A novel two-stage peak alignment algorithm, DISCO2, was developed for analysis of comprehensive two-dimensional gas chromatography time-of-flight mass spectrometry (GC×GC-TOFMS) data. This algorithm uses a mixture similarity measure to determine whether two peaks were generated by the same type of compound in different experiments. In the first stage, the algorithm detects and merges multiple peak entries of the same compound into one peak entry in each input peak list. Landmark peaks are selected from all samples based on two-dimensional retention times and mass spectral similarity. In the second stage, the original retention time shifts in the two-dimensional GC are corrected using a local linear fitting method. A progressive retention time mapping method is then employed to align peaks in all samples based on the parameters optimized in the first alignment stage.