Enabling proteomics discovery through visual analysis
This article presents the motivation for developing visual analysis tools for proteomic data and demonstrates their application to proteomics research with a visualization tool named Peptide Permutation and Protein Prediction, or PQuad, a functioning visual analytic tool for the study of systems bio...
Gespeichert in:
| Veröffentlicht in: | IEEE Engineering in Medicine and Biology Magazine, 24(3):50-57 24(3):50-57, 2005-05, Vol.24 (3), p.50-57 |
|---|---|
| Hauptverfasser: | , , , , |
| Format: | Artikel |
| Sprache: | eng |
| Schlagworte: | |
| Online-Zugang: | Volltext bestellen |
| Tags: |
Tag hinzufügen
Keine Tags, Fügen Sie den ersten Tag hinzu!
|
| container_end_page | 57 |
|---|---|
| container_issue | 3 |
| container_start_page | 50 |
| container_title | IEEE Engineering in Medicine and Biology Magazine, 24(3):50-57 |
| container_volume | 24 |
| creator | Havre, S.L. Singhal, M. Payne, D.A. Weir Lipton, M.S. Webb-Robertson, B.-J.M. |
| description | This article presents the motivation for developing visual analysis tools for proteomic data and demonstrates their application to proteomics research with a visualization tool named Peptide Permutation and Protein Prediction, or PQuad, a functioning visual analytic tool for the study of systems biology, is in operation at the Pacific Northwest National Laboratory (PNNL). PQuad supports the exploration of proteins identified by proteomic techniques in the context of supplemental biological information. In particular, PQuad supports differential proteomics by simplifying the comparison of peptide sets from different experimental conditions as well as different proteins identification or confidence scoring techniques. Finally, PQuad supports data validation and quality control by providing a variety of resolutions for huge amounts of data to reveal errors undetected by other methods. |
| doi_str_mv | 10.1109/MEMB.2005.1436460 |
| format | Article |
| fullrecord | <record><control><sourceid>proquest_RIE</sourceid><recordid>TN_cdi_ieee_primary_1436460</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><ieee_id>1436460</ieee_id><sourcerecordid>29375046</sourcerecordid><originalsourceid>FETCH-LOGICAL-c413t-234fd4fc21004569214b19e57dd4d8684ab4946e2256aaee77b518e81f47f043</originalsourceid><addsrcrecordid>eNqFkUtLxEAQhAdRdH38APESFLxlnU56XkeV9QGKF-_D7KTjjmQzmkmE_fdm3QXBi6c-9FdFdxVjp8CnANxcPc-eb6YF52IKWEqUfIdNwJQqR9Byl024Kk0uQIkDdpjSO-eAqMQ-OwBhFGiECROz1s2b0L5lH13sKS6DT1kVko9f1K2yftHF4W2RfYU0uCZzrWtWKaRjtle7JtHJdh6x17vZ6-1D_vRy_3h7_ZR7hLLPixLrCmtfAOcopCkA52BIqKrCSkuNbo4GJRWFkM4RKTUXoElDjarmWB6xi41tTH2wyYee_MLHtiXfWxAcpCrFSF1uqPGDz4FSb5fj_dQ0rqU4JFuMiQiO8n9QK0TU_F9wTFSrkpsRPP8DvsehG0NKVksDhYEfN9hAvospdVTbjy4sXbeywO26R7vu0a57tNseR83ZRhOI6Jffbr8Bd8iUlQ</addsrcrecordid><sourcetype>Open Access Repository</sourcetype><iscdi>true</iscdi><recordtype>article</recordtype><pqid>869129180</pqid></control><display><type>article</type><title>Enabling proteomics discovery through visual analysis</title><source>IEEE Electronic Library (IEL)</source><creator>Havre, S.L. ; Singhal, M. ; Payne, D.A. ; Weir Lipton, M.S. ; Webb-Robertson, B.-J.M.</creator><creatorcontrib>Havre, S.L. ; Singhal, M. ; Payne, D.A. ; Weir Lipton, M.S. ; Webb-Robertson, B.-J.M. ; Pacific Northwest National Lab. (PNNL), Richland, WA (United States)</creatorcontrib><description>This article presents the motivation for developing visual analysis tools for proteomic data and demonstrates their application to proteomics research with a visualization tool named Peptide Permutation and Protein Prediction, or PQuad, a functioning visual analytic tool for the study of systems biology, is in operation at the Pacific Northwest National Laboratory (PNNL). PQuad supports the exploration of proteins identified by proteomic techniques in the context of supplemental biological information. In particular, PQuad supports differential proteomics by simplifying the comparison of peptide sets from different experimental conditions as well as different proteins identification or confidence scoring techniques. Finally, PQuad supports data validation and quality control by providing a variety of resolutions for huge amounts of data to reveal errors undetected by other methods.</description><identifier>ISSN: 0739-5175</identifier><identifier>EISSN: 1937-4186</identifier><identifier>DOI: 10.1109/MEMB.2005.1436460</identifier><identifier>PMID: 15971841</identifier><identifier>CODEN: IEMBDE</identifier><language>eng</language><publisher>New York: IEEE</publisher><subject>Amino acids ; BASIC BIOLOGICAL SCIENCES ; Bioinformatics ; BIOLOGY ; DISEASES ; EXPLORATION ; FORECASTING ; Genomics ; Mass spectroscopy ; MINING ; Organisms ; PEPTIDES ; PROTEINS ; Proteomics ; Sequences ; visual analysis, mass spectrometry ; visualization</subject><ispartof>IEEE Engineering in Medicine and Biology Magazine, 24(3):50-57, 2005-05, Vol.24 (3), p.50-57</ispartof><rights>Copyright The Institute of Electrical and Electronics Engineers, Inc. (IEEE) 2005</rights><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c413t-234fd4fc21004569214b19e57dd4d8684ab4946e2256aaee77b518e81f47f043</citedby><cites>FETCH-LOGICAL-c413t-234fd4fc21004569214b19e57dd4d8684ab4946e2256aaee77b518e81f47f043</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktohtml>$$Uhttps://ieeexplore.ieee.org/document/1436460$$EHTML$$P50$$Gieee$$H</linktohtml><link.rule.ids>314,777,781,793,882,27905,27906,54739</link.rule.ids><linktorsrc>$$Uhttps://ieeexplore.ieee.org/document/1436460$$EView_record_in_IEEE$$FView_record_in_$$GIEEE</linktorsrc><backlink>$$Uhttps://www.osti.gov/biblio/15016735$$D View this record in Osti.gov$$Hfree_for_read</backlink></links><search><creatorcontrib>Havre, S.L.</creatorcontrib><creatorcontrib>Singhal, M.</creatorcontrib><creatorcontrib>Payne, D.A.</creatorcontrib><creatorcontrib>Weir Lipton, M.S.</creatorcontrib><creatorcontrib>Webb-Robertson, B.-J.M.</creatorcontrib><creatorcontrib>Pacific Northwest National Lab. (PNNL), Richland, WA (United States)</creatorcontrib><title>Enabling proteomics discovery through visual analysis</title><title>IEEE Engineering in Medicine and Biology Magazine, 24(3):50-57</title><addtitle>EMB-M</addtitle><description>This article presents the motivation for developing visual analysis tools for proteomic data and demonstrates their application to proteomics research with a visualization tool named Peptide Permutation and Protein Prediction, or PQuad, a functioning visual analytic tool for the study of systems biology, is in operation at the Pacific Northwest National Laboratory (PNNL). PQuad supports the exploration of proteins identified by proteomic techniques in the context of supplemental biological information. In particular, PQuad supports differential proteomics by simplifying the comparison of peptide sets from different experimental conditions as well as different proteins identification or confidence scoring techniques. Finally, PQuad supports data validation and quality control by providing a variety of resolutions for huge amounts of data to reveal errors undetected by other methods.</description><subject>Amino acids</subject><subject>BASIC BIOLOGICAL SCIENCES</subject><subject>Bioinformatics</subject><subject>BIOLOGY</subject><subject>DISEASES</subject><subject>EXPLORATION</subject><subject>FORECASTING</subject><subject>Genomics</subject><subject>Mass spectroscopy</subject><subject>MINING</subject><subject>Organisms</subject><subject>PEPTIDES</subject><subject>PROTEINS</subject><subject>Proteomics</subject><subject>Sequences</subject><subject>visual analysis, mass spectrometry</subject><subject>visualization</subject><issn>0739-5175</issn><issn>1937-4186</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2005</creationdate><recordtype>article</recordtype><sourceid>RIE</sourceid><recordid>eNqFkUtLxEAQhAdRdH38APESFLxlnU56XkeV9QGKF-_D7KTjjmQzmkmE_fdm3QXBi6c-9FdFdxVjp8CnANxcPc-eb6YF52IKWEqUfIdNwJQqR9Byl024Kk0uQIkDdpjSO-eAqMQ-OwBhFGiECROz1s2b0L5lH13sKS6DT1kVko9f1K2yftHF4W2RfYU0uCZzrWtWKaRjtle7JtHJdh6x17vZ6-1D_vRy_3h7_ZR7hLLPixLrCmtfAOcopCkA52BIqKrCSkuNbo4GJRWFkM4RKTUXoElDjarmWB6xi41tTH2wyYee_MLHtiXfWxAcpCrFSF1uqPGDz4FSb5fj_dQ0rqU4JFuMiQiO8n9QK0TU_F9wTFSrkpsRPP8DvsehG0NKVksDhYEfN9hAvospdVTbjy4sXbeywO26R7vu0a57tNseR83ZRhOI6Jffbr8Bd8iUlQ</recordid><startdate>20050501</startdate><enddate>20050501</enddate><creator>Havre, S.L.</creator><creator>Singhal, M.</creator><creator>Payne, D.A.</creator><creator>Weir Lipton, M.S.</creator><creator>Webb-Robertson, B.-J.M.</creator><general>IEEE</general><general>The Institute of Electrical and Electronics Engineers, Inc. (IEEE)</general><scope>97E</scope><scope>RIA</scope><scope>RIE</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7QO</scope><scope>8FD</scope><scope>FR3</scope><scope>P64</scope><scope>7U5</scope><scope>L7M</scope><scope>7TB</scope><scope>OTOTI</scope></search><sort><creationdate>20050501</creationdate><title>Enabling proteomics discovery through visual analysis</title><author>Havre, S.L. ; Singhal, M. ; Payne, D.A. ; Weir Lipton, M.S. ; Webb-Robertson, B.-J.M.</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c413t-234fd4fc21004569214b19e57dd4d8684ab4946e2256aaee77b518e81f47f043</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2005</creationdate><topic>Amino acids</topic><topic>BASIC BIOLOGICAL SCIENCES</topic><topic>Bioinformatics</topic><topic>BIOLOGY</topic><topic>DISEASES</topic><topic>EXPLORATION</topic><topic>FORECASTING</topic><topic>Genomics</topic><topic>Mass spectroscopy</topic><topic>MINING</topic><topic>Organisms</topic><topic>PEPTIDES</topic><topic>PROTEINS</topic><topic>Proteomics</topic><topic>Sequences</topic><topic>visual analysis, mass spectrometry</topic><topic>visualization</topic><toplevel>online_resources</toplevel><creatorcontrib>Havre, S.L.</creatorcontrib><creatorcontrib>Singhal, M.</creatorcontrib><creatorcontrib>Payne, D.A.</creatorcontrib><creatorcontrib>Weir Lipton, M.S.</creatorcontrib><creatorcontrib>Webb-Robertson, B.-J.M.</creatorcontrib><creatorcontrib>Pacific Northwest National Lab. (PNNL), Richland, WA (United States)</creatorcontrib><collection>IEEE All-Society Periodicals Package (ASPP) 2005-present</collection><collection>IEEE All-Society Periodicals Package (ASPP) 1998-Present</collection><collection>IEEE Electronic Library (IEL)</collection><collection>CrossRef</collection><collection>Biotechnology Research Abstracts</collection><collection>Technology Research Database</collection><collection>Engineering Research Database</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Solid State and Superconductivity Abstracts</collection><collection>Advanced Technologies Database with Aerospace</collection><collection>Mechanical & Transportation Engineering Abstracts</collection><collection>OSTI.GOV</collection><jtitle>IEEE Engineering in Medicine and Biology Magazine, 24(3):50-57</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext_linktorsrc</fulltext></delivery><addata><au>Havre, S.L.</au><au>Singhal, M.</au><au>Payne, D.A.</au><au>Weir Lipton, M.S.</au><au>Webb-Robertson, B.-J.M.</au><aucorp>Pacific Northwest National Lab. (PNNL), Richland, WA (United States)</aucorp><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Enabling proteomics discovery through visual analysis</atitle><jtitle>IEEE Engineering in Medicine and Biology Magazine, 24(3):50-57</jtitle><stitle>EMB-M</stitle><date>2005-05-01</date><risdate>2005</risdate><volume>24</volume><issue>3</issue><spage>50</spage><epage>57</epage><pages>50-57</pages><issn>0739-5175</issn><eissn>1937-4186</eissn><coden>IEMBDE</coden><abstract>This article presents the motivation for developing visual analysis tools for proteomic data and demonstrates their application to proteomics research with a visualization tool named Peptide Permutation and Protein Prediction, or PQuad, a functioning visual analytic tool for the study of systems biology, is in operation at the Pacific Northwest National Laboratory (PNNL). PQuad supports the exploration of proteins identified by proteomic techniques in the context of supplemental biological information. In particular, PQuad supports differential proteomics by simplifying the comparison of peptide sets from different experimental conditions as well as different proteins identification or confidence scoring techniques. Finally, PQuad supports data validation and quality control by providing a variety of resolutions for huge amounts of data to reveal errors undetected by other methods.</abstract><cop>New York</cop><pub>IEEE</pub><pmid>15971841</pmid><doi>10.1109/MEMB.2005.1436460</doi><tpages>8</tpages></addata></record> |
| fulltext | fulltext_linktorsrc |
| identifier | ISSN: 0739-5175 |
| ispartof | IEEE Engineering in Medicine and Biology Magazine, 24(3):50-57, 2005-05, Vol.24 (3), p.50-57 |
| issn | 0739-5175 1937-4186 |
| language | eng |
| recordid | cdi_ieee_primary_1436460 |
| source | IEEE Electronic Library (IEL) |
| subjects | Amino acids BASIC BIOLOGICAL SCIENCES Bioinformatics BIOLOGY DISEASES EXPLORATION FORECASTING Genomics Mass spectroscopy MINING Organisms PEPTIDES PROTEINS Proteomics Sequences visual analysis, mass spectrometry visualization |
| title | Enabling proteomics discovery through visual analysis |
| url | https://sfx.bib-bvb.de/sfx_tum?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2025-01-18T18%3A50%3A56IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-proquest_RIE&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=Enabling%20proteomics%20discovery%20through%20visual%20analysis&rft.jtitle=IEEE%20Engineering%20in%20Medicine%20and%20Biology%20Magazine,%2024(3):50-57&rft.au=Havre,%20S.L.&rft.aucorp=Pacific%20Northwest%20National%20Lab.%20(PNNL),%20Richland,%20WA%20(United%20States)&rft.date=2005-05-01&rft.volume=24&rft.issue=3&rft.spage=50&rft.epage=57&rft.pages=50-57&rft.issn=0739-5175&rft.eissn=1937-4186&rft.coden=IEMBDE&rft_id=info:doi/10.1109/MEMB.2005.1436460&rft_dat=%3Cproquest_RIE%3E29375046%3C/proquest_RIE%3E%3Curl%3E%3C/url%3E&disable_directlink=true&sfx.directlink=off&sfx.report_link=0&rft_id=info:oai/&rft_pqid=869129180&rft_id=info:pmid/15971841&rft_ieee_id=1436460&rfr_iscdi=true |