Asphaltenes are among the most challenging components in petroleum processing because they contain high amounts of heteroatoms (i.e., S, N, O, V, and Ni) thought to be responsible for strong aggregation tendencies, precipitation, and fouling problems. The role of vanadium- and nickel-containing petroleum compounds (i.e., petroporphyrins) in aggregation and fouling is not completely understood because asphaltene composition and structure is still a subject of debate in the petroleum chemistry community. Characterization of asphaltenes, namely, molecular analysis that employs no chromatographic separation, often fails to reveal their comprehensive composition. The work herein presents asphaltene fractionation by (1) solid/liquid extraction, which allows for separation of single-core (“island”) and multicore (“archipelago”) structural motifs and by (2) high-performance thin layer chromatography (HPTLC) with cellulose as the stationary phase and DCM/MeOH as the eluent, which facilitates access to petroporphyrins. Characterization is performed by laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS) and matrix-assisted laser desorption ionization Fourier transform ion cyclotron resonance mass spectrometry (MALDI FT-ICR MS). The results demonstrate that even with multiple separation steps, a large quantity of vanadyl porphyrins remains inaccessible for molecular analysis by MALDI FT-ICR MS, which raises the question of what portion of a complex sample of asphaltene can be revealed by ultrahigh resolution mass spectrometry. Furthermore, the results show that easily accessible porphyrins migrate with the solvent front in HPTLC. Thus, HPTLC can be used to isolate and identify “free” porphyrins not locked into asphaltene aggregates; however, further development of separation methods is required to access the most difficult and problematic asphaltene fractions, which do not migrate and impose analytical challenges due to their stronger aggregation tendency.