{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,29]],"date-time":"2025-11-29T10:51:40Z","timestamp":1764413500224,"version":"build-2065373602"},"reference-count":21,"publisher":"Wiley","issue":"23-24","license":[{"start":{"date-parts":[[2014,11,19]],"date-time":"2014-11-19T00:00:00Z","timestamp":1416355200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/onlinelibrary.wiley.com\/termsAndConditions#vor"}],"funder":[{"name":"Proteogenomics Research Program","award":["NRF-2012M3A9B9036675"],"award-info":[{"award-number":["NRF-2012M3A9B9036675"]}]},{"DOI":"10.13039\/501100003725","name":"National Research Foundation of Korea","doi-asserted-by":"crossref","id":[{"id":"10.13039\/501100003725","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100010446","name":"Institute for Basic Science","doi-asserted-by":"crossref","award":["CA1308"],"award-info":[{"award-number":["CA1308"]}],"id":[{"id":"10.13039\/501100010446","id-type":"DOI","asserted-by":"crossref"}]},{"name":"NRF","award":["NRF-2012M3A9D1054452","NRF-2014M3C7A1046047"],"award-info":[{"award-number":["NRF-2012M3A9D1054452","NRF-2014M3C7A1046047"]}]}],"content-domain":{"domain":["analyticalsciencejournals.onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["Proteomics"],"published-print":{"date-parts":[[2014,12]]},"abstract":"<jats:p>\n                    In proteogenomic analysis, construction of a compact, customized database from mRNA\u2010seq data and a sensitive search of both reference and customized databases are essential to accurately determine protein abundances and structural variations at the protein level. However, these tasks have not been systematically explored, but rather performed in an\n                    <jats:italic>ad\u2010hoc<\/jats:italic>\n                    fashion. Here, we present an effective method for constructing a compact database containing comprehensive sequences of sample\u2010specific variants\u2014single nucleotide variants, insertions\/deletions, and stop\u2010codon mutations derived from Exome\u2010seq and RNA\u2010seq data. It, however, occupies less space by storing variant peptides, not variant proteins. We also present an efficient search method for both customized and reference databases. The separate searches of the two databases increase the search time, and a unified search is less sensitive to identify variant peptides due to the smaller size of the customized database, compared to the reference database, in the target\u2010decoy setting. Our method searches the unified database once, but performs target\u2010decoy validations separately. Experimental results show that our approach is as fast as the unified search and as sensitive as the separate searches. Our customized database includes mutation information in the headers of variant peptides, thereby facilitating the inspection of peptide\u2010spectrum matches.\n                  <\/jats:p>","DOI":"10.1002\/pmic.201400225","type":"journal-article","created":{"date-parts":[[2014,10,15]],"date-time":"2014-10-15T05:13:42Z","timestamp":1413350022000},"page":"2742-2749","update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":29,"title":["Compact variant\u2010rich customized sequence database and a fast and sensitive database search for efficient proteogenomic analyses"],"prefix":"10.1002","volume":"14","author":[{"given":"Heejin","family":"Park","sequence":"first","affiliation":[{"name":"Department of Computer Science and Engineering Hanyang University  Seoul Republic of Korea"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Junwoo","family":"Bae","sequence":"additional","affiliation":[{"name":"Department of Computer Science and Engineering Hanyang University  Seoul Republic of Korea"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hyunwoo","family":"Kim","sequence":"additional","affiliation":[{"name":"Department of Computer Science and Engineering Hanyang University  Seoul Republic of Korea"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sangok","family":"Kim","sequence":"additional","affiliation":[{"name":"Department of Life Science and Ewha Research Center for Systems Biology Ewha Womans University  Seoul Republic of Korea"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hokeun","family":"Kim","sequence":"additional","affiliation":[{"name":"Department of Chemistry Research Institute for Natural Sciences Korea University  Seoul Republic of Korea"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Dong\u2010Gi","family":"Mun","sequence":"additional","affiliation":[{"name":"Department of Chemistry Research Institute for Natural Sciences 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