There is an increasing usage of ion mobility-mass spectrometry (IMMS) in proteomics. IMMS combines the features of ion mobility spectrometry (IMS) and mass spectrometry (MS). It separates and detects peptide ions on a millisecond time-scale. IMS separates peptide ions based on drift time that is determined by the collision cross-section of each peptide ion in a given experiment condition. A peptide ions collision cross-section is related to the ion size and shape resulted from the peptide amino acid sequence and their modifications. This inherent relation between the drift time of peptide ion and peptide sequence indicates that the drift time of peptide ions can be used to infer peptide sequence and therefore, for peptide identification.