{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,5,21]],"date-time":"2025-05-21T13:45:00Z","timestamp":1747835100402,"version":"3.37.3"},"reference-count":9,"publisher":"Oxford University Press (OUP)","issue":"6","license":[{"start":{"date-parts":[[2016,12,16]],"date-time":"2016-12-16T00:00:00Z","timestamp":1481846400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/about_us\/legal\/notices"}],"funder":[{"name":"Key Program of National Natural Science Foundation of China","award":["61432005"],"award-info":[{"award-number":["61432005"]}]},{"name":"National Outstanding Youth Science Program of National Natural Science Foundation of China","award":["61625202"],"award-info":[{"award-number":["61625202"]}]},{"name":"International Science & Technology Cooperation Program of China","award":["2015DFA11240, 2014DFB30010"],"award-info":[{"award-number":["2015DFA11240, 2014DFB30010"]}]},{"name":"National High-tech R&D Program of China","award":["2015AA015305"],"award-info":[{"award-number":["2015AA015305"]}]},{"name":"Ministry of Science and Technology of China","award":["2013CB910801, 2014DFB30010, 2015AA020108"],"award-info":[{"award-number":["2013CB910801, 2014DFB30010, 2015AA020108"]}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"crossref","award":["61303073"],"award-info":[{"award-number":["61303073"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2017,3,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>Tandem mass spectrometry-based de novo peptide sequencing is a complex and time-consuming process. The current algorithms for de novo peptide sequencing cannot rapidly and thoroughly process large mass spectrometry datasets. In this paper, we propose MRUniNovo, a novel tool for parallel de novo peptide sequencing. MRUniNovo parallelizes UniNovo based on the Hadoop compute platform. Our experimental results demonstrate that MRUniNovo significantly reduces the computation time of de novo peptide sequencing without sacrificing the correctness and accuracy of the results, and thus can process very large datasets that UniNovo cannot.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and Implementation<\/jats:title>\n                  <jats:p>MRUniNovo is an open source software tool implemented in java. The source code and the parameter settings are available at http:\/\/bioinfo.hupo.org.cn\/MRUniNovo\/index.php<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btw721","type":"journal-article","created":{"date-parts":[[2016,12,20]],"date-time":"2016-12-20T01:48:36Z","timestamp":1482198516000},"page":"944-946","source":"Crossref","is-referenced-by-count":13,"title":["MRUniNovo: an efficient tool for <i>de novo<\/i> peptide sequencing utilizing the hadoop distributed computing framework"],"prefix":"10.1093","volume":"33","author":[{"given":"Chuang","family":"Li","sequence":"first","affiliation":[{"name":"College of Information Science and Engineering, Hunan University, National Supercomputing Center in Changsha, Changsha, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Tao","family":"Chen","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences, Beijing Institute of Radiation Medicine, Beijing, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Qiang","family":"He","sequence":"additional","affiliation":[{"name":"School of Software and Electrical Engineering, Swinburne University of Technology, Melbourne, Victoria, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yunping","family":"Zhu","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences, Beijing Institute of Radiation Medicine, Beijing, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kenli","family":"Li","sequence":"additional","affiliation":[{"name":"College of Information Science and Engineering, Hunan University, National Supercomputing Center in Changsha, Changsha, China"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2016,12,16]]},"reference":[{"key":"2023020204511664200_btw721-B1","doi-asserted-by":"crossref","first-page":"107","DOI":"10.1145\/1327452.1327492","article-title":"MapReduce: simplified data processing","volume":"51","author":"Dean","year":"2008","journal-title":"On Large Clusters, Communications of the ACM"},{"key":"2023020204511664200_btw721-B2","doi-asserted-by":"crossref","first-page":"1953","DOI":"10.1093\/bioinformatics\/btt338","article-title":"UniNovo: a universal tool for de novo peptide sequencing","volume":"29","author":"Jeong","year":"2013","journal-title":"Bioinformatics"},{"key":"2023020204511664200_btw721-B3","doi-asserted-by":"crossref","first-page":"3072","DOI":"10.1093\/bioinformatics\/btr523","article-title":"MapReduce implementation of a hybrid spectral library-database search method for large-scale peptide identification","volume":"27","author":"Kalyanaraman","year":"2011","journal-title":"Bioinformatics"},{"key":"2023020204511664200_btw721-B4","doi-asserted-by":"crossref","first-page":"575","DOI":"10.1038\/nature13302","article-title":"A draft map of the human proteome","volume":"509","author":"Kim","year":"2014","journal-title":"Nature"},{"key":"2023020204511664200_btw721-B5","doi-asserted-by":"crossref","first-page":"136","DOI":"10.1093\/bioinformatics\/btr615","article-title":"MR-Tandem: parallel X!Tandem using Hadoop MapReduce on Amazon Web Services","volume":"28","author":"Pratt","year":"2012","journal-title":"Bioinformatics"},{"key":"2023020204511664200_btw721-B6","doi-asserted-by":"crossref","first-page":"4653","DOI":"10.1002\/pmic.200900216","article-title":"Proteomics data repositories","volume":"9","author":"Riffle","year":"2009","journal-title":"Proteomics"},{"key":"2023020204511664200_btw721-B7","doi-asserted-by":"crossref","first-page":"582","DOI":"10.1038\/nature13319","article-title":"Mass-spectrometry-based draft of the human proteome","volume":"509","author":"Wilhelm","year":"2014","journal-title":"Nature"},{"key":"2023020204511664200_btw721-B8","doi-asserted-by":"crossref","first-page":"382","DOI":"10.1038\/nature13438","article-title":"Proteogenomic characterization of human colon and rectal cancer","volume":"513","author":"Zhang","year":"2014","journal-title":"Nature"},{"key":"2023020204511664200_btw721-B9","doi-asserted-by":"crossref","first-page":"M111","DOI":"10.1074\/mcp.M111.010587","article-title":"PEAKS DB: de novo sequencing assisted database search for sensitive and accurate peptide identification","volume":"11","author":"Zhang","year":"2012","journal-title":"Mol. 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