Comprehensive identification of peptides in tandem mass spectra using an efficient open search engine
Peptide identification in proteomics data is improved using an efficient open search engine. We present a sequence-tag-based search engine, Open-pFind, to identify peptides in an ultra-large search space that includes coeluting peptides, unexpected modifications and digestions. Our method detects pe...
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| Veröffentlicht in: | Nature biotechnology 2018-12, Vol.36 (11), p.1059-1061 |
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| container_title | Nature biotechnology |
| container_volume | 36 |
| creator | Chi, Hao Liu, Chao Yang, Hao Zeng, Wen-Feng Wu, Long Zhou, Wen-Jing Wang, Rui-Min Niu, Xiu-Nan Ding, Yue-He Zhang, Yao Wang, Zhao-Wei Chen, Zhen-Lin Sun, Rui-Xiang Liu, Tao Tan, Guang-Ming Dong, Meng-Qiu Xu, Ping Zhang, Pei-Heng He, Si-Min |
| description | Peptide identification in proteomics data is improved using an efficient open search engine.
We present a sequence-tag-based search engine, Open-pFind, to identify peptides in an ultra-large search space that includes coeluting peptides, unexpected modifications and digestions. Our method detects peptides with higher precision and speed than seven other search engines. Open-pFind identified 70–85% of the tandem mass spectra in four large-scale datasets and 14,064 proteins, each supported by at least two protein-unique peptides, in a human proteome dataset. |
| doi_str_mv | 10.1038/nbt.4236 |
| format | Article |
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We present a sequence-tag-based search engine, Open-pFind, to identify peptides in an ultra-large search space that includes coeluting peptides, unexpected modifications and digestions. Our method detects peptides with higher precision and speed than seven other search engines. Open-pFind identified 70–85% of the tandem mass spectra in four large-scale datasets and 14,064 proteins, each supported by at least two protein-unique peptides, in a human proteome dataset.</description><identifier>ISSN: 1087-0156</identifier><identifier>EISSN: 1546-1696</identifier><identifier>DOI: 10.1038/nbt.4236</identifier><identifier>PMID: 30295672</identifier><language>eng</language><publisher>New York: Nature Publishing Group US</publisher><subject>631/114/2784 ; 631/114/794 ; 631/1647/2067 ; 631/61/475 ; 82/58 ; Agriculture ; Bioinformatics ; Biomedical Engineering/Biotechnology ; Biomedicine ; Biotechnology ; brief-communication ; Life Sciences ; Mass spectra ; Mass spectrometry ; Mass spectroscopy ; Online information services ; Peptides ; Proteins ; Proteomes ; Proteomics ; Search engines</subject><ispartof>Nature biotechnology, 2018-12, Vol.36 (11), p.1059-1061</ispartof><rights>Springer Nature America, Inc. 2018</rights><rights>COPYRIGHT 2018 Nature Publishing Group</rights><rights>Copyright Nature Publishing Group Nov 2018</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c551t-740289ac95190358bff841140213db44b906921e38511f762ecde815b59571c13</citedby><cites>FETCH-LOGICAL-c551t-740289ac95190358bff841140213db44b906921e38511f762ecde815b59571c13</cites><orcidid>0000-0002-6094-1182 ; 0000-0002-7898-2599</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://link.springer.com/content/pdf/10.1038/nbt.4236$$EPDF$$P50$$Gspringer$$H</linktopdf><linktohtml>$$Uhttps://link.springer.com/10.1038/nbt.4236$$EHTML$$P50$$Gspringer$$H</linktohtml><link.rule.ids>314,776,780,27901,27902,41464,42533,51294</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/30295672$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Chi, Hao</creatorcontrib><creatorcontrib>Liu, Chao</creatorcontrib><creatorcontrib>Yang, Hao</creatorcontrib><creatorcontrib>Zeng, Wen-Feng</creatorcontrib><creatorcontrib>Wu, Long</creatorcontrib><creatorcontrib>Zhou, Wen-Jing</creatorcontrib><creatorcontrib>Wang, Rui-Min</creatorcontrib><creatorcontrib>Niu, Xiu-Nan</creatorcontrib><creatorcontrib>Ding, Yue-He</creatorcontrib><creatorcontrib>Zhang, Yao</creatorcontrib><creatorcontrib>Wang, Zhao-Wei</creatorcontrib><creatorcontrib>Chen, Zhen-Lin</creatorcontrib><creatorcontrib>Sun, Rui-Xiang</creatorcontrib><creatorcontrib>Liu, Tao</creatorcontrib><creatorcontrib>Tan, Guang-Ming</creatorcontrib><creatorcontrib>Dong, Meng-Qiu</creatorcontrib><creatorcontrib>Xu, Ping</creatorcontrib><creatorcontrib>Zhang, Pei-Heng</creatorcontrib><creatorcontrib>He, Si-Min</creatorcontrib><title>Comprehensive identification of peptides in tandem mass spectra using an efficient open search engine</title><title>Nature biotechnology</title><addtitle>Nat Biotechnol</addtitle><addtitle>Nat Biotechnol</addtitle><description>Peptide identification in proteomics data is improved using an efficient open search engine.
We present a sequence-tag-based search engine, Open-pFind, to identify peptides in an ultra-large search space that includes coeluting peptides, unexpected modifications and digestions. Our method detects peptides with higher precision and speed than seven other search engines. 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| subjects | 631/114/2784 631/114/794 631/1647/2067 631/61/475 82/58 Agriculture Bioinformatics Biomedical Engineering/Biotechnology Biomedicine Biotechnology brief-communication Life Sciences Mass spectra Mass spectrometry Mass spectroscopy Online information services Peptides Proteins Proteomes Proteomics Search engines |
| title | Comprehensive identification of peptides in tandem mass spectra using an efficient open search engine |
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