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mzQuality: An Open-Source Software Tool for Quality Monitoring and Reporting of Targeted Mass Spectrometry Measurements.

dc.rights.licenseopenen_US
dc.contributor.authorVAN DER PEET, Marielle
dc.contributor.authorMAAS, Pascal
dc.contributor.authorWEGRZYN, Agnieszka
dc.contributor.authorLAMONT, Lieke
dc.contributor.authorFLEMING, Ronan
hal.structure.identifierBordeaux population health [BPH]
dc.contributor.authorBORDES, Constance
hal.structure.identifierBordeaux population health [BPH]
dc.contributor.authorDEBETTE, Stéphanie
dc.contributor.authorHARMS, Amy
dc.contributor.authorHANKEMEIER, Thomas
dc.contributor.authorKINDT, Alida
dc.date.accessioned2025-08-29T08:30:29Z
dc.date.available2025-08-29T08:30:29Z
dc.date.issued2025-08-06
dc.identifier.issn1879-1123en_US
dc.identifier.urihttps://oskar-bordeaux.fr/handle/20.500.12278/207525
dc.description.abstractEnAnalyzing metabolites using mass spectrometry provides valuable insight into an individual's health or disease status. However, various sources of experimental variation can be introduced during sample handling, preparation, and measurement, which can negatively affect the data. Quality assurance and quality control practices are essential to ensuring accurate and reproducible metabolomics data. These practices include measuring reference samples to monitor instrument stability, blank samples to evaluate the background signal, and strategies to correct for changes in instrumental performance. In this context, we introduce mzQuality, a user-friendly, open-source R-Shiny app designed to assess and correct technical variations in mass spectrometry-based metabolomics data. It processes peak-integrated data independently of vendor software and provides essential quality control features, including batch correction, outlier detection, and background signal assessment, and it visualizes trends in signal or retention time. We demonstrate its functionality using a data set of 419 samples measured across six batches, including quality control samples. mzQuality visualizes data through sample plots, PCA plots, and violin plots, which illustrate its ability to reduce the effect of experiment variation. Compound quality is further assessed by evaluating the relative standard deviation of quality control samples and the background signal from blank samples. Based on these quality metrics, compounds are classified into confidence levels. mzQuality provides an accessible solution to improve the data quality without requiring prior programming skills. Its customizable settings integrate seamlessly into research workflows, enhancing the accuracy and reproducibility of the metabolomics data. Additionally, with an R-compatible output, the data are ready for statistical analysis and biological interpretation.
dc.language.isoENen_US
dc.rightsAttribution 3.0 United States*
dc.rights.urihttp://creativecommons.org/licenses/by/3.0/us/*
dc.subject.enSoftware
dc.subject.enQuality Control
dc.subject.enMetabolomics
dc.subject.enMass Spectrometry
dc.subject.enReproducibility of Results
dc.subject.enHumans
dc.title.enmzQuality: An Open-Source Software Tool for Quality Monitoring and Reporting of Targeted Mass Spectrometry Measurements.
dc.title.alternativeJ Am Soc Mass Spectromen_US
dc.typeArticle de revueen_US
dc.identifier.doi10.1021/jasms.5c00073en_US
dc.subject.halSciences du Vivant [q-bio]/Santé publique et épidémiologie
dc.identifier.pubmed40711931en_US
bordeaux.journalJournal of The American Society for Mass Spectrometryen_US
bordeaux.page1669-1676en_US
bordeaux.volume36en_US
bordeaux.hal.laboratoriesBordeaux Population Health Research Center (BPH) - UMR 1219en_US
bordeaux.issue8en_US
bordeaux.institutionUniversité de Bordeauxen_US
bordeaux.institutionINSERMen_US
bordeaux.teamELEANOR_BPHen_US
bordeaux.peerReviewedouien_US
bordeaux.inpressnonen_US
bordeaux.identifier.funderIDHorizon 2020 Framework Programmeen_US
bordeaux.import.sourcepubmed
hal.identifierhal-05229522
hal.version1
hal.date.transferred2025-08-30T23:05:06Z
hal.popularnonen_US
hal.audienceInternationaleen_US
hal.exporttrue
workflow.import.sourcepubmed
dc.rights.ccPas de Licence CCen_US
bordeaux.COinSctx_ver=Z39.88-2004&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.jtitle=Journal%20of%20The%20American%20Society%20for%20Mass%20Spectrometry&rft.date=2025-08-06&rft.volume=36&rft.issue=8&rft.spage=1669-1676&rft.epage=1669-1676&rft.eissn=1879-1123&rft.issn=1879-1123&rft.au=VAN%20DER%20PEET,%20Marielle&MAAS,%20Pascal&WEGRZYN,%20Agnieszka&LAMONT,%20Lieke&FLEMING,%20Ronan&rft.genre=article


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