{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,28]],"date-time":"2025-11-28T17:24:28Z","timestamp":1764350668726,"version":"3.37.3"},"reference-count":37,"publisher":"Oxford University Press (OUP)","issue":"24","license":[{"start":{"date-parts":[[2021,7,29]],"date-time":"2021-07-29T00:00:00Z","timestamp":1627516800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001102","name":"Cancer Council NSW","doi-asserted-by":"publisher","award":["IG-18-01"],"award-info":[{"award-number":["IG-18-01"]}],"id":[{"id":"10.13039\/501100001102","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000947","name":"Australian Cancer Research Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100000947","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001171","name":"Cancer Institute New South Wales","doi-asserted-by":"publisher","award":["2017\/TPG001","REG171150"],"award-info":[{"award-number":["2017\/TPG001","REG171150"]}],"id":[{"id":"10.13039\/501100001171","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100008810","name":"NSW Ministry of Health","doi-asserted-by":"publisher","award":["CMP-01"],"award-info":[{"award-number":["CMP-01"]}],"id":[{"id":"10.13039\/501100008810","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001774","name":"The University of Sydney","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100001774","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001102","name":"Cancer Council NSW","doi-asserted-by":"publisher","award":["IG 18-01"],"award-info":[{"award-number":["IG 18-01"]}],"id":[{"id":"10.13039\/501100001102","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001047","name":"Ian Potter Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100001047","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Medical Research Futures Fund"},{"DOI":"10.13039\/501100000925","name":"National Health and Medical Research Council","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100000925","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Australia European Union","award":["GNT1170739"],"award-info":[{"award-number":["GNT1170739"]}]},{"name":"European Commission\u2019s Horizon 2020 Program","award":["H2020-SC1-DTH-2018-1"],"award-info":[{"award-number":["H2020-SC1-DTH-2018-1"]}]},{"name":"iPC\u2014individualizedPaediatricCure","award":["826121"],"award-info":[{"award-number":["826121"]}]},{"DOI":"10.13039\/501100001026","name":"National Breast Cancer Foundation","doi-asserted-by":"publisher","award":["IIRS-18-164"],"award-info":[{"award-number":["IIRS-18-164"]}],"id":[{"id":"10.13039\/501100001026","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Memorandum of Understanding between Children's Medical Research Institute"},{"name":"U.S. National Cancer Institute\u2019s International Cancer Proteogenome Consortium"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,12,11]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>The output of electrospray ionization\u2013liquid chromatography mass spectrometry (ESI-LC-MS) is influenced by multiple sources of noise and major contributors can be broadly categorized as baseline, random and chemical noise. Noise has a negative impact on the identification and quantification of peptides, which influences the reliability and reproducibility of MS-based proteomics data. Most attempts at denoising have been made on either spectra or chromatograms independently, thus, important 2D information is lost because the mass-to-charge ratio and retention time dimensions are not considered jointly.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>This article presents a novel technique for denoising raw ESI-LC-MS data via 2D undecimated wavelet transform, which is applied to proteomics data acquired by data-independent acquisition MS (DIA-MS). We demonstrate that denoising DIA-MS data results in the improvement of peptide identification and quantification in complex biological samples.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>The software is available on Github (https:\/\/github.com\/CMRI-ProCan\/CRANE). The datasets were obtained from ProteomeXchange (Identifiers\u2014PXD002952 and PXD008651). Preliminary data and intermediate files are available via ProteomeXchange (Identifiers\u2014PXD020529 and PXD025103).<\/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\/btab563","type":"journal-article","created":{"date-parts":[[2021,7,28]],"date-time":"2021-07-28T11:13:43Z","timestamp":1627470823000},"page":"4719-4726","source":"Crossref","is-referenced-by-count":9,"title":["Improved identification and quantification of peptides in mass spectrometry data via chemical and random additive noise elimination (CRANE)"],"prefix":"10.1093","volume":"37","author":[{"given":"Akila J","family":"Seneviratne","sequence":"first","affiliation":[{"name":"ProCan\u00ae, Children\u2019s Medical Research Institute, Faculty of Medicine and Health, The University of Sydney , Westmead, NSW, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sean","family":"Peters","sequence":"additional","affiliation":[{"name":"ProCan\u00ae, Children\u2019s Medical Research Institute, Faculty of Medicine and Health, The University of Sydney , Westmead, NSW, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"David","family":"Clarke","sequence":"additional","affiliation":[{"name":"ProCan\u00ae, Children\u2019s Medical Research Institute, Faculty of Medicine and Health, The University of Sydney , Westmead, NSW, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Michael","family":"Dausmann","sequence":"additional","affiliation":[{"name":"ProCan\u00ae, Children\u2019s Medical Research Institute, Faculty of Medicine and Health, The University of Sydney , Westmead, NSW, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Michael","family":"Hecker","sequence":"additional","affiliation":[{"name":"ProCan\u00ae, Children\u2019s Medical Research Institute, Faculty of Medicine and Health, The University of Sydney , Westmead, NSW, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6892-2771","authenticated-orcid":false,"given":"Brett","family":"Tully","sequence":"additional","affiliation":[{"name":"ProCan\u00ae, Children\u2019s Medical Research Institute, Faculty of Medicine and Health, The University of Sydney , Westmead, NSW, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Peter G","family":"Hains","sequence":"additional","affiliation":[{"name":"ProCan\u00ae, Children\u2019s Medical Research Institute, Faculty of Medicine and Health, The University of Sydney , Westmead, NSW, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5340-301X","authenticated-orcid":false,"given":"Qing","family":"Zhong","sequence":"additional","affiliation":[{"name":"ProCan\u00ae, Children\u2019s Medical Research Institute, Faculty of Medicine and Health, The University of Sydney , Westmead, NSW, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2021,7,29]]},"reference":[{"key":"2023051607140789900_btab563-B1","doi-asserted-by":"crossref","first-page":"347","DOI":"10.1038\/nature19949","article-title":"Mass-spectrometric exploration of proteome structure and function","volume":"537","author":"Aebersold","year":"2016","journal-title":"Nature"},{"key":"2023051607140789900_btab563-B2","doi-asserted-by":"crossref","first-page":"1518","DOI":"10.1093\/bioinformatics\/btw023","article-title":"MS-REDUCE: an ultrafast technique for reduction of big mass spectrometry data for high-throughput processing","volume":"32","author":"Awan","year":"2016","journal-title":"Bioinformatics"},{"key":"2023051607140789900_btab563-B3","doi-asserted-by":"crossref","first-page":"327","DOI":"10.1038\/s41580-020-0231-2","article-title":"Proteomic and interactomic insights into the molecular basis of cell functional diversity","volume":"21","author":"Bludau","year":"2020","journal-title":"Nat. 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