To produce peroxynitrite RAW 264.7 cells were pretreated overnight with interferon γ (IFN, 50 U/ml) and lipopolysaccharide (LPS, 1 μg/ml) followed by addition of PMA (1 μM) in the presence or absence of diphenyleneiodonium (DPI, 1 μM). During stimulation with PMA, o-MitoPhB(OH)2 (50 μM) was present and incubated for 1 h. Cell pellets were collected and processed as described in the protocol. The intensities of o-MitoPhOH were multiplied by a factor of 10 and intensities of cyclo-o-MitoPh and o-MitoPhNO2 were multiplied by 200 and 2000, respectively, to fit the same scale as of o-MitoPhB(OH)2. Solid lines represent the dominant transitions used for quantification and the dashed lines represent the reference transitions used for confirmation of peak identity.