{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,24]],"date-time":"2026-09-24T21:10:57Z","timestamp":1790284257962,"version":"4.1.0"},"reference-count":37,"publisher":"Oxford University Press (OUP)","issue":"5","license":[{"start":{"date-parts":[[2026,9,2]],"date-time":"2026-09-02T00:00:00Z","timestamp":1788307200000},"content-version":"vor","delay-in-days":1,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,9,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Comprehensive two-dimensional gas chromatography\u2013mass spectrometry (GC\u2009\u00d7\u2009GC\u2013MS) is a powerful tool for analysing complex mixtures, but its wide use is limited by the lack of robust and transparent inter-sample peak alignment workflows. Commercial solutions often rely on proprietary algorithms, while user-friendly open-source alternatives remain scarce. Here, we introduce jAligner4GCxGC, a new open-access Julia package for inter-sample GC\u2009\u00d7\u2009GC\u2013MS peak alignment and benchmark its performance within practical GC\u2009\u00d7\u2009GC\u2013MS data processing workflows against Guineu (open-source) and ChromaTOF Sync 2D (commercial). The package performs data preprocessing, alignment, and postprocessing including feature merging, library searching, and compound data retrieval. Three indoor dust samples, including certified reference material, were spiked with &amp;gt;150 reference compounds at concentrations of 0.5, 5.0, and 50\u00a0pg\/\u03bcl and analysed using workflows optimized for each application. Performance was evaluated based on recovery of correctly aligned spiked compounds and workflow processing time. Because the software packages differ in peak detection and preprocessing, comparisons involving Sync 2D should be interpreted at workflow rather than alignment algorithm level. At 50\u00a0pg\/\u03bcl, Guineu and jAligner4GCxGC detected 94% and 92% of compounds, respectively, outperforming Sync 2D (82%). At 5 and 0.5\u00a0pg\/\u03bcl, Sync 2D detected the highest proportions (79% and 71%), whereas Guineu and jAligner4GCxGC performed identically (68% and 33%). Alignment-related processing required seconds for Guineu, 4\u00a0min for jAligner4GCxGC, and 9\u00a0min for Sync 2D. However, Sync 2D provided the quickest end-to-end workflow. These results highlight practical trade-offs between commercial and open-source workflows and demonstrate that jAligner4GCxGC provides a transparent and reproducible solution for GC\u2009\u00d7\u2009GC\u2013MS peak alignment.<\/jats:p>","DOI":"10.1093\/bib\/bbag458","type":"journal-article","created":{"date-parts":[[2026,8,5]],"date-time":"2026-08-05T11:44:35Z","timestamp":1785930275000},"source":"Crossref","is-referenced-by-count":1,"title":["Evaluation of peak alignment performance of commercial and open-source tools for GC\u00d7GC\u2013MS based non-targeted screening"],"prefix":"10.1093","volume":"27","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-0090-809X","authenticated-orcid":false,"given":"Andriy","family":"Rebryk","sequence":"first","affiliation":[{"name":"Department of Chemistry, Chemical Biological Centre (KBC), Ume\u00e5 University , Linnaeus v\u00e4g 6, 901 87 Ume\u00e5 ,","place":["Sweden"]},{"name":"Amsterdam Institute for Life and Environment (A-LIFE), Faculty of Science, Vrije Universiteit Amsterdam , De Boelelaan 1108, 1081 HZ Amsterdam ,","place":["The Netherlands"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Denice","family":"van Herwerden","sequence":"additional","affiliation":[{"name":"Van \u2019t Hoff Institute for Molecular Sciences (HIMS), University of Amsterdam , 1090 GD Amsterdam ,","place":["The Netherlands"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Saer","family":"Samanipour","sequence":"additional","affiliation":[{"name":"Van \u2019t Hoff Institute for Molecular Sciences (HIMS), University of Amsterdam , 1090 GD Amsterdam ,","place":["The Netherlands"]},{"name":"UvA Data Science Center, University of Amsterdam , 1090 GD Amsterdam ,","place":["The Netherlands"]},{"name":"Queensland Alliance for Environmental Health Sciences (QAEHS), The University of Queensland , Cornwall Street, Woolloongabba 4102, QLD ,","place":["Australia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Peter","family":"Haglund","sequence":"additional","affiliation":[{"name":"Department of Chemistry, Chemical Biological Centre (KBC), Ume\u00e5 University , Linnaeus v\u00e4g 6, 901 87 Ume\u00e5 ,","place":["Sweden"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2026,9,2]]},"reference":[{"key":"2026090214054962500_ref1","doi-asserted-by":"publisher","first-page":"3058","DOI":"10.1021\/ac103308x","article-title":"Data analysis tool for comprehensive two-dimensional gas chromatography\/time-of-flight mass spectrometry","volume":"83","author":"Castillo","year":"2011","journal-title":"Anal Chem"},{"key":"2026090214054962500_ref2","doi-asserted-by":"publisher","first-page":"177639","DOI":"10.1016\/j.scitotenv.2024.177639","article-title":"Comprehensive characterization of European house dust contaminants: concentrations and profiles, geographical 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