We report a multivariate curve resolution (MCR)-based spectral deconvolution workflow for untargeted gas chromatography-mass spectrometry metabolomics. As an essential step in preprocessing such data, spectral deconvolution computationally separates ions that are in the same mass spectrum but belong to coeluting compounds that are not resolved completely by chromatography. As a result of this computational separation, spectral deconvolution produces pure fragmentation mass spectra. Traditionally, spectral deconvolution has been achieved by using a model peak approach. We describe the fundamental differences between the model peak-based and the MCR-based spectral deconvolution and report ADAP-GC 4.0 that employs the latter approach while overcoming the associated computational complexity. ADAP-GC 4.0 has been evaluated using GC-TOF data sets from a 27-standards mixture at different dilutions and urine with the mixture spiked in, and GC Orbitrap data sets from mixtures of different standards. It produced the average matching scores 960, 959, and 926 respectively. Moreover, its performance has been compared against MS-DIAL, eRah, and ADAP-GC 3.2, and ADAP-GC 4.0 demonstrated a higher number of matched compounds and up to 6% increase of the average matching score.