCBI PubMed", "callNumber": "", "rights": "", "extra": "PMID: 16901219", "tags": [], "collections": [ "3EF9VTPK" ], "relations": {}, "dateAdded": "2011-12-05T09:52:32Z", "dateModified": "2011-12-05T09:52:32Z" } }, { "key": "67IEHM7G", "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/67IEHM7G", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/xavier.robin/items/67IEHM7G", "type": "text/html" } }, "meta": { "createdByUser": { "id": 12953, "username": "Calimo", "name": "Xavier Robin", "links": { "alternate": { "href": "https://www.zotero.org/calimo", "type": "text/html" } } }, "creatorSummary": "Prince et al.", "parsedDate": "2004-04", "numChildren": 0 }, "data": { "key": "67IEHM7G", "version": 1, "itemType": "journalArticle", "title": "The need for a public proteomics repository", "creators": [ { "creatorType": "author", "firstName": "John T", "lastName": "Prince" }, { "creatorType": "author", "firstName": "Mark W", "lastName": "Carlson" }, { "creatorType": "author", "firstName": "Rong", "lastName": "Wang" }, { "creatorType": "author", "firstName": "Peng", "lastName": "Lu" }, { "creatorType": "author", "firstName": "Edward M", "lastName": "Marcotte" } ], "abstractNote": "", "publicationTitle": "Nature Biotechnology", "publisher": "", "place": "", "date": "April 2004", "volume": "22", "issue": "4", "section": "", "partNumber": "", "partTitle": "", "pages": "471-472", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "Nat Biotech", "DOI": "10.1038/nbt0404-471", "citationKey": "", "url": "http://dx.doi.org/10.1038/nbt0404-471", "accessDate": "2009-11-11T16:51:43Z", "PMID": "", "PMCID": "", "ISSN": "1087-0156", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "Nature", "callNumber": "", "rights": "", "extra": "", "tags": [], "collections": [ "3EF9VTPK" ], "relations": {}, "dateAdded": "2011-12-05T09:52:32Z", "dateModified": "2011-12-05T09:52:32Z" } }, { "key": "5XGT42K6", "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/5XGT42K6", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/xavier.robin/items/5XGT42K6", "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": "2004", "numChildren": 0 }, "data": { "key": "5XGT42K6", "version": 1, "itemType": "journalArticle", "title": "SWISS-2DPAGE, ten years later", "creators": [ { "creatorType": "author", "firstName": "Christine", "lastName": "Hoogland" }, { "creatorType": "author", "firstName": "Khaled", "lastName": "Mostaguir" }, { "creatorType": "author", "firstName": "Jean-Charles", "lastName": "Sanchez" }, { "creatorType": "author", "firstName": "Denis F.", "lastName": "Hochstrasser" }, { "creatorType": "author", "firstName": "Ron D.", "lastName": "Appel" } ], "abstractNote": "The SWISS-2DPAGE database was established in 1993 and is maintained collaboratively by the Swiss Institute of Bioinformatics (SIB) and the Biomedical Proteomics Research Group (BPRG) of the Geneva University Hospital. During these years, SWISS-2DPAGE underwent constant modification and improvement. Current content includes about 4000 identified spots corresponding to 1200 different protein entries in 36 reference maps from human, mouse, Arabidopsis thaliana, Dictyostelium discoideum, Escherichia coli, Saccharomyces cerevisiae and Staphylococcus aureus origins. With a high level of annotation and integration with other relevant databases, SWISS-2DPAGE is a reference source in the proteomics world. 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