The compound identification in gas chromatography-mass spectrometry (GC-MS) is achieved by matching the experimental mass spectrum to the mass spectra in a spectral library. It is known that the intensities with higher m/z value in the GC-MS mass spectrum are the most diagnostic. Therefore, to increase the relative significance of peak intensities of higher m/z value, the intensities and m/z values are usually transformed with a set of weight factors. A poor quality of weight factors can significantly decrease the accuracy of compound identification. With the significant enrichment of the mass spectral database and the broad application of GC-MS, it is important to re-visit the methods of discovering the optimal weight factors for high confident compound identification.