{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,23]],"date-time":"2026-06-23T01:47:19Z","timestamp":1782179239204,"version":"3.54.5"},"reference-count":5,"publisher":"Oxford University Press (OUP)","issue":"6","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2010,3,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: XDIA is a computational strategy for analyzing multiplexed spectra acquired using electron transfer dissociation and collision-activated dissociation; it significantly increases identified spectra (\u223c250%) and unique peptides (\u223c30%) when compared with the data-dependent ETCaD analysis on middle-down, single-phase shotgun proteomic analysis. Increasing identified spectra and peptides improves quantitation statistics confidence and protein coverage, respectively.<\/jats:p>\n               <jats:p>Availability: The software and data produced in this work are freely available for academic use at http:\/\/fields.scripps.edu\/XDIA<\/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\/btq031","type":"journal-article","created":{"date-parts":[[2010,1,28]],"date-time":"2010-01-28T01:13:21Z","timestamp":1264641201000},"page":"847-848","source":"Crossref","is-referenced-by-count":87,"title":["XDIA: improving on the label-free data-independent analysis"],"prefix":"10.1093","volume":"26","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, Brazil, 2 Department of Chemical Physiology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA and 3 Biophysics Institute Carlos Chagas Filho, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil"},{"name":"1 Systems Engineering and Computer Science Program, COPPE, Federal University of Rio de Janeiro, Caixa Postal 68511, 21941-972 Rio de Janeiro, Brazil, 2 Department of Chemical Physiology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA and 3 Biophysics Institute Carlos Chagas Filho, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"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, Brazil, 2 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