A method to optimize different objectives (total analysis time, total peak capacity, and total dilution) has been applied to comprehensive two-dimensional liquid chromatography. The approach is based on Pareto-optimality, and it yields optimal parameters (column particle sizes, column diameters, and modulation times). Losses in the peak capacities in the first dimension (due to undersampling) and in the second dimension (due to high injection volumes) have been taken into account. The first effect (detection band broadening) reduces the original peak capacity by about a half, the second effect can reduce the total peak capacity by an additional half. Thus, the total loss in peak capacity may be 75% of its theoretical value. Analytical expressions to calculate these effects under gradient and isocratic conditions are derived. Of particular interest is the study of the optimal modulation times, which corresponded to between 2 and 3 two-dimensional runs per one-dimensional peak. The effects of using gradient or isocratic elution, conventional (40 MPa) or "ultra-high" (100 MPa) pressures, and focusing between the first and second dimensions were also studied. A trade-off between total peak capacity, total analysis time, and total dilution can be established.

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