Abstract: The structural principle of the linear ion trap-Fourier transform ion cyclotron resonance mass spectrometry(LTQ-FT-MS)was introduced using the LTQ-FT-MS produced by Thermo Corporation as an example.Also its application in proteomics was introduced briefly.Using liquid chromatographymass spectrometry(LC-MS) coupling technique,LTQ-FT-MS could provide high measure accuracy,routinely at 1-2 μg/g,which could significantly enhance the validation of peptide identification.This FT-MS could use electron capture dissociation technique,getting more information in structural identification.The top-down multiple mass spectrometer analysis of protein molecules could also be applied,which could identify some protein sequence from high homogeneity family.