Coupling of multiway and multiset modeling methods with hyphenated chromatographic data for second-order calibration purposes allows the quantification of multiple target analytes in highly complex samples, which otherwise would be impossible or at least a very hard task using univariate calibration scenario. In this regard, there are some chromatographic challenges that complicate attaining the best quantification efficiency through the highlighted advantages such as increased sensitivity and selectivity and the well-known second-order advantage. The present paper tries to overview these issues and to address the most usable strategies for their handling with a special focus on the relevant recent studies in quantitation field. KEYWORDS challenges, complex samples, hyphenated chromatography, multiway and multiset methods, quantitation 1 | INTRODUCTION One of the most important factors that enhances the quality of our life is the depth of our information about the composition of natural or synthetic materials, such as the presence of toxic or potentially dangerous substances in food products, personal care products, environmental resources, and so on. In fact, numerous similar and highly concerned examples can be noted, in addition to the cases that are recently spotlighted, like identification and quantification of new banned drugs in slimming herbal products.Chromatographic analytical systems have been widely used for analysis of complex samples, such as bioanalytical field, food analysis, and metabolomics. Hyphenated chromatographic techniques, such as high-performance liquid chromatography coupled with diode array detection or fast-scanning fluorescence detection (HPLC-DAD/FSFD), liquid chromatography mass spectrometry (LC-MS), and gas chromatography mass spectrometry (GC-MS), have found their place in most of analytical laboratories and routinely provide valuable qualitative and quantitative information. As a result, such powerful techniques enable the analyst to efficiently analyze much more complex samples of various nature. This is especially true for chromatographic systems coupled with mass spectrometric detection, because of additional selectivity and sensitivity, which is the intrinsic and advantageous property of mass spectrometers. However, parameter optimizations in chromatographic systems (especially in LC systems) is a necessary and often laborious step in the path to obtain the best performance of the instrument. In fact, success of the chromatographic separation, robustness and stability of the outcome signal, strongly depends on chromatographic equipment, such as pumping and solvent delivery system, detector performance, column type and its steadiness, and temperature control. Although some chromatographic troubles such as problematic solvent peak, a nonstable or nonuniform background offset, peak tailing or fronting, coelution of analytes with each other or matrix constituents, retention time shifts in different runs, peak shape changes, and a narrow linear response range may usually exist.Fi...