Abstract Applied cold atmospheric plasma allows for the controlled delivery of reactive oxygen and nitrogen species tailored for specific applications. Through the manipulation of the plasma parameters, feed gases, and careful consideration of the environment surrounding the treatment target, selective chemistries that preferentially influence the target can be produced and delivered. To demonstrate this, the COST reference microscale atmospheric pressure plasma jet is used to study the generation and transport of O and <?CDATA $^\cdot$?> <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" overflow="scroll"> <mml:mrow> <mml:msup> <mml:mrow /> <mml:mo>⋅</mml:mo> </mml:msup> </mml:mrow> </mml:math> OH from the gas phase through the liquid to the biological model target cysteine. Relative and absolute species densities of <?CDATA $^\cdot$?> <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" overflow="scroll"> <mml:mrow> <mml:msup> <mml:mrow /> <mml:mo>⋅</mml:mo> </mml:msup> </mml:mrow> </mml:math> OH and O are measured in the gas phase through laser induced fluorescence (LIF) and two-photon absorption LIF respectively. The transport of these species is followed into the liquid phase by hydrogen peroxide quantification and visualized by a fluorescence assay. Modifications to the model biological sample cysteine exposed to <?CDATA $^\cdot$?> <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" overflow="scroll"> <mml:mrow> <mml:msup> <mml:mrow /> <mml:mo>⋅</mml:mo> </mml:msup> </mml:mrow> </mml:math> OH and H 2 O 2 dominated chemistry (He/H 2 O (0.25%)) and O dominated chemistry (He/O 2 (0.6%)) is measured by FTIR spectroscopy. The origin of these species that modify cysteine is considered through the use of heavy water (H <?CDATA $_2^{18}$?> <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" overflow="scroll"> <mml:mrow> <mml:msubsup> <mml:mrow /> <mml:mn>2</mml:mn> <mml:mrow> <mml:mn>18</mml:mn> </mml:mrow> </mml:msubsup> </mml:mrow> </mml:math> O) and mass spectrometry. It is found that the reaction pathways differ significantly for He/O 2 and He/H 2 O. Hydrogen peroxide is formed mainly in the liquid phase in the presence of a substrate for He/O 2 whereas for He/H 2 O it forms in the gas phase. The liquid chemistry resulting from the He/O 2 admixture mainly targets the sulfur moiety of cysteine for oxidation up to irreversible oxidation states, while He/H 2 O treatment leads preferentially to reversible oxidation products. The more O or OH/H 2 O 2 dominated chemistry produced by the two gas admixtures studied offers the possibility to select species for target modification.