Mass spectrometers on board spacecraft typically use either impact ionization or electron ionization (EI) as ion sources. Understanding the similarities and differences in the spectral signatures and fragmentation patterns produced by different techniques in mass spectrometry could elucidate the composition of organic compounds. Here we present a comparison between the mass spectra obtained through laser-induced liquid beam ion desorption (LILBID; proven to simulate the impact ionization mass spectra of ice grains) and EI mass spectra of pairs of low-mass, isomeric aldehydes and ketones. Our comparison confirms that EI produces more fragmentation of carbonyl compounds, particularly aldehydes, than LILBID. We find protonated molecular ions [M+H]+ in LILBID but molecular ions [M]+ in EI spectra. From the evaluated species, LILBID generally produces oxygen-carrying fragment ions (e.g., [CHO]+ and [C2H3O]+) in the mass ranges 26–30 and 39–44 u, while in EI, most ions in these ranges correspond to hydrocarbon fragments. The LILBID spectra additionally show mostly protonated oxygen-bearing fragments [CH3O]+ and [C2H5O]+ at m/z 31 and 45, less commonly observed in EI spectra. We observe a decrease in the relative intensities of cation fragment mass lines between m/z 26 and 33 and an increase between m/z 39 and 45, with an increasing carbon number for ketones and aldehydes with LILBID and EI, respectively. Our study provides a basis for complementary compositional analysis to identify the structural properties of organic species in a space environment using different spaceborne mass spectrometers (e.g., SUrface Dust Analyzer and MAss Spectrometer for Planetary EXploration) on board NASA’s future Europa Clipper space mission.