This study probes the nanoaggregation behavior of asphaltenes by gel permeation chromatography (GPC). Compounds containing sulfur, vanadium, and nickel were monitored online with elemental detection by inductively coupled plasma mass spectrometry (ICP-MS), and four fractions that vary in nanoaggregation state were analyzed by positive atmospheric pressure photoionization 9.4 T Fourier transform ion cyclotron resonance mass spectrometry ((+)APPI FT-ICR MS). We also highlight some of the challenges associated with the analysis of asphaltene fractions by direct infusion. Nanoaggregate size and monomer ion yield were inversely correlated. The extremely low ionization efficiency for the largest aggregate GPC fractions collected from the asphaltenes limited their characterization to only a few of the most abundant heteroatom classes. However, for all of the characterizable heteroatom classes, aggregation closely correlated with increased relative abundance of larger, more aliphatic compounds. These observations agree with results from the parent whole crude oil, suggesting that the interactions among the more alkylated compounds in asphaltenes may be a major contributor to asphaltene nanoaggregation.