{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T16:06:26Z","timestamp":1772121986520,"version":"3.50.1"},"reference-count":14,"publisher":"Oxford University Press (OUP)","issue":"20","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":2606,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/2.0\/uk\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2009,10,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: YADA can deisotope and decharge high-resolution mass spectra from large peptide molecules, link the precursor monoisotopic peak information to the corresponding tandem mass spectrum, and account for different co-fragmenting ion species (multiplexed spectra). We describe how YADA enables a pipeline consisting of ProLuCID and DTASelect for analyzing large-scale middle-down proteomics data.<\/jats:p>\n               <jats:p>Availability: \u00a0http:\/\/fields.scripps.edu\/yada<\/jats:p>\n               <jats:p>Contact: \u00a0paulo@pcarvalho.com<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btp489","type":"journal-article","created":{"date-parts":[[2009,8,15]],"date-time":"2009-08-15T00:39:07Z","timestamp":1250296747000},"page":"2734-2736","source":"Crossref","is-referenced-by-count":72,"title":["YADA: a tool for taking the most out of high-resolution spectra"],"prefix":"10.1093","volume":"25","author":[{"given":"Paulo C.","family":"Carvalho","sequence":"first","affiliation":[{"name":"1 Systems Engineering and Computer Science Program, COPPE, Federal University of Rio de Janeiro, Caixa Postal 68511, 21941-972 Rio de Janeiro - RJ, Brazil and 2 Department of Chemical Physiology, The Scripps Research Institute, N Torrey Pines 10550, La Jolla, CA 92037, USA"},{"name":"1 Systems Engineering and Computer Science Program, COPPE, Federal University of Rio de Janeiro, Caixa Postal 68511, 21941-972 Rio de Janeiro - RJ, Brazil and 2 Department of Chemical Physiology, The Scripps Research Institute, N Torrey Pines 10550, La Jolla, CA 92037, USA"}]},{"given":"Tao","family":"Xu","sequence":"additional","affiliation":[{"name":"1 Systems Engineering and Computer Science Program, COPPE, Federal University of Rio de Janeiro, Caixa Postal 68511, 21941-972 Rio de Janeiro - RJ, Brazil and 2 Department of Chemical Physiology, The Scripps Research Institute, N Torrey Pines 10550, La Jolla, CA 92037, USA"}]},{"given":"Xuemei","family":"Han","sequence":"additional","affiliation":[{"name":"1 Systems Engineering and Computer Science Program, COPPE, Federal University of Rio de Janeiro, Caixa Postal 68511, 21941-972 Rio de Janeiro - RJ, Brazil and 2 Department of Chemical Physiology, The Scripps Research Institute, N Torrey Pines 10550, La Jolla, CA 92037, USA"}]},{"given":"Daniel","family":"Cociorva","sequence":"additional","affiliation":[{"name":"1 Systems Engineering and Computer Science Program, COPPE, Federal University of Rio de Janeiro, Caixa Postal 68511, 21941-972 Rio de Janeiro - RJ, Brazil and 2 Department of Chemical Physiology, The Scripps Research Institute, N Torrey Pines 10550, La Jolla, CA 92037, USA"}]},{"given":"Valmir C.","family":"Barbosa","sequence":"additional","affiliation":[{"name":"1 Systems Engineering and Computer Science Program, COPPE, Federal University of Rio de Janeiro, Caixa Postal 68511, 21941-972 Rio de Janeiro - RJ, Brazil and 2 Department of Chemical Physiology, The Scripps Research Institute, N Torrey Pines 10550, La Jolla, CA 92037, USA"}]},{"suffix":"III","given":"John R.","family":"Yates","sequence":"additional","affiliation":[{"name":"1 Systems Engineering and Computer Science Program, COPPE, Federal University of Rio de Janeiro, Caixa Postal 68511, 21941-972 Rio de Janeiro - RJ, Brazil and 2 Department of Chemical Physiology, The Scripps Research Institute, N Torrey Pines 10550, La Jolla, CA 92037, USA"}]}],"member":"286","published-online":{"date-parts":[[2009,8,14]]},"reference":[{"key":"2023013112131109500_B1","doi-asserted-by":"crossref","first-page":"374","DOI":"10.1021\/pr800635m","article-title":"Tandem mass spectrometry with ultrahigh mass accuracy clarifies peptide identification by database retrieval","volume":"8","author":"Boyne","year":"2009","journal-title":"J. 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