Electrospray ionization(ESI) and matrix-assisted laser desorption ionization(MALDI) are two kinds of newly-developed mass spectrometry techniques. The application of mass spectrometry is described in the proteome research such as MS charting, determination of molecular weight, peptide mass fingerprinting(PMF) and peptide sequence validation. The advantages of mass spectrometry are sensitive, accurate, rapid, high-throughput and automated. They have been proved a powerful technique and can be used as an important method for proteome research.