Molecular composition of petroleum asphaltenes has been a major research challenge for petroleum chemistry community both in upstream and downstream of petroleum industry. Heavy petroleum asphaltenes and their subfractions were characterized by using negative ion electrospray ionization (ESI) Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometry (MS). The composition of heteroatoms in heavy petroleum samples and asphaltenes is rather complex. Class species such as N₁, N₁O₁, N₁O₁S₁, N₁O₂, N₁S₁, O₂, O₂S₁, O₂S₂, O₂S₃, O₃, O₃S₁, O_4are identified with high resolution FT-ICR MS. Oxygen and multi-heteroatom containing species tend to precipitate into asphalenes. Heptane derived asphaltenes have higher molecular condensation degree than pentane derived asphaltenes. Molecular composition of asphaltenes from various crude oil is very different. Asphaltenes derived from Canada vacuum topped bitumen(VTB) have more heteroatom classes and higher molecular condensation degree than that of Sudan heavy oil asphaltenes. Sulfur species are absent from Sudan heavy oil asphaltenes in which oxygen class species show a very high relative abundance. Minimal variations in molecular condensation degree can lead to significant changes in asphaltene solubility in solvents. The research results provide evidence at molecular level that compounds with high molecular condensation degree and/or multi heteroatoms tend to precipitate from solvent with non or weak polarity. The characterization on neutral nitrogen and acidic oxygen compounds reveals the compositional complexity of asphaltenes. Under current conditions only limited amount of asphaltene moieties are revealed in negative ion ESI analysis, however a significant amount of small molecules are highly likely to present in petroleum asphaltenes.