{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,23]],"date-time":"2026-10-23T19:21:20Z","timestamp":1792783280998,"version":"4.5.0"},"reference-count":31,"publisher":"Springer Science and Business Media LLC","issue":"5","license":[{"start":{"date-parts":[[2026,9,25]],"date-time":"2026-09-25T00:00:00Z","timestamp":1790294400000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2026,9,25]],"date-time":"2026-09-25T00:00:00Z","timestamp":1790294400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"funder":[{"name":"Curtin University","id":[{"id":"https:\/\/ror.org\/02n415q13","id-type":"ROR","asserted-by":"crossref"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Metabolomics"],"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Introduction<\/jats:title>\n                    <jats:p>Targeted metabolic phenotyping by liquid chromatography\u2013tandem mass spectrometry (LC-MS\/MS) relies on a fragmented toolchain of proprietary vendor formats, manual integration steps, and ad hoc quality-control (QC) scripts, introducing user- and laboratory-level variation that undermines reproducibility and confounds cross-laboratory and retrospective comparison.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Objectives<\/jats:title>\n                    <jats:p>To provide an open-source, R-native workflow for targeted multiple reaction monitoring (MRM\/SRM) mass spectrometry data that consolidates vendor file conversion, peak integration, and QC reporting into a single reproducible pipeline while preserving auditable, human-in-the-loop peak review.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Methods<\/jats:title>\n                    <jats:p>MStargetR builds on msConvert and Skyline through three modules: msConvertR (vendor-to-mzML conversion), PeakForgeR (peak boundary optimisation and automated peak integration executed through Skyline), and qcCheckR (normalisation, concentration calculation, signal and batch correction, and reporting). Additionally, MStargetR has a standalone correction module and a Shiny graphical user interface. Third-party tools are pinned in version-controlled Docker images (with Apptainer support for high-performance computing), and each analytical plate emits a fully populated sky document for inspection and reimport.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>Applied to a published targeted lipidomics dataset of 128 human plasma samples targeting 1,161 lipid species, MStargetR processed all samples end-to-end, recovering all 1,161 targeted lipid features, 949 of which (81.7%) were detected and returned RSD\u2009&lt;\u200930% across replicated long-term reference QCs. Analysis scaled linearly to 4,200 samples, averaging 4.1\u00a0s per sample.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusion<\/jats:title>\n                    <jats:p>MStargetR delivers automated batch processing, auditable peak review, and a documented QC layer in a single reproducible pipeline, supporting FAIR-aligned targeted metabolomics.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1007\/s11306-026-02541-2","type":"journal-article","created":{"date-parts":[[2026,9,25]],"date-time":"2026-09-25T17:55:52Z","timestamp":1790358952000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["MStargetR: a reproducible, containerised workflow for end-to-end targeted (MRM\/SRM) mass spectrometry data processing in R"],"prefix":"10.1007","volume":"22","author":[{"ORCID":"https:\/\/orcid.org\/0009-0008-5829-540X","authenticated-orcid":false,"given":"Harrison","family":"Szemray","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5384-6788","authenticated-orcid":false,"given":"Vimalnath","family":"Nambiar","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3823-8271","authenticated-orcid":false,"given":"Dana","family":"Hicks","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9193-0462","authenticated-orcid":false,"given":"Samantha","family":"Lodge","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3416-2572","authenticated-orcid":false,"given":"Julien","family":"Wist","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9649-425X","authenticated-orcid":false,"given":"Nathan G.","family":"Lawler","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9088-4799","authenticated-orcid":false,"given":"Luke","family":"Whiley","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2026,9,25]]},"reference":[{"key":"2541_CR1","doi-asserted-by":"crossref","unstructured":"Adams, K. 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