{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,16]],"date-time":"2026-10-16T09:44:37Z","timestamp":1792143877302,"version":"4.4.0"},"publisher-location":"New York, NY","reference-count":18,"publisher":"Springer US","isbn-type":[{"value":"9781071655184","type":"print"},{"value":"9781071655191","type":"electronic"}],"license":[{"start":{"date-parts":[[2026,10,16]],"date-time":"2026-10-16T00:00:00Z","timestamp":1792108800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"},{"start":{"date-parts":[[2026,10,16]],"date-time":"2026-10-16T00:00:00Z","timestamp":1792108800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2027]]},"DOI":"10.1007\/978-1-0716-5519-1_3","type":"book-chapter","created":{"date-parts":[[2026,10,16]],"date-time":"2026-10-16T03:45:40Z","timestamp":1792122340000},"page":"29-54","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["An Open Infrastructure for Mass Spectrometry Data in R"],"prefix":"10.1007","author":[{"given":"Johannes","family":"Rainer","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marilyn","family":"De Graeve","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Philippine","family":"Louail","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sebastien","family":"Gibb","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Laurent","family":"Gatto","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2026,10,16]]},"reference":[{"issue":"1","key":"3_CR1","doi-asserted-by":"publisher","first-page":"110","DOI":"10.1074\/mcp.R110.000133","volume":"10","author":"L Martens","year":"2011","unstructured":"Martens L, Chambers M, Sturm M, Kessner D, Levander F, Shofstahl J, Tang WH, R\u00a8ompp A, Neumann S, Pizarro AD, Montecchi-Palazzi L, Tasman N, Coleman M, Reisinger F, Souda P, Hermjakob H, Binz P-A, Deutsch EW (2011) mzML\u2013a community standard for mass spectrometry data. Mol Cell Proteomics 10(1):110","journal-title":"Mol Cell Proteomics"},{"key":"3_CR2","doi-asserted-by":"publisher","unstructured":"Holman JD, Tabb DL, Mallick P (2014) Employing ProteoWizard to convert raw mass spectrometry data. Curr Protoc Bioinform 46:13.24.1\u201313.24.9. https:\/\/doi.org\/10.1002\/robo0471250953.bi1324s46","DOI":"10.1002\/robo0471250953.bi1324s46"},{"key":"3_CR3","doi-asserted-by":"publisher","unstructured":"Louail P, Brunius C, Garcia-Aloy M, Kumler W, Storz N, Stanstrup J, Treutler H, Vangeenderhuysen P, Witting M, Neumann S, Rainer J (2025) Xcms in peak form: now anchoring a complete metabolomics data preprocessing and analysis software ecosystem. Anal Chem 97(50):27639\u201327645. https:\/\/doi.org\/10.1021\/acs.analchem.5c04338. Epub 2025 Dec 8. PMID: 41359826; PMCID: PMC12750407","DOI":"10.1021\/acs.analchem.5c04338"},{"issue":"10","key":"3_CR4","doi-asserted-by":"publisher","DOI":"10.1186\/gb-2004-5-10-r80","volume":"5","author":"RC Gentleman","year":"2004","unstructured":"Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004) Bioconductor: open software development for computational biology and bioinformatics. Genome Biol 5(10):80. https:\/\/doi.org\/10.1186\/gb-2004-5-10-r80","journal-title":"Genome Biol"},{"issue":"2","key":"3_CR5","doi-asserted-by":"publisher","first-page":"115","DOI":"10.1038\/nmeth.3252","volume":"12","author":"W Huber","year":"2015","unstructured":"Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Ole\u00b4s AK, Pag\u2019es H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015) Orchestrating high-throughput genomic analysis with bioconductor. Nat Methods 12(2):115\u2013121. https:\/\/doi.org\/10.1038\/nmeth.3252","journal-title":"Nat Methods"},{"issue":"1","key":"3_CR6","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(1):1063\u20131069. https:\/\/doi.org\/10.1021\/acs.jproteome.0c00313 Epub 2020 Sep 28. PMID: 32902283","journal-title":"J Proteome Res"},{"key":"3_CR7","doi-asserted-by":"publisher","unstructured":"Deflandre G, Gibb S, Gatto L (2025) PSMatch: an R\/Bioconductor package to explore proteomics identification data. OSF Preprints. https:\/\/doi.org\/10.31219\/osf.io\/62v9pv1.osf.io\/62v9pv1","DOI":"10.31219\/osf.io\/62v9pv1.osf.io\/62v9pv1"},{"issue":"7","key":"3_CR8","doi-asserted-by":"publisher","first-page":"1166","DOI":"10.1038\/s41592-024-02299-2","volume":"21","author":"WJ Hutchison","year":"2024","unstructured":"Hutchison WJ, Keyes TJ, tidyomics Consortium, Crowell HL, Serizay J, Soneson C, Davis ES, Sato N, Moses L, Tarlinton B, Nahid AA, Kosmac M, Clayssen Q, Yuan V, Mu W, Park J-E, Mamede I, Ryu MH, Axisa P-P, Paiz P, Poon C-L, Tang M, Gottardo R, Morgan M, Lee S, Lawrence M, Hicks SC, Nolan GP, Davis KL, Papenfuss AT, Love MI, Mangiola S (2024) The tidyomics ecosystem: enhancing omic data analyses. Nat Methods 21(7):1166\u20131170","journal-title":"Nat Methods"},{"issue":"109","key":"3_CR9","doi-asserted-by":"publisher","first-page":"8070","DOI":"10.21105\/joss.08070","volume":"10","author":"MD Graeve","year":"2025","unstructured":"Graeve MD, Bittremieux W, Naake T, Huber C, Anagho-Mattanovich M, Hoffmann N, Marchal P, Chrone V, Louail P, Hecht H, Witting M, Rainer J (2025) SpectriPy: enhancing cross-language mass spectrometry data analysis with R and Python. J Open Source Softw 10(109):8070. https:\/\/doi.org\/10.21105\/joss.08070","journal-title":"J Open Source Softw"},{"issue":"10","key":"3_CR10","doi-asserted-by":"publisher","first-page":"918","DOI":"10.1038\/nbt.2377","volume":"30","author":"MC Chambers","year":"2012","unstructured":"Chambers MC, Maclean B, Burke R, Amodei D, Ruderman DL, Neumann S, Gatto L, Fischer B, Pratt B, Egertson J, Hoff K, Kessner D, Tasman N, Shulman N, Frewen B, Baker TA, Brusniak M-Y, Paulse C, Creasy D, Flashner L, Kani K, Moulding C, Seymour SL, Nuwaysir LM, Lefebvre B, Kuhlmann F, Roark J, Rainer P, Detlev S, Hemenway T, Huhmer A, Langridge J, Connolly B, Chadick T, Holly K, Eckels J, Deutsch EW, Moritz RL, Katz JE, Agus DB, MacCoss M, Tabb DL, Mallick P (2012) A cross-platform toolkit for mass spectrometry and proteomics. Nat Biotechnol 30(10):918\u2013920","journal-title":"Nat Biotechnol"},{"key":"3_CR11","doi-asserted-by":"publisher","unstructured":"Databases (R-SIG-DB), RSIG, Wickham H, M\u00a8uller K (2024) DBI: R database interface. https:\/\/doi.org\/10.32614\/CRAN.package.DBI . R package version 1.2.3. https:\/\/CRAN.R-project.org\/package=DBI","DOI":"10.32614\/CRAN.package.DBI"},{"issue":"10","key":"3_CR12","doi-asserted-by":"publisher","first-page":"1","DOI":"10.18637\/jss.v059.i10","volume":"59","author":"H Wickham","year":"2014","unstructured":"Wickham H (2014) Tidy data. J Stat Softw 59(10):1\u201323","journal-title":"J Stat Softw"},{"issue":"52","key":"3_CR13","doi-asserted-by":"publisher","first-page":"2411","DOI":"10.21105\/joss.02411","volume":"5","author":"F Huber","year":"2020","unstructured":"Huber F, Verhoeven S, Meijer C, Spreeuw H, Castilla E, Geng C, Van Der Hooft J, Rogers S, Belloum A, Diblen F, Spaaks J (2020) matchms\u2014 processing and similarity evaluation of mass spectrometry data. J Open Source Softw 5(52):2411. https:\/\/doi.org\/10.21105\/joss.02411","journal-title":"J Open Source Softw"},{"issue":"1","key":"3_CR14","doi-asserted-by":"publisher","first-page":"659","DOI":"10.1021\/acs.analchem.9b04884","volume":"92","author":"W Bittremieux","year":"2020","unstructured":"Bittremieux W (2020) spectrum utils: a Python package for mass spectrometry data processing and visualization. Anal Chem 92(1):659\u2013661. https:\/\/doi.org\/10.1021\/acs.analchem.9b04884","journal-title":"Anal Chem"},{"key":"3_CR15","doi-asserted-by":"publisher","unstructured":"De Graeve et al (2025) SpectriPy: Enhancing cross-language mass spectrometry data analysis with R and Python. J. Open Source Softw 10(109):8070. https:\/\/doi.org\/10.21105\/joss.08070","DOI":"10.21105\/joss.08070"},{"key":"3_CR16","doi-asserted-by":"publisher","unstructured":"Ushey K, Allaire J, Tang Y (2025) Reticulate: interface to \u2018Python\u2019. https:\/\/doi.org\/10.32614\/CRAN.package.reticulate. R package version 1.41.0. https:\/\/github.com\/rstudio\/reticulate","DOI":"10.32614\/CRAN.package.reticulate"},{"issue":"11","key":"3_CR17","doi-asserted-by":"publisher","first-page":"1788","DOI":"10.1039\/d3em00181d","volume":"25","author":"A Elapavalore","year":"2023","unstructured":"Elapavalore A, Kondi\u00b4c T, Singh RR, Shoemaker BA, Thiessen PA, Zhang J, Bolton EE, Schymanski EL (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(11):1788\u20131801. https:\/\/doi.org\/10.1039\/d3em00181d","journal-title":"Environ Sci Process Impacts"},{"key":"3_CR18","doi-asserted-by":"publisher","unstructured":"Morgan M, Shepherd L (2025) AnnotationHub: client to access AnnotationHub resources. https:\/\/doi.org\/10.18129\/B9.bioc.AnnotationHub. R package version 3.16.0. https:\/\/bioconductor.org\/packages\/AnnotationHub","DOI":"10.18129\/B9.bioc.AnnotationHub"}],"container-title":["Methods in Molecular Biology","Bioinformatics for Mass Spectrometry"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/978-1-0716-5519-1_3","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,10,16]],"date-time":"2026-10-16T08:52:30Z","timestamp":1792140750000},"score":1,"resource":{"primary":{"URL":"https:\/\/link.springer.com\/chapter\/10.1007\/978-1-0716-5519-1_3"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,10,16]]},"ISBN":["9781071655184","9781071655191"],"references-count":18,"URL":"https:\/\/doi.org\/10.1007\/978-1-0716-5519-1_3","relation":{},"ISSN":["1064-3745","1940-6029"],"issn-type":[{"value":"1064-3745","type":"print"},{"value":"1940-6029","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,10,16]]},"assertion":[{"value":"16 October 2026","order":1,"name":"first_online","label":"First Online","group":{"name":"ChapterHistory","label":"Chapter History"}},{"value":"The authors report no competing interests.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing Interests"}}]}}