Evaluation of peak alignment performance of commercial and open-source tools for GC×GC-MS based non-targeted...

Comprehensive two-dimensional gas chromatography-mass spectrometry (GC × GC-MS) 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 × GC-MS peak alignment and benchmark its performance within practical GC × GC-MS 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 >150 reference compounds at concentrations of 0.5, 5.0, and 50 pg/μl 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 pg/μl, Guineu and jAligner4GCxGC detected 94% and 92% of compounds, respectively, outperforming Sync 2D (82%). At 5 and 0.5 pg/μl, 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 min for jAligner4GCxGC, and 9 min 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 × GC-MS peak alignment.