{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,13]],"date-time":"2026-07-13T23:14:12Z","timestamp":1783984452194,"version":"3.55.0"},"reference-count":19,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2023,12,20]],"date-time":"2023-12-20T00:00:00Z","timestamp":1703030400000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2023,12,20]],"date-time":"2023-12-20T00:00:00Z","timestamp":1703030400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"funder":[{"DOI":"10.13039\/501100007129","name":"Natural Science Foundation of Shandong Province","doi-asserted-by":"crossref","award":["2022HWYQ-081"],"award-info":[{"award-number":["2022HWYQ-081"]}],"id":[{"id":"10.13039\/501100007129","id-type":"DOI","asserted-by":"crossref"}]},{"name":"Academic promotion project of Shandong First Medical University"},{"name":"Jinan City"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"abstract":"<jats:title>Abstract<\/jats:title><jats:sec>\n                <jats:title>Background<\/jats:title>\n                <jats:p>Plate design is a necessary and time-consuming operation for GC\/LC-MS-based sample preparation. The implementation of the inter-batch balancing algorithm and the intra-batch randomization algorithm can have a significant impact on the final results. For researchers without programming skills, a stable and efficient online service for plate design is necessary.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Results<\/jats:title>\n                <jats:p>Here we describe InjectionDesign, a free online plate design service focused on GC\/LC-MS-based multi-omics experiment design. It offers the ability to separate the position design from the sequence design, making the output more compatible with the requirements of a modern mass spectrometer-based laboratory. In addition, it has implemented an optimized block randomization algorithm, which can be better applied to sample stratification with block randomization for an unbalanced distribution. It is easy to use, with built-in support for common instrument models and quick export to a worksheet.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Conclusions<\/jats:title>\n                <jats:p>InjectionDesign is an open-source project based on Java. Researchers can get the source code for the project from Github: <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"https:\/\/github.com\/CSi-Studio\/InjectionDesign\">https:\/\/github.com\/CSi-Studio\/InjectionDesign<\/jats:ext-link>. A free web service is also provided: <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/www.injection.design\">http:\/\/www.injection.design<\/jats:ext-link>.<\/jats:p>\n              <\/jats:sec>","DOI":"10.1186\/s12859-023-05598-1","type":"journal-article","created":{"date-parts":[[2023,12,20]],"date-time":"2023-12-20T17:02:24Z","timestamp":1703091744000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":2,"title":["Injectiondesign: web service of plate design with optimized stratified block randomization for modern GC\/LC-MS-based sample preparation"],"prefix":"10.1186","volume":"24","author":[{"given":"Miaoshan","family":"Lu","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hengxuan","family":"Jiang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ruimin","family":"Wang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shaowei","family":"An","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jiawei","family":"Wang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Changbin","family":"Yu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2023,12,20]]},"reference":[{"key":"5598_CR1","doi-asserted-by":"publisher","DOI":"10.1007\/s11306-018-1460-7","author":"RD Beger","year":"2019","unstructured":"Beger RD, Dunn WB, Bandukwala A, Bethan B, Broadhurst D, Clish CB, Dasari S, Derr L, Evans A, Fischer S, Flynn T, Hartung T, Herrington D, Higashi R, Hsu PC, Jones C, Kachman M, Karuso H, Kruppa G, Lippa K, Maruvada P, Mosley J, Ntai I, O\u2019Donovan C, Playdon M, Raftery D, Shaughnessy D, Souza A, Spaeder T, Spalholz B, Tayyari F, Ubhi B, Verma M, Walk T, Wilson I, Witkin K, Bearden DW, Zanetti KA. Towards quality assurance and quality control in untargeted metabolomics studies. Metabolomics. 2019. https:\/\/doi.org\/10.1007\/s11306-018-1460-7.","journal-title":"Metabolomics"},{"key":"5598_CR2","doi-asserted-by":"publisher","DOI":"10.1007\/s11306-020-01728-5","author":"AM Evans","year":"2020","unstructured":"Evans AM, O\u2019Donovan C, Playdon M, Beecher C, Beger RD, Bowden JA, Broadhurst D, Clish CB, Dasari S, Dunn WB, Griffin JL, Hartung T, Hsu PC, Huan T, Jans J, Jones CM, Kachman M, Kleensang A, Lewis MR, Monge ME, Mosley JD, Taylor E, Tayyari F, Theodoridis G, Torta F, Ubhi BK, Vuckovic D. Dissemination and analysis of the quality assurance (qa) and quality control (qc) practices of lc-ms based untargeted metabolomics practitioners. Metabolomics. 2020. https:\/\/doi.org\/10.1007\/s11306-020-01728-5.","journal-title":"Metabolomics"},{"key":"5598_CR3","doi-asserted-by":"publisher","DOI":"10.14573\/altex.1509161","author":"M Bouhifd","year":"2015","unstructured":"Bouhifd M, Beger R, Flynn T, Guo L, Harris G, Hogberg H, Kaddurah-Daouk R, Kamp H, Kleensang A, Maertens A, Odwin-DaCosta S, Pamies D, Robertson D, Smirnova L, Sun J, Zhao L, Hartung T. Quality assurance of metabolomics. Altex. 2015. https:\/\/doi.org\/10.14573\/altex.1509161.","journal-title":"Altex"},{"key":"5598_CR4","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jproteome.0c00536","author":"B Burger","year":"2021","unstructured":"Burger B, Vaudel M, Barsnes H. Importance of block randomization when designing proteomics experiments. J Proteome Res. 2021. https:\/\/doi.org\/10.1021\/acs.jproteome.0c00536.","journal-title":"J Proteome Res"},{"key":"5598_CR5","doi-asserted-by":"publisher","DOI":"10.1017\/CBO9780511611483","author":"RA Bailey","year":"2008","unstructured":"Bailey RA. Design of comparative experiments. Des Comp Exp. 2008. https:\/\/doi.org\/10.1017\/CBO9780511611483.","journal-title":"Des Comp Exp"},{"key":"5598_CR6","doi-asserted-by":"publisher","DOI":"10.1016\/j.chroma.2018.07.019","author":"I Surowiec","year":"2018","unstructured":"Surowiec I, Johansson E, Stenlund H, Rantap\u00e4\u00e4-Dahlqvist S, Bergstr\u00f6m S, Normark J, Trygg J. Quantification of run order effect on chromatography\u2014mass spectrometry profiling data. J Chromatogr A. 2018. https:\/\/doi.org\/10.1016\/j.chroma.2018.07.019.","journal-title":"J Chromatogr A"},{"key":"5598_CR7","doi-asserted-by":"publisher","first-page":"51","DOI":"10.1021\/acs.jproteome.0c00310","volume":"19","author":"T Zhang","year":"2020","unstructured":"Zhang T, Gaffrey MJ, Monroe ME, Thomas DG, Weitz KK, Piehowski PD, Petyuk VA, Moore RJ, Thrall BD, Qian WJ. Block design with common reference samples enables robust large-scale label-free quantitative proteome profiling. J Proteome Res. 2020;19:51. https:\/\/doi.org\/10.1021\/acs.jproteome.0c00310.","journal-title":"J Proteome Res"},{"key":"5598_CR8","doi-asserted-by":"crossref","unstructured":"Datta S, Mertens B. Statistical analysis of proteomics, metabolomics, and lipidomics data using mass spectrometry; 2016.","DOI":"10.1007\/978-3-319-45809-0"},{"key":"5598_CR9","doi-asserted-by":"publisher","first-page":"24","DOI":"10.1007\/s11306-021-01848-6","volume":"18","author":"KA Lippa","year":"2022","unstructured":"Lippa KA, Aristizabal-Henao JJ, Beger RD, Bowden JA, Broeckling C, Beecher C, Davis WC, Dunn WB, Flores R, Goodacre R, Gouveia GJ, Harms AC, Hartung T, Jones CM, Lewis MR, Ntai I, Percy AJ, Raftery D, Schock TB, Sun J, Theodoridis G, Tayyari F, Torta F, Ulmer CZ, Wilson I, Ubhi BK. Reference materials for ms-based untargeted metabolomics and lipidomics: a review by the metabolomics quality assurance and quality control consortium (mqacc). 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Artif Intell Life Sci. 2023;3:66. https:\/\/doi.org\/10.1016\/j.ailsci.2023.100073.","journal-title":"Artif Intell Life Sci"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-023-05598-1.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1186\/s12859-023-05598-1\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-023-05598-1.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,12,20]],"date-time":"2023-12-20T17:02:35Z","timestamp":1703091755000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/s12859-023-05598-1"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023,12,20]]},"references-count":19,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2023,12]]}},"alternative-id":["5598"],"URL":"https:\/\/doi.org\/10.1186\/s12859-023-05598-1","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2023,12,20]]},"assertion":[{"value":"29 March 2023","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"4 December 2023","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"20 December 2023","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"Not applicable.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethics approval and consent to participate"}},{"value":"Not applicable.","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Consent for publication"}},{"value":"The authors declare no conflict of interest regarding the company mentioned in this work. The InjectionDesign website () is supported by Carbon Silicon (Hangzhou) Biotechnology Co., Ltd., which is a research output transformation company the main authors established, responsible for long-term maintenance and commercial customization of all omics software we published.","order":4,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"489"}}