Partially premixed low temperature combustion (LTC) in diesel engines is a strategy for reducing soot and NOX formation, though it is accompanied by higher unburned hydrocarbon (UHC) emissions compared to conventional mixing-controlled diesel combustion. In this work, two independent methods of quantifying light UHC species from a diesel engine operating in early LTC (ELTC) modes were compared: Fourier transform infrared (FT-IR) spectroscopy and gas chromatography-mass spectroscopy (GC-MS). A sampling system was designed to capture and transfer exhaust samples for off-line GC-MS analysis, while the FT-IR sampled and quantified engine exhaust in real time. Three different ELTC modes with varying levels of exhaust gas recirculation (EGR) were implemented on a modern light-duty diesel engine. GC-MS and FT-IR concentrations were within 10 % for C2H2, C2H4, C2H6, and C2H4O. While C3H8 was identified and quantified by the FT-IR, it was not detected by the GCMS. Analysis of the spectral fitting residuals revealed features spanning 2700 cm-1 - 3100 cm-1, a region where propane, heavier hydrocarbons, and aldehydes absorb and in some cases are evaluated in the standard Diesel-SCR method. The list of components identified via GC-MS was used to help identify species fitting the spectral residual. Although GC-MS informed FT-IR analysis of low and mid UHC emitting LTC modes, it was not a factor in analysis of the LTC high UHC emitting mode. Results show that different species likely comprise the identified spectral residual for these different LTC modes. Although GC-MS can aid in FT-IR spectral analysis to further refine FT-IR methods for real time measurement of unconventional combustion mode exhaust species, its utility is dependent upon the chemical properties of the GC stationary phase responsible for speciation ahead of MS analysis.