In mass spectrometry (MS) based proteomics research, only the spectral biologically relevant in analysis applications such as biomarker discovery and disease classification. number and locations of peaks in different spectra are very likely to be different given the biological samples and variations of MS data acquisition conditions. Aligning peaks spectra and determining their locations is therefore an important task as all comparisons significant conclusions are based on the alignment results. Due to the fact that the shift curves peaks are non-linear, however, peak alignment still remains challenging even after instrument with internal markers. To address this problem, different methods have been proposed.