To begin HPTLC, a stationary phase has to be determined to separate different compounds within a mixture. Around 90% of all pharmaceutical separations are performed on normal phase silica gel; however, other stationary phases such as alumina can be used for samples with dissociating compounds and cellulose for ionic compounds. The reverse-phase HPTLC method (similar methodology to reverse-phase TLC) is used for compounds with high polarity. After the selection of the stationary phase, plates are generally washed with methanol and dried in an oven to remove excess solvent.
Selection for the mobile phase is one of the most important processes of HPTLC and follows a trial and error pathway. However, the PRISMA system stands as a guideline for finding the optimal mobile phase. The mobile phase is dependent on the absorptivity of the stationary phase and the composition of the compound of interest. The compound is first tested with solutions such as diethyl ether, ethanol, dichloromethane, chloroform for normal phase HPTLC, or solutions such as methanol, acetonitrile, and tetrahydrofuran for reverse phase HPTLC. The retardation factors (Rf) of the compounds with the selected solvent are then analyzed and the solvent that gives the largest Rf is chosen to be the mobile phase for the compound. Then, the mobile solvent strength is tested against hexane (for normal HPTLC) and water (for reverse-phase HPTLC) to determine the need for adjustment.
Notable HPTLC devices such as the Linomat 5 and the Automatic TLC Sampler 4 (ATS 4) by CAMAG function very similarly by having the automated spray-on sample application technique. This automated spray-on technique is useful to overcome the uncertainty in droplet size and position when the sample is applied to the TLC plate by hand.  Additionally, automation provides high resolution and narrow bands since the solvent evaporates immediately as the sample makes contact with the plate. One approach to automation has been the use of piezoelectric devices and inkjet printers for applying the sample. Alternatively, the Nanomat 4 and ATS 4 by CAMAG are manually operated where the sample is applied via spot application using a capillary pipette.
Upon chromatographic detection, HPTLC plates are usually developed in saturated twin-trough chambers with filter paper for optimal outcomes. However, flat-bottom chambers and horizontal-development chambers are also used for specific compounds. A general mechanism for the HPTLC device goes as follows. A fitted filter paper is placed in the rear trough of the chamber and the mobile phase is poured through the rear trough to ensure complete solvent absorption of the filter paper. The chamber is then tilted to ~45° so both troughs are equal in solvent volume and left alone to equilibrate for ~20 mins. Finally, the HPTLC plate is placed in the chamber to develop. Between each sample reading, the mobile phase and filter paper are changed to ensure the best outcomes.
The spot capacity (analogous to peak capacity in HPLC) can be increased by developing the plate with two different solvents, using two-dimensional chromatography. The procedure begins with development of a sample loaded plate with first solvent. After removing it, the plate is rotated 90° and developed with a second solvent.