Dataset_MStargetR_Szemray_2026

InformationDataset to reproduce the results in Szemray et al. (2026), MStargetR: A modular R package for automating targeted mass spectrometry-based metabolic phenotyping pipelines, submitted for review to Phenomics.HighlightsMStargetR runs on Windows, macOS, and Linux host systems that support AMD64 architecture.I/O: Input, proprietary vendor files and method templates. Output, standardised and reproducible analysis ready concentration data and a comprehensive quality control report.Pipeline consists of:MsConvertR wraps the ProteoWizard msConvert Docker image to convert proprietary vendor files into mzML, the HUPO‑PSI community standard.PeakForgeR performs retention time optimisation/tuning, peak boundary refinement, and integration via the Skyline Docker image, generating analytical plate-level results.QcCheckR implements single-point concentration calculation using internal standards, quality control sample-based signal drift correction (QC-RFSC), and comprehensive interactive control charts for quality control reporting.MaterialsThis repository contains all of the necessary resources to recreate the casestudy in Szemray et al. (2026), MStargetR: A modular R package for automating targeted mass spectrometry-based metabolic phenotyping pipelinesProject TeamHarrison Szemray 1,2, Vimalnath Nambiar1, Dana Hicks1,2, Samantha Lodge 1, Julien Wist 1,3, Nathan Lawler 1,4, and Luke Whiley* 1,5,6,71. Centre for Computational and Systems Medicine, Health Futures Institute, Murdoch University, Perth, Western Australia, Australia.2. School of Medical, Molecular, and Forensic Science, Murdoch University, Perth, Western Australia, Australia.3. Chemistry Department, Universidad del Valle, Cali, 76001, Colombia4. School of Allied Health, College of Health and Education, Murdoch University, Perth, Western Australia, Australia.5. Curtin Medical Research Institute, Curtin University, Perth, Western Australia, Australia6. School of Diagnostic and Therapeutic Sciences, Curtin University, Perth, Western Australia, Australia7. Dementia Centre of Excellence, Enable Institute, Curtin University, Perth, Western Australia, Australia*correspondence: [e-mail] and Funding: H.S. would like to acknowledge that this research was supported by an Australian Government Research Training Program (RTP) Scholarship [DOI: Research Training Program - Department of Education, Australian Government]. L.W. would like to acknowledge support from Dementia Australia and the Royce Simmons Foundation through their mid-career fellowship.Conflicts of Interest: The authors declare that they have no conflicts of interest.Author Contributions: H.S. and L.W. conceptualised and developed the software. H.S. wrote the manuscript. H.S., V.N., N.L., J.W., and L.W. contributed to the design of the software. H.S., D.H., and L.W. performed package testing. H.S., L.W., N.L., J.W., and S.L. contributed to the revision of the manuscript. All authors read and approved the final manuscript.Github link: https://github.com/Hszemray/MStargetR/tree/master