{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,27]],"date-time":"2026-02-27T04:28:31Z","timestamp":1772166511750,"version":"3.50.1"},"reference-count":36,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2025,6,20]],"date-time":"2025-06-20T00:00:00Z","timestamp":1750377600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2025,6,20]],"date-time":"2025-06-20T00:00:00Z","timestamp":1750377600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"funder":[{"DOI":"10.13039\/501100001866","name":"Fonds National de la Recherche Luxembourg","doi-asserted-by":"publisher","award":["A18\/BM\/12341006"],"award-info":[{"award-number":["A18\/BM\/12341006"]}],"id":[{"id":"10.13039\/501100001866","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001866","name":"Fonds National de la Recherche Luxembourg","doi-asserted-by":"publisher","award":["A18\/BM\/12341006"],"award-info":[{"award-number":["A18\/BM\/12341006"]}],"id":[{"id":"10.13039\/501100001866","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001866","name":"Fonds National de la Recherche Luxembourg","doi-asserted-by":"publisher","award":["A18\/BM\/12341006"],"award-info":[{"award-number":["A18\/BM\/12341006"]}],"id":[{"id":"10.13039\/501100001866","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001866","name":"Fonds National de la Recherche Luxembourg","doi-asserted-by":"publisher","award":["A18\/BM\/12341006"],"award-info":[{"award-number":["A18\/BM\/12341006"]}],"id":[{"id":"10.13039\/501100001866","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001866","name":"Fonds National de la Recherche Luxembourg","doi-asserted-by":"publisher","award":["A18\/BM\/12341006"],"award-info":[{"award-number":["A18\/BM\/12341006"]}],"id":[{"id":"10.13039\/501100001866","id-type":"DOI","asserted-by":"publisher"}]},{"name":"The European Union Research and Innovation program Horizon Europe for PARC","award":["101057014"],"award-info":[{"award-number":["101057014"]}]},{"name":"The European Union Research and Innovation program Horizon Europe for PARC","award":["101057014"],"award-info":[{"award-number":["101057014"]}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["J Cheminform"],"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>\n                    Shinyscreen is an R package and Shiny-based web application designed for the exploration, visualization, and quality assessment of raw data from high resolution mass spectrometry instruments. Its versatile list-based approach supports the curation of data starting from either known or \u201csuspected\u201d compounds (compound list-based screening) or detected masses (mass list-based screening), making it adaptable to diverse analytical needs (target, suspect or non-target screening). Shinyscreen can be operated in multiple modes, including as an R package, an interactive command-line tool, a self-documented web GUI, or a network-deployable service. Shinyscreen has been applied in environmental research, database enrichment, and educational initiatives, showcasing its broad utility. Shinyscreen is available in GitLab (\n                    <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" xlink:href=\"https:\/\/gitlab.com\/uniluxembourg\/lcsb\/eci\/shinyscreen\" ext-link-type=\"uri\">https:\/\/gitlab.com\/uniluxembourg\/lcsb\/eci\/shinyscreen<\/jats:ext-link>\n                    ) under the Apache License 2.0. The repository contains detailed instructions for deployment and use. Additionally, a pre-configured Docker image, designed for seamless installation and operation is available, with instructions also provided in the main repository.\n                    <jats:bold>Scientific Contribution<\/jats:bold>\n                    : Shinyscreen is a fully open source prescreening application to assist analysts in the high throughput quality control of the thousands of peaks detected in high resolution mass spectrometry experiments. As a vendor-independent, cross operating system application it covers an important niche in open mass spectrometry workflows. Shinyscreen supports quality control of data for further identification or upload of spectra to public data resources, as well as teaching efforts to educate students on the importance of data quality control and rigorous identification methods.\n                  <\/jats:p>","DOI":"10.1186\/s13321-025-01044-x","type":"journal-article","created":{"date-parts":[[2025,6,20]],"date-time":"2025-06-20T08:44:10Z","timestamp":1750409050000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Shinyscreen: mass spectrometry data inspection and quality checking utility"],"prefix":"10.1186","volume":"17","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-6662-4375","authenticated-orcid":false,"given":"Todor","family":"Kondi\u0107","sequence":"first","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0295-6618","authenticated-orcid":false,"given":"Anjana","family":"Elapavalore","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6986-5545","authenticated-orcid":false,"given":"Jessy","family":"Krier","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2985-6473","authenticated-orcid":false,"given":"Adelene","family":"Lai","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7820-4335","authenticated-orcid":false,"given":"Hiba Mohammed","family":"Taha","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5428-8183","authenticated-orcid":false,"given":"Mira","family":"Narayanan","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6868-8145","authenticated-orcid":false,"given":"Emma L.","family":"Schymanski","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2025,6,20]]},"reference":[{"key":"1044_CR1","doi-asserted-by":"publisher","first-page":"209","DOI":"10.1177\/14690667241278110","volume":"30","author":"AK Kuril","year":"2024","unstructured":"Kuril AK (2024) Exploring the versatility of mass spectrometry: applications across diverse scientific disciplines. Eur J Mass Spectrom 30:209\u2013220. https:\/\/doi.org\/10.1177\/14690667241278110. ([cito:citesAsAuthority])","journal-title":"Eur J Mass Spectrom"},{"key":"1044_CR2","doi-asserted-by":"publisher","first-page":"75","DOI":"10.1186\/s12302-023-00779-4","volume":"35","author":"J Hollender","year":"2023","unstructured":"Hollender J, Schymanski EL, Ahrens L et al (2023) NORMAN guidance on suspect and non-target screening in environmental monitoring. Environ Sci Eur 35:75. https:\/\/doi.org\/10.1186\/s12302-023-00779-4. ([cito:citesAsAuthority])","journal-title":"Environ Sci Eur"},{"key":"1044_CR3","doi-asserted-by":"publisher","first-page":"1788","DOI":"10.1039\/D3EM00181D","volume":"25","author":"A Elapavalore","year":"2023","unstructured":"Elapavalore A, Kondi\u0107 T, Singh RR et al (2023) Adding open spectral data to MassBank and PubChem using open source tools to support non-targeted exposomics of mixtures. Environ Sci Process Impacts 25:1788\u20131801. https:\/\/doi.org\/10.1039\/D3EM00181D. ([cito:citesAsAuthority])","journal-title":"Environ Sci Process Impacts"},{"key":"1044_CR4","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1007\/978-1-4939-9744-2","volume-title":"Mass spectrometry data analysis in proteomics","author":"R Matthiesen","year":"2020","unstructured":"Matthiesen R, Bunkenborg J (2020) Introduction to mass spectrometry-based proteomics. In: Matthiesen R (ed) Mass spectrometry data analysis in proteomics. Springer, New York, NY, pp 1\u201358 ([cito:citesAsAuthority])"},{"key":"1044_CR5","unstructured":"Thermo Scientific (2024) Xcalibur\u2122 Software. https:\/\/www.thermofisher.com\/order\/catalog\/product\/OPTON-30967. Accessed 2 Dec 2024"},{"key":"1044_CR6","doi-asserted-by":"publisher","first-page":"405","DOI":"10.1186\/1471-2105-11-405","volume":"11","author":"P Wenig","year":"2010","unstructured":"Wenig P, Odermatt J (2010) OpenChrom: a cross-platform open source software for the mass spectrometric analysis of chromatographic data. BMC Bioinformatics 11:405. https:\/\/doi.org\/10.1186\/1471-2105-11-405. ([cito:citesAsAuthority])","journal-title":"BMC Bioinformatics"},{"key":"1044_CR7","doi-asserted-by":"publisher","first-page":"163","DOI":"10.1186\/1471-2105-9-163","volume":"9","author":"M Sturm","year":"2008","unstructured":"Sturm M, Bertsch A, Gr\u00f6pl C et al (2008) OpenMS\u2014an open-source software framework for mass spectrometry. BMC Bioinformatics 9:163. https:\/\/doi.org\/10.1186\/1471-2105-9-163. ([cito:citesAsAuthority])","journal-title":"BMC Bioinformatics"},{"key":"1044_CR8","doi-asserted-by":"publisher","first-page":"134","DOI":"10.1038\/s41592-021-01339-5","volume":"19","author":"D Petras","year":"2022","unstructured":"Petras D, Phelan VV, Acharya D et al (2022) GNPS dashboard: collaborative exploration of mass spectrometry data in the web browser. Nat Methods 19:134\u2013136. https:\/\/doi.org\/10.1038\/s41592-021-01339-5. ([cito:citesAsAuthority])","journal-title":"Nat Methods"},{"key":"1044_CR9","unstructured":"Fischer B, Neumann S, Gatto L, Kou Q (2017) mzR: parser for netCDF, mzXML, mzData and mzML and mzIdentML files (mass spectrometry data). http:\/\/bioconductor.org\/packages\/mzR\/. Accessed 2 Dec 2024 [cito:citesAsAuthority]"},{"key":"1044_CR10","doi-asserted-by":"publisher","first-page":"1063","DOI":"10.1021\/acs.jproteome.0c00313","volume":"20","author":"L Gatto","year":"2021","unstructured":"Gatto L, Gibb S, Rainer J (2021) MSnbase, efficient and elegant R-based processing and visualization of raw mass spectrometry data. J Proteome Res 20:1063\u20131069. https:\/\/doi.org\/10.1021\/acs.jproteome.0c00313. ([cito:citesAsAuthority])","journal-title":"J Proteome Res"},{"key":"1044_CR11","unstructured":"Laurent Gatto JR (2017) MSnbase. https:\/\/bioconductor.org\/packages\/MSnbase. Accessed 24 May 2025 [cito:citesAsAuthority]"},{"key":"1044_CR12","unstructured":"Colin A. Smith <Csmith@Scripps. Edu> RTC (2024) Xcms: LC-MS and GC-MS Data Analysis. https:\/\/bioconductor.org\/packages\/xcms. Accessed 6 Dec 2024 [cito:citesAsAuthority]"},{"key":"1044_CR13","unstructured":"Gatto L, Gibb S, Rainer J (2024) R for mass spectrometry. https:\/\/www.rformassspectrometry.org\/. Accessed 6 Dec 2024"},{"key":"1044_CR14","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/s13321-020-00477-w","volume":"13","author":"R Helmus","year":"2021","unstructured":"Helmus R, ter Laak TL, van Wezel AP et al (2021) patRoon: open source software platform for environmental mass spectrometry based non-target screening. J Cheminform 13:1. https:\/\/doi.org\/10.1186\/s13321-020-00477-w. ([cito:citesAsAuthority])","journal-title":"J Cheminform"},{"key":"1044_CR15","doi-asserted-by":"publisher","first-page":"3","DOI":"10.1186\/s13321-016-0115-9","volume":"8","author":"C Ruttkies","year":"2016","unstructured":"Ruttkies C, Schymanski EL, Wolf S et al (2016) MetFrag relaunched: Incorporating strategies beyond in silico fragmentation. J Cheminform 8:3. https:\/\/doi.org\/10.1186\/s13321-016-0115-9. ([cito:citesAsAuthority])","journal-title":"J Cheminform"},{"key":"1044_CR16","unstructured":"Stravs M, Schymanski E, Neumann S, et al (2020) RMassBank: workflow to process tandem MS files and build MassBank records. https:\/\/bioconductor.org\/packages\/RMassBank\/. Accessed 20 Jan 2020 [cito:citesAsAuthority]"},{"key":"1044_CR17","doi-asserted-by":"publisher","first-page":"89","DOI":"10.1002\/jms.3131","volume":"48","author":"MA Stravs","year":"2013","unstructured":"Stravs MA, Schymanski EL, Singer HP, Hollender J (2013) Automatic recalibration and processing of tandem mass spectra using formula annotation: recalibration and processing of MS\/MS spectra. J Mass Spectrom 48:89\u201399. https:\/\/doi.org\/10.1002\/jms.3131. ([cito:citesAsAuthority])","journal-title":"J Mass Spectrom"},{"key":"1044_CR18","doi-asserted-by":"publisher","DOI":"10.1016\/j.envint.2021.106885","volume":"158","author":"J Krier","year":"2022","unstructured":"Krier J, Singh RR, Kondi\u0107 T et al (2022) Discovering pesticides and their TPs in Luxembourg waters using open cheminformatics approaches. Environ Int 158:106885. https:\/\/doi.org\/10.1016\/j.envint.2021.106885. ([cito:citesAsAuthority])","journal-title":"Environ Int"},{"key":"1044_CR19","unstructured":"Wikipedia (2025) Modular programming. In: Wikipedia. https:\/\/en.wikipedia.org\/wiki\/Modular_programming. Accessed 24 May 2025"},{"key":"1044_CR20","unstructured":"Cheng J, Sievert C, Schloerke B, et al (2024) Htmltools: tools for HTML. https:\/\/cran.r-project.org\/web\/packages\/htmltools\/index.html. Accessed 18 Nov 2024 [cito:citesAsAuthority]"},{"key":"1044_CR21","unstructured":"Hester J, Henry L, M\u00fcller K, et al (2024) Withr: run code \u2018With\u2019 temporarily modified global state. https:\/\/cran.r-project.org\/web\/packages\/withr\/index.html. Accessed 18 Nov 2024 [cito:citesAsAuthority]"},{"key":"1044_CR22","unstructured":"Barrett T, Dowle M, Srinivasan A, et al (2024) Data.table: extension of \u2019data.frame\u2019. https:\/\/cran.r-project.org\/web\/packages\/data.table\/index.html. Accessed 18 Nov 2024 [cito:citesAsAuthority]"},{"key":"1044_CR23","unstructured":"Garbett SP, Stephens J, Simonov K, et al (2024) Yaml: methods to convert R data to YAML and back. https:\/\/cran.r-project.org\/web\/packages\/yaml\/index.html. Accessed 18 Nov 2024 [cito:citesAsAuthority]"},{"key":"1044_CR24","unstructured":"Neuwirth E (2022) RColorBrewer: ColorBrewer Palettes. https:\/\/cran.r-project.org\/web\/packages\/RColorBrewer\/index.html. Accessed 17 Nov 2024 [cito:citesAsAuthority]"},{"key":"1044_CR25","unstructured":"Xie Y, Cheng J, Tan X, et al (2024) DT: a wrapper of the JavaScript library \u2019DataTables\u2019. https:\/\/cran.r-project.org\/web\/packages\/DT\/index.html. Accessed 18 Nov 2024 [cito:citesAsAuthority]"},{"key":"1044_CR26","doi-asserted-by":"publisher","first-page":"5738","DOI":"10.1021\/acs.analchem.5b00941","volume":"87","author":"M Loos","year":"2015","unstructured":"Loos M, Gerber C, Corona F et al (2015) Accelerated isotope fine structure calculation using pruned transition trees. Anal Chem 87:5738\u20135744. https:\/\/doi.org\/10.1021\/acs.analchem.5b00941. ([cito:citesAsAuthority])","journal-title":"Anal Chem"},{"key":"1044_CR27","doi-asserted-by":"publisher","unstructured":"Wickham H (2016) ggplot2. http:\/\/link.springer.com\/https:\/\/doi.org\/10.1007\/978-3-319-24277-4. Accessed 13 Nov 2024 [cito:citesAsAuthority]","DOI":"10.1007\/978-3-319-24277-4"},{"key":"1044_CR28","unstructured":"Wilke CO (2024) Cowplot: streamlined plot theme and plot annotations for \u2019ggplot2\u2019. https:\/\/cran.r-project.org\/web\/packages\/cowplot\/index.html. Accessed 18 Nov 2024 [cito:citesAsAuthority]"},{"key":"1044_CR29","doi-asserted-by":"publisher","first-page":"31","DOI":"10.1021\/ci00057a005","volume":"28","author":"D Weininger","year":"1988","unstructured":"Weininger D (1988) SMILES, a chemical language and information system. 1. introduction to methodology and encoding rules. J Chem Inf Comput Sci 28:31\u201336. https:\/\/doi.org\/10.1021\/ci00057a005. ([cito:citesAsAuthority])","journal-title":"J Chem Inf Comput Sci"},{"key":"1044_CR30","doi-asserted-by":"publisher","first-page":"208","DOI":"10.32614\/RJ-2021-048","volume":"13","author":"H Bengtsson","year":"2021","unstructured":"Bengtsson H (2021) A unifying framework for parallel and distributed processing in R using futures. R J 13:208. https:\/\/doi.org\/10.32614\/RJ-2021-048. ([cito:citesAsAuthority])","journal-title":"R J"},{"key":"1044_CR31","doi-asserted-by":"publisher","first-page":"19","DOI":"10.1186\/s13321-021-00489-0","volume":"13","author":"EL Schymanski","year":"2021","unstructured":"Schymanski EL, Kondi\u0107 T, Neumann S et al (2021) Empowering large chemical knowledge bases for exposomics: PubChemLite meets MetFrag. J Cheminform 13:19. https:\/\/doi.org\/10.1186\/s13321-021-00489-0. ([cito:citesAsAuthority])","journal-title":"J Cheminform"},{"key":"1044_CR32","doi-asserted-by":"publisher","DOI":"10.1021\/acs.estlett.4c01003","author":"A Elapavalore","year":"2025","unstructured":"Elapavalore A, Ross DH, Grou\u00e8s V et al (2025) PubChemLite plus collision cross section (CCS) values for enhanced interpretation of nontarget environmental data. Environ Sci Technol Lett. https:\/\/doi.org\/10.1021\/acs.estlett.4c01003. ([cito:citesAsAuthority])","journal-title":"Environ Sci Technol Lett"},{"key":"1044_CR33","unstructured":"Elapavalore A (2025) Shinyscreen container registry. In: GitLab. https:\/\/gitlab.com\/uniluxembourg\/lcsb\/eci\/shinyscreen\/container_registry. Accessed 19 Mar 2025 [cito:citesAsAuthority]"},{"key":"1044_CR34","doi-asserted-by":"publisher","first-page":"58","DOI":"10.1021\/acsenvironau.1c00008","volume":"1","author":"RR Singh","year":"2021","unstructured":"Singh RR, Lai A, Krier J et al (2021) Occurrence and distribution of pharmaceuticals and their transformation products in luxembourgish surface waters. ACS Environ Au 1:58\u201370. https:\/\/doi.org\/10.1021\/acsenvironau.1c00008. ([cito:citesAsAuthority])","journal-title":"ACS Environ Au"},{"key":"1044_CR35","unstructured":"IPB Halle (2024) MetFrag web. https:\/\/msbi.ipb-halle.de\/MetFrag\/. Accessed 3 Dec 2024"},{"key":"1044_CR36","unstructured":"IPB Halle (2024) MetFrag command line (CL). http:\/\/ipb-halle.github.io\/MetFrag\/projects\/metfragcl\/. Accessed 3 Dec 2024"}],"container-title":["Journal of Cheminformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s13321-025-01044-x.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1186\/s13321-025-01044-x\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s13321-025-01044-x.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,6,20]],"date-time":"2025-06-20T08:44:13Z","timestamp":1750409053000},"score":1,"resource":{"primary":{"URL":"https:\/\/jcheminf.biomedcentral.com\/articles\/10.1186\/s13321-025-01044-x"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,6,20]]},"references-count":36,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2025,12]]}},"alternative-id":["1044"],"URL":"https:\/\/doi.org\/10.1186\/s13321-025-01044-x","relation":{"has-preprint":[{"id-type":"doi","id":"10.26434\/chemrxiv-2025-kgz6g","asserted-by":"object"}]},"ISSN":["1758-2946"],"issn-type":[{"value":"1758-2946","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,6,20]]},"assertion":[{"value":"20 March 2025","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"12 June 2025","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"20 June 2025","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"The authors do not have any competing interests to declare.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"98"}}