Gas-chromatography hyphenated with low-resolution mass spectrometry is a very flexible tool for the cost-effective identification and quantification of volatile compounds in complex matrices. In some analytical fields, criteria for the agreement between retention time and mass spectra of the analyte in calibrators and samples are defined based on the general understanding of the performance of these parameters. However, since this harmonization is not based on experimental performance observed for specific GC-MS conditions and analyte it leads to false identifications. This research proposes a novel and robust tool for defining statistically sound criteria for the identification of compounds by GC-MS and LC-MS using experimental data. The Monte Carlo Method (MCM) simulation of the correlated abundance of characteristic ions of analyte mass spectrum allows simulating the abundance ratio difference of the analyte in a calibrator and sample used for statistically sound identifications. The Cholesky decomposition of the covariance matrix of ion abundances for MCM simulations allows the reliable use of many ion abundance ratios in identifications. The developed methodology was implemented in a user-friendly Excel spreadsheet and applied to the identification of tear gas agents in tear gas sprays. Criteria defined by SANTE for identifying pesticide residues in foodstuffs were compared with the developed tool. The cross-validation of computational and SANTE tools allowed concluding that the statistical control of retention time and mass spectra performs according to the defined confidence level. On the other hand, the SANTE criteria can produce up to 92% false identifications for being too strict considering signal dispersion.