{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,29]],"date-time":"2025-10-29T13:33:15Z","timestamp":1761744795557},"reference-count":7,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2018,7,23]],"date-time":"2018-07-23T00:00:00Z","timestamp":1532304000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,2,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>Large-scale peptide mass spectrometry (MS)\/MS reference libraries are essential for the comprehensive analysis of data-independent acquisition (DIA) MS datasets, providing a comprehensive set of spectra for identification and quantification of proteins. We have developed a novel web-based R-package (iSwathX) for combining reference libraries that is compatible with different DIA analysis software. This open-source web GUI automates the process of normalization and combination of spectral libraries and provides a user-friendly method for performing library format conversions, analysis and visualizations, with no need for programing familiarity.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>iSwathX is freely accessible at https:\/\/biolinfo.shinyapps.io\/iSwathX with the R-package and Shiny source code available from GitHub (https:\/\/github.com\/znoor\/iSwathX).<\/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\/bty660","type":"journal-article","created":{"date-parts":[[2018,7,20]],"date-time":"2018-07-20T13:59:58Z","timestamp":1532095198000},"page":"538-539","source":"Crossref","is-referenced-by-count":8,"title":["iSwathX: an interactive web-based application for extension of DIA peptide reference libraries"],"prefix":"10.1093","volume":"35","author":[{"given":"Zainab","family":"Noor","sequence":"first","affiliation":[{"name":"Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jemma X","family":"Wu","sequence":"additional","affiliation":[{"name":"Australian Proteome Analysis Facility (APAF), Macquarie University, Sydney, NSW, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Dana","family":"Pascovici","sequence":"additional","affiliation":[{"name":"Australian Proteome Analysis Facility (APAF), Macquarie University, Sydney, NSW, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Abidali","family":"Mohamedali","sequence":"additional","affiliation":[{"name":"Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mark P","family":"Molloy","sequence":"additional","affiliation":[{"name":"Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia"},{"name":"Australian Proteome Analysis Facility (APAF), Macquarie University, Sydney, NSW, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mark S","family":"Baker","sequence":"additional","affiliation":[{"name":"Department of Biomedical Sciences, Macquarie University, Sydney, NSW, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Shoba","family":"Ranganathan","sequence":"additional","affiliation":[{"name":"Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2018,7,23]]},"reference":[{"key":"2023013107245626300_bty660-B1","doi-asserted-by":"crossref","first-page":"35","DOI":"10.1038\/nmeth.3234","article-title":"DIA mass spectrometry","volume":"12","author":"Doerr","year":"2015","journal-title":"Nat. Methods"},{"key":"2023013107245626300_bty660-B3","doi-asserted-by":"crossref","first-page":"1130","DOI":"10.1038\/nbt.3685","article-title":"A multicenter study benchmarks software tools for label-free proteome quantification","volume":"34","author":"Navarro","year":"2016","journal-title":"Nat. Biotechnol."},{"key":"2023013107245626300_bty660-B4","doi-asserted-by":"crossref","first-page":"2221","DOI":"10.1002\/pmic.201600007","article-title":"Effect of peptide assay library size and composition in targeted data-independent acquisition-MS analyses","volume":"16","author":"Parker","year":"2016","journal-title":"Proteomics"},{"key":"2023013107245626300_bty660-B5","volume-title":"R: A Language and Environment for Statistical Computing","author":"R Core Team","year":"2017"},{"key":"2023013107245626300_bty660-B6","doi-asserted-by":"crossref","first-page":"921","DOI":"10.1038\/nmeth.4398","article-title":"Statistical control of peptide and protein error rates in large-scale targeted data-independent acquisition analyses","volume":"14","author":"Rosenberger","year":"2017","journal-title":"Nat. Methods"},{"key":"2023013107245626300_bty660-B8","doi-asserted-by":"crossref","first-page":"2384","DOI":"10.1021\/acs.jproteome.6b00928","article-title":"Improvements in mass spectrometry assay library generation for targeted proteomics","volume":"16","author":"Teleman","year":"2017","journal-title":"J. Proteome Res."},{"key":"2023013107245626300_bty660-B9","doi-asserted-by":"crossref","first-page":"2501","DOI":"10.1074\/mcp.M115.055558","article-title":"SWATH Mass Spectrometry Performance Using Extended Peptide MS\/MS Assay Libraries","volume":"15","author":"Wu","year":"2016","journal-title":"Mol. Cell Proteomics"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/35\/3\/538\/48965520\/bioinformatics_35_3_538.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/35\/3\/538\/48965520\/bioinformatics_35_3_538.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,31]],"date-time":"2023-01-31T10:18:34Z","timestamp":1675160314000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/35\/3\/538\/5057156"}},"subtitle":[],"editor":[{"given":"Jonathan","family":"Wren","sequence":"additional","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2018,7,23]]},"references-count":7,"journal-issue":{"issue":"3","published-print":{"date-parts":[[2019,2,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/bty660","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2019,2,1]]},"published":{"date-parts":[[2018,7,23]]}}}