AMASS: Software for Automatically Validating the Quality of MS/MS Spectrum from SEQUEST Results
Time-consuming and experience-dependent manual validations of tandem mass spectra are usually applied to SEQUEST results. This inefficient method has become a significant bottleneck for MS/MS data processing. Here we introduce a program AMASS (advanced mass spectrum screener), which can filter the t...
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| Veröffentlicht in: | Molecular & cellular proteomics 2004-12, Vol.3 (12), p.1194-1199 |
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| container_title | Molecular & cellular proteomics |
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| creator | Sun, Wei Li, Fuxin Wang, Jue Zheng, Dexian Gao, Youhe |
| description | Time-consuming and experience-dependent manual validations of tandem mass spectra are usually applied to SEQUEST results.
This inefficient method has become a significant bottleneck for MS/MS data processing. Here we introduce a program AMASS (advanced
mass spectrum screener), which can filter the tandem mass spectra of SEQUEST results by measuring the match percentage of
high-abundant ions and the continuity of matched fragment ions in b, y series. Compared with Xcorr and DeltaCn filter, AMASS
can increase the number of positives and reduce the number of negatives in 22 datasets generated from 18 known protein mixtures.
It effectively removed most noisy spectra, false interpretations, and about half of poor fragmentation spectra, and AMASS
can work synergistically with Rscore filter. We believe the use of AMASS and Rscore can result in a more accurate identification
of peptide MS/MS spectra and reduce the time and energy for manual validation. |
| doi_str_mv | 10.1074/mcp.M400120-MCP200 |
| format | Article |
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This inefficient method has become a significant bottleneck for MS/MS data processing. Here we introduce a program AMASS (advanced
mass spectrum screener), which can filter the tandem mass spectra of SEQUEST results by measuring the match percentage of
high-abundant ions and the continuity of matched fragment ions in b, y series. Compared with Xcorr and DeltaCn filter, AMASS
can increase the number of positives and reduce the number of negatives in 22 datasets generated from 18 known protein mixtures.
It effectively removed most noisy spectra, false interpretations, and about half of poor fragmentation spectra, and AMASS
can work synergistically with Rscore filter. We believe the use of AMASS and Rscore can result in a more accurate identification
of peptide MS/MS spectra and reduce the time and energy for manual validation.</description><identifier>ISSN: 1535-9476</identifier><identifier>EISSN: 1535-9484</identifier><identifier>DOI: 10.1074/mcp.M400120-MCP200</identifier><identifier>PMID: 15489460</identifier><language>eng</language><publisher>United States: American Society for Biochemistry and Molecular Biology</publisher><subject>Algorithms ; Animals ; Automation ; Cattle ; Computational Biology - methods ; Databases as Topic ; Humans ; Mass Spectrometry - methods ; Models, Statistical ; Peptides - chemistry ; Proteins - chemistry ; Proteomics - methods ; Sequence Analysis, Protein - methods ; Software ; Statistics as Topic</subject><ispartof>Molecular & cellular proteomics, 2004-12, Vol.3 (12), p.1194-1199</ispartof><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c371t-dccb17f5d9a24c93ed24899459c1bc2a018c2f70c60e5042fd9d94e0702b4e763</citedby><cites>FETCH-LOGICAL-c371t-dccb17f5d9a24c93ed24899459c1bc2a018c2f70c60e5042fd9d94e0702b4e763</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><link.rule.ids>314,776,780,27901,27902</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/15489460$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Sun, Wei</creatorcontrib><creatorcontrib>Li, Fuxin</creatorcontrib><creatorcontrib>Wang, Jue</creatorcontrib><creatorcontrib>Zheng, Dexian</creatorcontrib><creatorcontrib>Gao, Youhe</creatorcontrib><title>AMASS: Software for Automatically Validating the Quality of MS/MS Spectrum from SEQUEST Results</title><title>Molecular & cellular proteomics</title><addtitle>Mol Cell Proteomics</addtitle><description>Time-consuming and experience-dependent manual validations of tandem mass spectra are usually applied to SEQUEST results.
This inefficient method has become a significant bottleneck for MS/MS data processing. Here we introduce a program AMASS (advanced
mass spectrum screener), which can filter the tandem mass spectra of SEQUEST results by measuring the match percentage of
high-abundant ions and the continuity of matched fragment ions in b, y series. Compared with Xcorr and DeltaCn filter, AMASS
can increase the number of positives and reduce the number of negatives in 22 datasets generated from 18 known protein mixtures.
It effectively removed most noisy spectra, false interpretations, and about half of poor fragmentation spectra, and AMASS
can work synergistically with Rscore filter. We believe the use of AMASS and Rscore can result in a more accurate identification
of peptide MS/MS spectra and reduce the time and energy for manual validation.</description><subject>Algorithms</subject><subject>Animals</subject><subject>Automation</subject><subject>Cattle</subject><subject>Computational Biology - methods</subject><subject>Databases as Topic</subject><subject>Humans</subject><subject>Mass Spectrometry - methods</subject><subject>Models, Statistical</subject><subject>Peptides - chemistry</subject><subject>Proteins - chemistry</subject><subject>Proteomics - methods</subject><subject>Sequence Analysis, Protein - methods</subject><subject>Software</subject><subject>Statistics as Topic</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>eNpFkMtOwzAQRS0EgvL4ARbIbNiFjh0nrtlVVXlIRDwCbC3HsdugpC62I9S_J6gVrGZGOvdqdBA6J3BNgLNxp9fXBQMgFJJi9kwB9tCIZGmWCDZh-387z4_QcQifABQIzw7REcnYRLAcRkhOi2lZ3uDS2fitvMHWeTzto-tUbLRq2w3-UG1TD9dqgePS4Jd-uOMGO4uLclyUuFwbHX3fYetdh8v5y_u8fMOvJvRtDKfowKo2mLPdPEHvt_O32X3y-HT3MJs-JjrlJCa11hXhNquFokyL1NR0-FCwTGhSaaqATDS1HHQOJgNGbS1qwQxwoBUzPE9P0NW2d-3dV29ClF0TtGlbtTKuDzLnRBCawwDSLai9C8EbK9e-6ZTfSALyV6sctMqdVrnVOoQudu191Zn6P7LzOACXW2DZLJbfjTeyapxemk6mklBJiGDpD0uPfk4</recordid><startdate>20041201</startdate><enddate>20041201</enddate><creator>Sun, Wei</creator><creator>Li, Fuxin</creator><creator>Wang, Jue</creator><creator>Zheng, Dexian</creator><creator>Gao, Youhe</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>20041201</creationdate><title>AMASS: Software for Automatically Validating the Quality of MS/MS Spectrum from SEQUEST Results</title><author>Sun, Wei ; Li, Fuxin ; Wang, Jue ; Zheng, Dexian ; Gao, Youhe</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c371t-dccb17f5d9a24c93ed24899459c1bc2a018c2f70c60e5042fd9d94e0702b4e763</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2004</creationdate><topic>Algorithms</topic><topic>Animals</topic><topic>Automation</topic><topic>Cattle</topic><topic>Computational Biology - methods</topic><topic>Databases as Topic</topic><topic>Humans</topic><topic>Mass Spectrometry - methods</topic><topic>Models, Statistical</topic><topic>Peptides - chemistry</topic><topic>Proteins - chemistry</topic><topic>Proteomics - methods</topic><topic>Sequence Analysis, Protein - methods</topic><topic>Software</topic><topic>Statistics as Topic</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Sun, Wei</creatorcontrib><creatorcontrib>Li, Fuxin</creatorcontrib><creatorcontrib>Wang, Jue</creatorcontrib><creatorcontrib>Zheng, Dexian</creatorcontrib><creatorcontrib>Gao, Youhe</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>Sun, Wei</au><au>Li, Fuxin</au><au>Wang, Jue</au><au>Zheng, Dexian</au><au>Gao, Youhe</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>AMASS: Software for Automatically Validating the Quality of MS/MS Spectrum from SEQUEST Results</atitle><jtitle>Molecular & cellular proteomics</jtitle><addtitle>Mol Cell Proteomics</addtitle><date>2004-12-01</date><risdate>2004</risdate><volume>3</volume><issue>12</issue><spage>1194</spage><epage>1199</epage><pages>1194-1199</pages><issn>1535-9476</issn><eissn>1535-9484</eissn><abstract>Time-consuming and experience-dependent manual validations of tandem mass spectra are usually applied to SEQUEST results.
This inefficient method has become a significant bottleneck for MS/MS data processing. Here we introduce a program AMASS (advanced
mass spectrum screener), which can filter the tandem mass spectra of SEQUEST results by measuring the match percentage of
high-abundant ions and the continuity of matched fragment ions in b, y series. Compared with Xcorr and DeltaCn filter, AMASS
can increase the number of positives and reduce the number of negatives in 22 datasets generated from 18 known protein mixtures.
It effectively removed most noisy spectra, false interpretations, and about half of poor fragmentation spectra, and AMASS
can work synergistically with Rscore filter. We believe the use of AMASS and Rscore can result in a more accurate identification
of peptide MS/MS spectra and reduce the time and energy for manual validation.</abstract><cop>United States</cop><pub>American Society for Biochemistry and Molecular Biology</pub><pmid>15489460</pmid><doi>10.1074/mcp.M400120-MCP200</doi><tpages>6</tpages><oa>free_for_read</oa></addata></record> |
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| ispartof | Molecular & cellular proteomics, 2004-12, Vol.3 (12), p.1194-1199 |
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| language | eng |
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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 Automation Cattle Computational Biology - methods Databases as Topic Humans Mass Spectrometry - methods Models, Statistical Peptides - chemistry Proteins - chemistry Proteomics - methods Sequence Analysis, Protein - methods Software Statistics as Topic |
| title | AMASS: Software for Automatically Validating the Quality of MS/MS Spectrum from SEQUEST Results |
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