The present disclosure relates to the use of aptamers in solid phase extraction, chromatography and chromatography-mass spectrometry systems. More specifically, the present disclosure relates to the use of aptamers in SPE and chromatography systems to selectively retain, extract and/or pre-concentrate target molecule(s) having a specific affinity for the particular aptamer(s). The target molecule(s) can be further analyzed by mass spectrometry with limited interferences and/or enhanced sensitivity.