Comprehensive two-dimensional gas chromatography coupled to mass spectrometry (GC×GC- MS) is one of the most powerful analytical platforms suitable for the qualitative and quantitative investigation of complex samples. However, while qualitative analysis has been the main area of interest in many GC×GC studies, the focus on quantitative analysis is still less frequently reported. Several quantitative approaches have been proposed, but they often require labour-intensive procedures and the need for constant user supervision. However, the time consumption of those procedures and specific problems are usually not described in detail. Peak integration plays a pivotal role in the reliability of quantitative results. Although many improvements have been made in GC×GC, data handling and data integration are still some of the most challenging and timeconsuming steps during data processing, representing a major source of uncertainty in the results. The development of GC×GC data analysis has already made a lot of progress but is not yet fully mature. Here we provide an overview of the most common quantification approaches currently applied to GC×GC data, with focus on peak integration strategies, as well as on their merits and limitations. Moreover, common challenges regarding peak finding and subsequent integration, such as peak splitting, misassignment, or inconsistent integration, which typically have to be corrected manually, will be discussed. In practice, especially the comparison and analysis of large sample sets demands robust and automated data handling approaches, to avoid time-consuming post-processing. Finally, we introduce the principles of a simplified approach for reliable quantification of polycyclic aromatic hydrocarbons (PAHs) in complex real-world samples, such as atmospheric particulate matter. Acknowledgments This Project is supported by the Federal Ministry for Economic Affairs and Climate Action (BMWK) on the basis of a decision by the German Bundestag (grant ID: KK5037301JO0).