{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,12,5]],"date-time":"2025-12-05T12:22:56Z","timestamp":1764937376610,"version":"3.37.3"},"reference-count":21,"publisher":"Oxford University Press (OUP)","issue":"8","license":[{"start":{"date-parts":[[2022,2,16]],"date-time":"2022-02-16T00:00:00Z","timestamp":1644969600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/501100001809","name":"Natural Science Foundation of China","doi-asserted-by":"publisher","award":["61732009"],"award-info":[{"award-number":["61732009"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"Natural Science Foundation of China","doi-asserted-by":"publisher","award":["61972329"],"award-info":[{"award-number":["61972329"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Hong Kong Special Administrative Region, P. R. China","award":["CityU 11210119","CityU 11206120"],"award-info":[{"award-number":["CityU 11210119","CityU 11206120"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,4,12]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:sec><jats:title>Motivation<\/jats:title><jats:p>Drawing peaks in a data window of an MS dataset happens at all time in MS data visualization applications. This asks to retrieve from an MS dataset some selected peaks in a data window whose image in a display window reflects the visual feature of all peaks in the data window. If an algorithm for this purpose is asked to output high-quality solutions in real time, then the most fundamental dependence of it is on the storage format of the MS dataset.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>We present mzMD, a new storage format of MS datasets and an algorithm to query this format of a storage system for a summary (a set of selected representative peaks) of a given data window. We propose a criterion Q-score to examine the quality of data window summaries. Experimental statistics on real MS datasets verified the high speed of mzMD in retrieving high-quality data window summaries. mzMD reported summaries of data windows whose Q-score outperforms those mzTree reported. The query speed of mzMD is the same as that of mzTree whereas its query speed stability is better than that of mzTree.<\/jats:p><\/jats:sec><jats:sec><jats:title>Availability and implementation<\/jats:title><jats:p>The source code is freely available at https:\/\/github.com\/yrm9837\/mzMD-java.<\/jats:p><\/jats:sec><jats:sec><jats:title>Supplementary information<\/jats:title><jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p><\/jats:sec>","DOI":"10.1093\/bioinformatics\/btac098","type":"journal-article","created":{"date-parts":[[2022,2,14]],"date-time":"2022-02-14T13:39:26Z","timestamp":1644845966000},"page":"2333-2340","source":"Crossref","is-referenced-by-count":1,"title":["mzMD: visualization-oriented MS data storage and retrieval"],"prefix":"10.1093","volume":"38","author":[{"given":"Runmin","family":"Yang","sequence":"first","affiliation":[{"name":"School of Computer Science and Technology, Shandong University , Qingdao 266237, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jingjing","family":"Ma","sequence":"additional","affiliation":[{"name":"School of Computer Science and Technology, Shandong University , Qingdao 266237, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Shu","family":"Zhang","sequence":"additional","affiliation":[{"name":"School of Computer Science and Technology, Shandong University , Qingdao 266237, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yu","family":"Zheng","sequence":"additional","affiliation":[{"name":"School of Computer Science and Technology, Shandong University , Qingdao 266237, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4344-8791","authenticated-orcid":false,"given":"Lusheng","family":"Wang","sequence":"additional","affiliation":[{"name":"Department of Computer Science, City University of Hong Kong , Hong Kong, China"},{"name":"City University of Hong Kong Shenzhen Research Institute , Shenzhen 518057, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9395-7247","authenticated-orcid":false,"given":"Daming","family":"Zhu","sequence":"additional","affiliation":[{"name":"School of Computer Science and Technology, Shandong University , Qingdao 266237, China"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2022,2,16]]},"reference":[{"key":"2023020109024231800_btac098-B1","doi-asserted-by":"crossref","first-page":"198","DOI":"10.1038\/nature01511","article-title":"Mass spectrometry-based proteomics","volume":"422","author":"Aebersold","year":"2003","journal-title":"Nature"},{"key":"2023020109024231800_btac098-B2","doi-asserted-by":"crossref","first-page":"2500","DOI":"10.1021\/acs.jproteome.6b00021","article-title":"BatMass: a Java software platform for LC\u2013MS data visualization in proteomics and metabolomics","volume":"15","author":"Avtonomov","year":"2016","journal-title":"J. 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