In this study, we analyzed purine derivatives using multimatrix variation matrix-assisted laser desorption ionization mass spectrometry (MALDI MS) with α-cyano-4-hydroxycinnamic acid (CHCA), 1,5-diaminonaphtalene (DAN), 5-formylsalicylic acid (FSA), and 5-nitrosalicylic acid (NSA) as matrices. Further, we focused on the abstraction/attachment of hydrogen from/to analytes and detected [M - H]+, [M + 2H]+• and/or [M + 3H]+ in MALDI MS spectra of compounds containing nitrogen and/or carbonyl oxygen. Although [M - H]+ generation of purine compounds in MALDI MS with conventional matrices was challenging, NSA-MALDI MS effectively yielded the [M - H]+species of purine derivatives compared with CHCA, FSA, and DAN, and the [M - H]+/[M + H]+ ratios reflected their structures, such as the substituting groups and positions. We speculated that the molecular ion [M]+• generated and the subsequent hydrogen radical abstraction proceeded by NSA matrix from the α-carbon of the amine group. The nitro group (-NO2) of NSA can withdraw hydrogen radicals in photochemical reactions. The [M - H]+ of adenosine, guanosine, and inosine suggested that hydrogen abstraction occurred in the ribose unit. The xanthine isomer of paraxanthine was distinguished from those of theophylline and theobromine using their [M - H]+/[M + H]+ ratios obtained with NSA-MALDI MS. Additionally, [M + 2H]+• generated in DAN-MALDI MS of xanthine derivatives due to their carbonyl groups. The relative abundances of [M + 2H]+• of xanthine derivatives were much higher than those of the other purine derivatives such as adenine derivatives which generated [M + 3H]+ in their DAN-MALDI MS. DAN induced the hydrogen attachment of purine compounds because the amine group (-NH2) of DAN can give hydrogen radicals in photochemical reactions. NSA- and DAN-MALDI MS characterized purine derivatives and were useful for their structure categorization.