Informatics Platform for Global Proteomic Profiling and Biomarker Discovery Using Liquid Chromatography-Tandem Mass Spectrometry
We have developed an integrated suite of algorithms, statistical methods, and computer applications to support large-scale LC-MS-based gel-free shotgun profiling of complex protein mixtures using basic experimental procedures. The programs automatically detect and quantify large numbers of peptide p...
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| Veröffentlicht in: | Molecular & cellular proteomics 2004-10, Vol.3 (10), p.984-997 |
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| container_title | Molecular & cellular proteomics |
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| creator | Radulovic, Dragan Jelveh, Salomeh Ryu, Soyoung Hamilton, T Guy Foss, Eric Mao, Yongyi Emili, Andrew |
| description | We have developed an integrated suite of algorithms, statistical methods, and computer applications to support large-scale
LC-MS-based gel-free shotgun profiling of complex protein mixtures using basic experimental procedures. The programs automatically
detect and quantify large numbers of peptide peaks in feature-rich ion mass chromatograms, compensate for spurious fluctuations
in peptide signal intensities and retention times, and reliably match related peaks across many different datasets. Application
of this toolkit markedly facilitates pattern recognition and biomarker discovery in global comparative proteomic studies,
simplifying mechanistic investigation of physiological responses and the detection of proteomic signatures of disease. |
| doi_str_mv | 10.1074/mcp.M400061-MCP200 |
| format | Article |
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LC-MS-based gel-free shotgun profiling of complex protein mixtures using basic experimental procedures. The programs automatically
detect and quantify large numbers of peptide peaks in feature-rich ion mass chromatograms, compensate for spurious fluctuations
in peptide signal intensities and retention times, and reliably match related peaks across many different datasets. Application
of this toolkit markedly facilitates pattern recognition and biomarker discovery in global comparative proteomic studies,
simplifying mechanistic investigation of physiological responses and the detection of proteomic signatures of disease.</description><identifier>ISSN: 1535-9476</identifier><identifier>EISSN: 1535-9484</identifier><identifier>DOI: 10.1074/mcp.M400061-MCP200</identifier><identifier>PMID: 15269249</identifier><language>eng</language><publisher>United States: American Society for Biochemistry and Molecular Biology</publisher><subject>Algorithms ; Animals ; Biomarkers - analysis ; Cell Extracts ; Chromatography, High Pressure Liquid ; Chromatography, Liquid - methods ; Computational Biology ; Humans ; Liver - chemistry ; Mass Spectrometry - methods ; Mice ; Mice, Inbred C57BL ; Myocardium - chemistry ; Protein Array Analysis ; Proteins - analysis ; Proteomics - methods ; Serum - chemistry ; Troponin - analysis</subject><ispartof>Molecular & cellular proteomics, 2004-10, Vol.3 (10), p.984-997</ispartof><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c436t-976726e09963b4ddc432f2c8588baefb4caae56249976149ccfedf7382a65d233</citedby><cites>FETCH-LOGICAL-c436t-976726e09963b4ddc432f2c8588baefb4caae56249976149ccfedf7382a65d233</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><link.rule.ids>314,780,784,27922,27923</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/15269249$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Radulovic, Dragan</creatorcontrib><creatorcontrib>Jelveh, Salomeh</creatorcontrib><creatorcontrib>Ryu, Soyoung</creatorcontrib><creatorcontrib>Hamilton, T Guy</creatorcontrib><creatorcontrib>Foss, Eric</creatorcontrib><creatorcontrib>Mao, Yongyi</creatorcontrib><creatorcontrib>Emili, Andrew</creatorcontrib><title>Informatics Platform for Global Proteomic Profiling and Biomarker Discovery Using Liquid Chromatography-Tandem Mass Spectrometry</title><title>Molecular & cellular proteomics</title><addtitle>Mol Cell Proteomics</addtitle><description>We have developed an integrated suite of algorithms, statistical methods, and computer applications to support large-scale
LC-MS-based gel-free shotgun profiling of complex protein mixtures using basic experimental procedures. The programs automatically
detect and quantify large numbers of peptide peaks in feature-rich ion mass chromatograms, compensate for spurious fluctuations
in peptide signal intensities and retention times, and reliably match related peaks across many different datasets. Application
of this toolkit markedly facilitates pattern recognition and biomarker discovery in global comparative proteomic studies,
simplifying mechanistic investigation of physiological responses and the detection of proteomic signatures of disease.</description><subject>Algorithms</subject><subject>Animals</subject><subject>Biomarkers - analysis</subject><subject>Cell Extracts</subject><subject>Chromatography, High Pressure Liquid</subject><subject>Chromatography, Liquid - methods</subject><subject>Computational Biology</subject><subject>Humans</subject><subject>Liver - chemistry</subject><subject>Mass Spectrometry - methods</subject><subject>Mice</subject><subject>Mice, Inbred C57BL</subject><subject>Myocardium - chemistry</subject><subject>Protein Array Analysis</subject><subject>Proteins - analysis</subject><subject>Proteomics - methods</subject><subject>Serum - chemistry</subject><subject>Troponin - analysis</subject><issn>1535-9476</issn><issn>1535-9484</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2004</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNpFkM1u2zAQhImgQeymfYEeCp56k8s_UeKxdZrUgI0YSHImKGplsZVMhZQb-JZHDwUbzYXc5X4z4A5CXyhZUFKI770dFhtBCJE02yy3jJALNKc5zzMlSvHhf13IGfoY4x9CGKFFfoVmNGdSMaHm6HW1b3zozehsxNvOjFOH04HvOl-ZDm-DH8H3zk5V4zq332Gzr_FP53sT_kLANy5a_w_CET_Fabp2zwdX42UbEjH6XTBDe8wekwh6vDEx4ocB7JimMIbjJ3TZmC7C5_N9jZ5ufz0uf2fr-7vV8sc6s4LLMVOFLJgEopTklajr9MoaZsu8LCsDTSWsMZDLtFMiqVDWNlA3BS-ZkXnNOL9G306-Q_DPB4ij7tO_oevMHvwhailVzllJE8hOoA0-xgCNHoJLqx41JXrKXafc9Tl3fco9ib6e3Q9VD_W75Bx0AvAJaN2ufXEBdOW8baHXfPJVpeBv3-iNCA</recordid><startdate>20041001</startdate><enddate>20041001</enddate><creator>Radulovic, Dragan</creator><creator>Jelveh, Salomeh</creator><creator>Ryu, Soyoung</creator><creator>Hamilton, T Guy</creator><creator>Foss, Eric</creator><creator>Mao, Yongyi</creator><creator>Emili, Andrew</creator><general>American Society for Biochemistry and Molecular Biology</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7X8</scope></search><sort><creationdate>20041001</creationdate><title>Informatics Platform for Global Proteomic Profiling and Biomarker Discovery Using Liquid Chromatography-Tandem Mass Spectrometry</title><author>Radulovic, Dragan ; Jelveh, Salomeh ; Ryu, Soyoung ; Hamilton, T Guy ; Foss, Eric ; Mao, Yongyi ; Emili, Andrew</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c436t-976726e09963b4ddc432f2c8588baefb4caae56249976149ccfedf7382a65d233</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2004</creationdate><topic>Algorithms</topic><topic>Animals</topic><topic>Biomarkers - analysis</topic><topic>Cell Extracts</topic><topic>Chromatography, High Pressure Liquid</topic><topic>Chromatography, Liquid - methods</topic><topic>Computational Biology</topic><topic>Humans</topic><topic>Liver - chemistry</topic><topic>Mass Spectrometry - methods</topic><topic>Mice</topic><topic>Mice, Inbred C57BL</topic><topic>Myocardium - chemistry</topic><topic>Protein Array Analysis</topic><topic>Proteins - analysis</topic><topic>Proteomics - methods</topic><topic>Serum - chemistry</topic><topic>Troponin - analysis</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Radulovic, Dragan</creatorcontrib><creatorcontrib>Jelveh, Salomeh</creatorcontrib><creatorcontrib>Ryu, Soyoung</creatorcontrib><creatorcontrib>Hamilton, T Guy</creatorcontrib><creatorcontrib>Foss, Eric</creatorcontrib><creatorcontrib>Mao, Yongyi</creatorcontrib><creatorcontrib>Emili, Andrew</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>MEDLINE - Academic</collection><jtitle>Molecular & cellular proteomics</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Radulovic, Dragan</au><au>Jelveh, Salomeh</au><au>Ryu, Soyoung</au><au>Hamilton, T Guy</au><au>Foss, Eric</au><au>Mao, Yongyi</au><au>Emili, Andrew</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Informatics Platform for Global Proteomic Profiling and Biomarker Discovery Using Liquid Chromatography-Tandem Mass Spectrometry</atitle><jtitle>Molecular & cellular proteomics</jtitle><addtitle>Mol Cell Proteomics</addtitle><date>2004-10-01</date><risdate>2004</risdate><volume>3</volume><issue>10</issue><spage>984</spage><epage>997</epage><pages>984-997</pages><issn>1535-9476</issn><eissn>1535-9484</eissn><abstract>We have developed an integrated suite of algorithms, statistical methods, and computer applications to support large-scale
LC-MS-based gel-free shotgun profiling of complex protein mixtures using basic experimental procedures. The programs automatically
detect and quantify large numbers of peptide peaks in feature-rich ion mass chromatograms, compensate for spurious fluctuations
in peptide signal intensities and retention times, and reliably match related peaks across many different datasets. Application
of this toolkit markedly facilitates pattern recognition and biomarker discovery in global comparative proteomic studies,
simplifying mechanistic investigation of physiological responses and the detection of proteomic signatures of disease.</abstract><cop>United States</cop><pub>American Society for Biochemistry and Molecular Biology</pub><pmid>15269249</pmid><doi>10.1074/mcp.M400061-MCP200</doi><tpages>14</tpages><oa>free_for_read</oa></addata></record> |
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| source | MEDLINE; EZB-FREE-00999 freely available EZB journals; Alma/SFX Local Collection; Free Full-Text Journals in Chemistry |
| subjects | Algorithms Animals Biomarkers - analysis Cell Extracts Chromatography, High Pressure Liquid Chromatography, Liquid - methods Computational Biology Humans Liver - chemistry Mass Spectrometry - methods Mice Mice, Inbred C57BL Myocardium - chemistry Protein Array Analysis Proteins - analysis Proteomics - methods Serum - chemistry Troponin - analysis |
| title | Informatics Platform for Global Proteomic Profiling and Biomarker Discovery Using Liquid Chromatography-Tandem Mass Spectrometry |
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