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A simple, rapid chemical coating and patterning method was developed and optimized for paper-based substrates for use in paper spray mass spectrometry (PS-MS). A variety of chlorosilanes were explored for coating paper substrates, and their effectiveness in forming hydrophobic surfaces was characterized via contact angle goniometry, scanning electron microscopy, and energy dispersive X-ray spectroscopy. Trichloromethylsilane was selected as the primary coating agent because of the short time required to produce a hydrophobic surface (contact angle > 130°), as well as the ease of patterning. Patterning was performed using 3D-printed masks and an oxygen/plasma cleaner. Optimal mask thickness and oxygen/plasma cleaning parameters were determined to produce channels varying from 0.5 to 2.5 mm in width. The effectiveness of the patterned substrates for PS-MS was determined via analysis of four antiretrovirals: emtricitabine, lamivudine, efavirenz, and dolutegravir. Calibration curves were made for each antiretroviral at varying channel widths, and the limits of detection and limits of quantification for each drug were determined. These results show that this patterning method results in an average 7.2-fold improvement in sensitivity and an average 190-fold improvement in limits of detection over uncoated paper substrates in a neat matrix. In a proof-of-concept experiment, calibration curves were generated for each antiretroviral in urine. A patterned paper substrate with a 2-mm channel resulted in an average 7.4-fold improvement in sensitivity and an average 18-fold improvement in limits of detection over uncoated paper substrates.