This study describes the use of gel permeation chromatography inductively coupled plasma high-resolution mass spectrometry (GPC ICP HRMS) to examine and explain two important petroleum industry catalytic processes: hydrodemetallization (HDM) and hydrodesulfurization (HDS). The sulfur, nickel and vanadium species size distributions in atmospheric residue fractions were studied to track their evolution during both catalytic processes and examine their mechanisms, especially those mechanisms linked to changes in temperature and initial deactivation via coke laydown. Chromatogram shapes as well as peak areas were used to study the V, Ni and S aggregate types and concentrations in the feedstock as well as in the product after varying the operating temperature and residence time at a constant temperature. For the V and Ni compounds, the low and medium molecular weight (LMW and MMW, respectively) aggregates are easily hydrotreated under all conditions, while the high molecular weight (HMW) compounds are more refractory. For the S compounds, a different reactivity pattern was observed whereby the LMW, MMW and HMW aggregates were more similar in their reactivity, showing that the catalyst is less selective towards a certain aggregate size for the S compounds compared to the V or Ni compounds.