Analysis of the Saccharomyces cerevisiae proteome with PeptideAtlas
We present the Saccharomyces cerevisiae PeptideAtlas composed from 47 diverse experiments and 4.9 million tandem mass spectra. The observed peptides align to 61% of Saccharomyces Genome Database (SGD) open reading frames (ORFs), 49% of the uncharacterized SGD ORFs, 54% of S. cerevisiae ORFs with a G...
Gespeichert in:
| Veröffentlicht in: | Genome Biology (Online Edition) 2006-11, Vol.7 (11), p.R106-R106, Article R106 |
|---|---|
| Hauptverfasser: | , , , , , , , , , , , , , |
| Format: | Artikel |
| Sprache: | eng |
| Schlagworte: | |
| Online-Zugang: | Volltext |
| Tags: |
Tag hinzufügen
Keine Tags, Fügen Sie den ersten Tag hinzu!
|
| container_end_page | R106 |
|---|---|
| container_issue | 11 |
| container_start_page | R106 |
| container_title | Genome Biology (Online Edition) |
| container_volume | 7 |
| creator | King, Nichole L Deutsch, Eric W Ranish, Jeffrey A Nesvizhskii, Alexey I Eddes, James S Mallick, Parag Eng, Jimmy Desiere, Frank Flory, Mark Martin, Daniel B Kim, Bong Lee, Hookeun Raught, Brian Aebersold, Ruedi |
| description | We present the Saccharomyces cerevisiae PeptideAtlas composed from 47 diverse experiments and 4.9 million tandem mass spectra. The observed peptides align to 61% of Saccharomyces Genome Database (SGD) open reading frames (ORFs), 49% of the uncharacterized SGD ORFs, 54% of S. cerevisiae ORFs with a Gene Ontology annotation of 'molecular function unknown', and 76% of ORFs with Gene names. We highlight the use of this resource for data mining, construction of high quality lists for targeted proteomics, validation of proteins, and software development. |
| doi_str_mv | 10.1186/gb-2006-7-11-r106 |
| format | Article |
| fullrecord | <record><control><sourceid>gale_pubme</sourceid><recordid>TN_cdi_pubmedcentral_primary_oai_pubmedcentral_nih_gov_1794584</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><galeid>A603113918</galeid><sourcerecordid>A603113918</sourcerecordid><originalsourceid>FETCH-LOGICAL-b565t-7a9305f02c40e5a718c81516b05fd6283ca632188d7aec67b2f60757e4a83d593</originalsourceid><addsrcrecordid>eNp1kk1r3DAQhkVoaL76A3IpPhV6cKKxrQ9fCsumSUMCDTSF3oQsj70qtrWVtGn330fLLk0WWnSQmHnfh9HLEHIO9AJA8su-yQtKeS5ygNwD5QfkGCpR5YLTH29evY_ISQg_KYW6KvhbcgQCKFAGx2Q-m_SwDjZkrsviArNv2piF9m5cGwyZQY9PNliN2dK7iG7E7LeNi-wBl9G2OIuDDmfksNNDwHe7-5R8v_78OP-S33-9uZ3P7vOGcRZzoeuSso4WpqLItABpJDDgTSq2vJCl0bwsQMpWaDRcNEXHqWACKy3LltXlKfm05S5XzYitwSl6Pailt6P2a-W0VfudyS5U754UiLpiskqAqy2gse4_gP2OcaPqG7UJWQkFoDYhJ8yH3Rze_VphiGq0weAw6AndKigui5pRSZPwYivs9YDKTp1LVJNOi6M1bsLOpvqM0xKgrEEmw8c9Q9JE_BN7vQpB3T3c7mthqzXeheCx-_sPoGqzHv-c_P3rBF8cu30onwG5TLc7</addsrcrecordid><sourcetype>Open Access Repository</sourcetype><iscdi>true</iscdi><recordtype>article</recordtype><pqid>68295080</pqid></control><display><type>article</type><title>Analysis of the Saccharomyces cerevisiae proteome with PeptideAtlas</title><source>MEDLINE</source><source>DOAJ Directory of Open Access Journals</source><source>Elektronische Zeitschriftenbibliothek - Frei zugängliche E-Journals</source><source>Springer Nature OA Free Journals</source><source>PubMed Central</source><source>SpringerLink Journals - AutoHoldings</source><creator>King, Nichole L ; Deutsch, Eric W ; Ranish, Jeffrey A ; Nesvizhskii, Alexey I ; Eddes, James S ; Mallick, Parag ; Eng, Jimmy ; Desiere, Frank ; Flory, Mark ; Martin, Daniel B ; Kim, Bong ; Lee, Hookeun ; Raught, Brian ; Aebersold, Ruedi</creator><creatorcontrib>King, Nichole L ; Deutsch, Eric W ; Ranish, Jeffrey A ; Nesvizhskii, Alexey I ; Eddes, James S ; Mallick, Parag ; Eng, Jimmy ; Desiere, Frank ; Flory, Mark ; Martin, Daniel B ; Kim, Bong ; Lee, Hookeun ; Raught, Brian ; Aebersold, Ruedi</creatorcontrib><description>We present the Saccharomyces cerevisiae PeptideAtlas composed from 47 diverse experiments and 4.9 million tandem mass spectra. The observed peptides align to 61% of Saccharomyces Genome Database (SGD) open reading frames (ORFs), 49% of the uncharacterized SGD ORFs, 54% of S. cerevisiae ORFs with a Gene Ontology annotation of 'molecular function unknown', and 76% of ORFs with Gene names. We highlight the use of this resource for data mining, construction of high quality lists for targeted proteomics, validation of proteins, and software development.</description><identifier>ISSN: 1474-760X</identifier><identifier>ISSN: 1465-6906</identifier><identifier>EISSN: 1474-760X</identifier><identifier>EISSN: 1465-6914</identifier><identifier>DOI: 10.1186/gb-2006-7-11-r106</identifier><identifier>PMID: 17101051</identifier><language>eng</language><publisher>England: BioMed Central Ltd</publisher><subject>Analysis ; Codon ; Data mining ; Databases, Protein ; Genes, Fungal ; Genomes ; Genomics ; Hydrophobic and Hydrophilic Interactions ; Mass Spectrometry ; Messenger RNA ; Method ; Molecular Weight ; Open Reading Frames - genetics ; Peptides ; Peptides - chemistry ; Peptides - metabolism ; Proteins ; Proteome - chemistry ; Proteome - genetics ; Proteome - metabolism ; Proteomics ; RNA ; Saccharomyces cerevisiae - chemistry ; Saccharomyces cerevisiae - genetics ; Saccharomyces cerevisiae - metabolism ; Saccharomyces cerevisiae Proteins - chemistry ; Saccharomyces cerevisiae Proteins - genetics ; Saccharomyces cerevisiae Proteins - metabolism ; Spectroscopy ; User-Computer Interface</subject><ispartof>Genome Biology (Online Edition), 2006-11, Vol.7 (11), p.R106-R106, Article R106</ispartof><rights>COPYRIGHT 2006 BioMed Central Ltd.</rights><rights>Copyright © 2006 King et al.; licensee BioMed Central Ltd. 2006 King et al.; licensee BioMed Central Ltd.</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-b565t-7a9305f02c40e5a718c81516b05fd6283ca632188d7aec67b2f60757e4a83d593</citedby><cites>FETCH-LOGICAL-b565t-7a9305f02c40e5a718c81516b05fd6283ca632188d7aec67b2f60757e4a83d593</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC1794584/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC1794584/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,727,780,784,864,885,27924,27925,53791,53793</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/17101051$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>King, Nichole L</creatorcontrib><creatorcontrib>Deutsch, Eric W</creatorcontrib><creatorcontrib>Ranish, Jeffrey A</creatorcontrib><creatorcontrib>Nesvizhskii, Alexey I</creatorcontrib><creatorcontrib>Eddes, James S</creatorcontrib><creatorcontrib>Mallick, Parag</creatorcontrib><creatorcontrib>Eng, Jimmy</creatorcontrib><creatorcontrib>Desiere, Frank</creatorcontrib><creatorcontrib>Flory, Mark</creatorcontrib><creatorcontrib>Martin, Daniel B</creatorcontrib><creatorcontrib>Kim, Bong</creatorcontrib><creatorcontrib>Lee, Hookeun</creatorcontrib><creatorcontrib>Raught, Brian</creatorcontrib><creatorcontrib>Aebersold, Ruedi</creatorcontrib><title>Analysis of the Saccharomyces cerevisiae proteome with PeptideAtlas</title><title>Genome Biology (Online Edition)</title><addtitle>Genome Biol</addtitle><description>We present the Saccharomyces cerevisiae PeptideAtlas composed from 47 diverse experiments and 4.9 million tandem mass spectra. The observed peptides align to 61% of Saccharomyces Genome Database (SGD) open reading frames (ORFs), 49% of the uncharacterized SGD ORFs, 54% of S. cerevisiae ORFs with a Gene Ontology annotation of 'molecular function unknown', and 76% of ORFs with Gene names. We highlight the use of this resource for data mining, construction of high quality lists for targeted proteomics, validation of proteins, and software development.</description><subject>Analysis</subject><subject>Codon</subject><subject>Data mining</subject><subject>Databases, Protein</subject><subject>Genes, Fungal</subject><subject>Genomes</subject><subject>Genomics</subject><subject>Hydrophobic and Hydrophilic Interactions</subject><subject>Mass Spectrometry</subject><subject>Messenger RNA</subject><subject>Method</subject><subject>Molecular Weight</subject><subject>Open Reading Frames - genetics</subject><subject>Peptides</subject><subject>Peptides - chemistry</subject><subject>Peptides - metabolism</subject><subject>Proteins</subject><subject>Proteome - chemistry</subject><subject>Proteome - genetics</subject><subject>Proteome - metabolism</subject><subject>Proteomics</subject><subject>RNA</subject><subject>Saccharomyces cerevisiae - chemistry</subject><subject>Saccharomyces cerevisiae - genetics</subject><subject>Saccharomyces cerevisiae - metabolism</subject><subject>Saccharomyces cerevisiae Proteins - chemistry</subject><subject>Saccharomyces cerevisiae Proteins - genetics</subject><subject>Saccharomyces cerevisiae Proteins - metabolism</subject><subject>Spectroscopy</subject><subject>User-Computer Interface</subject><issn>1474-760X</issn><issn>1465-6906</issn><issn>1474-760X</issn><issn>1465-6914</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2006</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>KPI</sourceid><recordid>eNp1kk1r3DAQhkVoaL76A3IpPhV6cKKxrQ9fCsumSUMCDTSF3oQsj70qtrWVtGn330fLLk0WWnSQmHnfh9HLEHIO9AJA8su-yQtKeS5ygNwD5QfkGCpR5YLTH29evY_ISQg_KYW6KvhbcgQCKFAGx2Q-m_SwDjZkrsviArNv2piF9m5cGwyZQY9PNliN2dK7iG7E7LeNi-wBl9G2OIuDDmfksNNDwHe7-5R8v_78OP-S33-9uZ3P7vOGcRZzoeuSso4WpqLItABpJDDgTSq2vJCl0bwsQMpWaDRcNEXHqWACKy3LltXlKfm05S5XzYitwSl6Pailt6P2a-W0VfudyS5U754UiLpiskqAqy2gse4_gP2OcaPqG7UJWQkFoDYhJ8yH3Rze_VphiGq0weAw6AndKigui5pRSZPwYivs9YDKTp1LVJNOi6M1bsLOpvqM0xKgrEEmw8c9Q9JE_BN7vQpB3T3c7mthqzXeheCx-_sPoGqzHv-c_P3rBF8cu30onwG5TLc7</recordid><startdate>20061113</startdate><enddate>20061113</enddate><creator>King, Nichole L</creator><creator>Deutsch, Eric W</creator><creator>Ranish, Jeffrey A</creator><creator>Nesvizhskii, Alexey I</creator><creator>Eddes, James S</creator><creator>Mallick, Parag</creator><creator>Eng, Jimmy</creator><creator>Desiere, Frank</creator><creator>Flory, Mark</creator><creator>Martin, Daniel B</creator><creator>Kim, Bong</creator><creator>Lee, Hookeun</creator><creator>Raught, Brian</creator><creator>Aebersold, Ruedi</creator><general>BioMed Central Ltd</general><general>BioMed Central</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>KPI</scope><scope>IAO</scope><scope>7X8</scope><scope>5PM</scope></search><sort><creationdate>20061113</creationdate><title>Analysis of the Saccharomyces cerevisiae proteome with PeptideAtlas</title><author>King, Nichole L ; Deutsch, Eric W ; Ranish, Jeffrey A ; Nesvizhskii, Alexey I ; Eddes, James S ; Mallick, Parag ; Eng, Jimmy ; Desiere, Frank ; Flory, Mark ; Martin, Daniel B ; Kim, Bong ; Lee, Hookeun ; Raught, Brian ; Aebersold, Ruedi</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-b565t-7a9305f02c40e5a718c81516b05fd6283ca632188d7aec67b2f60757e4a83d593</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2006</creationdate><topic>Analysis</topic><topic>Codon</topic><topic>Data mining</topic><topic>Databases, Protein</topic><topic>Genes, Fungal</topic><topic>Genomes</topic><topic>Genomics</topic><topic>Hydrophobic and Hydrophilic Interactions</topic><topic>Mass Spectrometry</topic><topic>Messenger RNA</topic><topic>Method</topic><topic>Molecular Weight</topic><topic>Open Reading Frames - genetics</topic><topic>Peptides</topic><topic>Peptides - chemistry</topic><topic>Peptides - metabolism</topic><topic>Proteins</topic><topic>Proteome - chemistry</topic><topic>Proteome - genetics</topic><topic>Proteome - metabolism</topic><topic>Proteomics</topic><topic>RNA</topic><topic>Saccharomyces cerevisiae - chemistry</topic><topic>Saccharomyces cerevisiae - genetics</topic><topic>Saccharomyces cerevisiae - metabolism</topic><topic>Saccharomyces cerevisiae Proteins - chemistry</topic><topic>Saccharomyces cerevisiae Proteins - genetics</topic><topic>Saccharomyces cerevisiae Proteins - metabolism</topic><topic>Spectroscopy</topic><topic>User-Computer Interface</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>King, Nichole L</creatorcontrib><creatorcontrib>Deutsch, Eric W</creatorcontrib><creatorcontrib>Ranish, Jeffrey A</creatorcontrib><creatorcontrib>Nesvizhskii, Alexey I</creatorcontrib><creatorcontrib>Eddes, James S</creatorcontrib><creatorcontrib>Mallick, Parag</creatorcontrib><creatorcontrib>Eng, Jimmy</creatorcontrib><creatorcontrib>Desiere, Frank</creatorcontrib><creatorcontrib>Flory, Mark</creatorcontrib><creatorcontrib>Martin, Daniel B</creatorcontrib><creatorcontrib>Kim, Bong</creatorcontrib><creatorcontrib>Lee, Hookeun</creatorcontrib><creatorcontrib>Raught, Brian</creatorcontrib><creatorcontrib>Aebersold, Ruedi</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Gale In Context: Global Issues</collection><collection>Gale Academic OneFile</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Genome Biology (Online Edition)</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>King, Nichole L</au><au>Deutsch, Eric W</au><au>Ranish, Jeffrey A</au><au>Nesvizhskii, Alexey I</au><au>Eddes, James S</au><au>Mallick, Parag</au><au>Eng, Jimmy</au><au>Desiere, Frank</au><au>Flory, Mark</au><au>Martin, Daniel B</au><au>Kim, Bong</au><au>Lee, Hookeun</au><au>Raught, Brian</au><au>Aebersold, Ruedi</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Analysis of the Saccharomyces cerevisiae proteome with PeptideAtlas</atitle><jtitle>Genome Biology (Online Edition)</jtitle><addtitle>Genome Biol</addtitle><date>2006-11-13</date><risdate>2006</risdate><volume>7</volume><issue>11</issue><spage>R106</spage><epage>R106</epage><pages>R106-R106</pages><artnum>R106</artnum><issn>1474-760X</issn><issn>1465-6906</issn><eissn>1474-760X</eissn><eissn>1465-6914</eissn><abstract>We present the Saccharomyces cerevisiae PeptideAtlas composed from 47 diverse experiments and 4.9 million tandem mass spectra. The observed peptides align to 61% of Saccharomyces Genome Database (SGD) open reading frames (ORFs), 49% of the uncharacterized SGD ORFs, 54% of S. cerevisiae ORFs with a Gene Ontology annotation of 'molecular function unknown', and 76% of ORFs with Gene names. We highlight the use of this resource for data mining, construction of high quality lists for targeted proteomics, validation of proteins, and software development.</abstract><cop>England</cop><pub>BioMed Central Ltd</pub><pmid>17101051</pmid><doi>10.1186/gb-2006-7-11-r106</doi><oa>free_for_read</oa></addata></record> |
| fulltext | fulltext |
| identifier | ISSN: 1474-760X |
| ispartof | Genome Biology (Online Edition), 2006-11, Vol.7 (11), p.R106-R106, Article R106 |
| issn | 1474-760X 1465-6906 1474-760X 1465-6914 |
| language | eng |
| recordid | cdi_pubmedcentral_primary_oai_pubmedcentral_nih_gov_1794584 |
| source | MEDLINE; DOAJ Directory of Open Access Journals; Elektronische Zeitschriftenbibliothek - Frei zugängliche E-Journals; Springer Nature OA Free Journals; PubMed Central; SpringerLink Journals - AutoHoldings |
| subjects | Analysis Codon Data mining Databases, Protein Genes, Fungal Genomes Genomics Hydrophobic and Hydrophilic Interactions Mass Spectrometry Messenger RNA Method Molecular Weight Open Reading Frames - genetics Peptides Peptides - chemistry Peptides - metabolism Proteins Proteome - chemistry Proteome - genetics Proteome - metabolism Proteomics RNA Saccharomyces cerevisiae - chemistry Saccharomyces cerevisiae - genetics Saccharomyces cerevisiae - metabolism Saccharomyces cerevisiae Proteins - chemistry Saccharomyces cerevisiae Proteins - genetics Saccharomyces cerevisiae Proteins - metabolism Spectroscopy User-Computer Interface |
| title | Analysis of the Saccharomyces cerevisiae proteome with PeptideAtlas |
| url | https://sfx.bib-bvb.de/sfx_tum?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2025-01-05T06%3A19%3A13IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-gale_pubme&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=Analysis%20of%20the%20Saccharomyces%20cerevisiae%20proteome%20with%20PeptideAtlas&rft.jtitle=Genome%20Biology%20(Online%20Edition)&rft.au=King,%20Nichole%20L&rft.date=2006-11-13&rft.volume=7&rft.issue=11&rft.spage=R106&rft.epage=R106&rft.pages=R106-R106&rft.artnum=R106&rft.issn=1474-760X&rft.eissn=1474-760X&rft_id=info:doi/10.1186/gb-2006-7-11-r106&rft_dat=%3Cgale_pubme%3EA603113918%3C/gale_pubme%3E%3Curl%3E%3C/url%3E&disable_directlink=true&sfx.directlink=off&sfx.report_link=0&rft_id=info:oai/&rft_pqid=68295080&rft_id=info:pmid/17101051&rft_galeid=A603113918&rfr_iscdi=true |