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We propose to assess the selectivity of hydrotreatment catalysts by two complementary analytical methods: (1) high-resolution mass spectrometry (MS), called “petroleomic” analysis, by Fourier transform ion cyclotron resonance (FT ICR, 9.4T) MS for species heavier than m/z of about 200 Da and (2) quantitative GC*GC (heart-cutting)/MS-flame ionization detector (FID) analysis of lighter species. The methodology is illustrated on methanol-soluble bio-oils produced by lignin pyrolysis and hydrotreated by iron-based catalysts. GC*GC analysis is calibrated by a combination of internal standard and prediction of response factors on the FID. Laser desorption ionization (LDI) and electro spray ionization (ESI) in negative-ion mode are combined for the petroleomic analysis. The selectivity of hydrotreatment (catalytic fixed bed, 1 atm, 400 °C) is assessed as a function of catalyst loads and iron support (silica and activated carbon). Hundreds of species are analyzed by GC*GC and petroleomic and mapped in Van Krevelen diagrams. The high selectivity of reduced iron for the hydrodeoxygenation of lignin pyrolysis vapors is demonstrated. The effect of the catalytic treatment on oxygen content and unsaturation is studied for a broad range of species: from C2 to C14 by GC analysis and from C8 to C37 by petroleomic. Many heavy lignin oligomers produced by the pyrolysis are trapped by the catalytic bed, highlighting the need of new catalytic systems to convert them into valuable fuels or chemicals.