A method for obtaining information on the primary structure of peptides comprising fragmenting the proteins, which enables automation of obtaining information on the primary structure of a peptide sample; a device for use in the method; and an automatic analysis system on the primary structure of the peptides. The method for obtaining information on the primary structure of peptides comprising the steps of: denaturing, reducing, and alkylating a protein; immobilizing the reduced alkylated protein obtained on a hydrophobic microparticulate carrier; chemically or enzymatically fragmenting the immobilized protein obtained; and obtaining information on the primary structure of the peptides fragmented. The automatic analysis system on the primary structure of the peptides comprising an automatic fragmentation element for automatically fragmenting a reduced and alkylated protein, an automatic mass spectrometry element for automatically analyzing the fragmented peptides by mass spectrometry, and a data analysis element for analyzing the data obtained by the automatic mass spectrometry element. The automatic fragmentation of the reduced and alkylated protein is conducted using a hydrophobic microparticulate carrier.