Asphaltene nanoaggregates for three diverse source materials—coal-derived asphaltenes dominated by aromatic carbon, petroleum asphaltenes with comparable abundances of aromatic and aliphatic carbon, and immature source-rock asphaltenes dominated by aliphatic carbon—are examined by means of surface-assisted laser desorption ionization mass spectrometer (SALDI-MS) coupled with laser desorption laser ionization mass spectrometry (L2MS). All three types of asphaltenes form nanoaggregates with aggregation numbers close to 7. Molecular dynamics calculations for proposed island molecular structures show the important roles that π-stacking and alkane steric hindrance play in nanoaggregate formation. These results are discussed in terms of entropy and enthalpy changes. All results are consistent with the Yen-Mullins model, which bodes well for its expanded use in oilfield reservoir evaluations.