Analyzing the most unstable fractions is fundamental to understanding the mechanisms involved in asphaltenes precipitation. For this, Fourier transform ion cyclotron resonance mass spectrometers (FT-ICR MS) play a significant role due to their capability to provide information at the molecular level of complex samples. However, asphaltenes deposition in capillaries during ionization hinders the analysis of unstable fractions. In our previous work (10.1016/j.fuel.2022.124418), we demonstrated laser desorption ionization (LDI) as an alternative to FT-ICR MS analysis of unstable asphaltene fractions without the occurrence of any capillary obstructions. Herein, we present a new fractionation methodology that separates asphaltenes with the most significant aggregation tendencies. Then, asphaltenes from two oil samples were fractionated and characterized by LDI (+) FT-ICR MS. The results made it possible to verify correlations between the instability of the samples with the proportions of archipelago-type molecules. Also, higher contents of heteroatoms O and S were verified in the most unstable fractions isolated by the developed fractionation methodology.