Patent ID: 8296300

Claim:
A method for screening a protein comprising: i) grouping proteins having a required homology from a primary database by using clustering software which minimizes overlapping of proteins, thereby generating one or more protein groups, and then recording sequence information of each protein group on a recording system of a computer; ii) designating a representative protein in each protein group and then constructing a representative protein database composed of the representative proteins, followed by recording the representative protein database and sequence information of the representative proteins on a recording system of a computer; iii) screening tandem mass spectra of one or more protein samples obtained by a mass spectrometer, using sequence searching software with the representative protein database, and then preparing a primary protein list comprising representative proteins from the representative database identified by the sequence searching software as matching the one or more protein samples; iv) constructing a secondary protein database comprising proteins from each protein group having a representative protein from the primary protein list, and then recording the secondary protein database and sequence information of the secondary database proteins on a recording system of a computer; v) screening tandem mass spectra of each protein sample obtained by the mass spectrometer using sequence searching software with the secondary protein database and then preparing a secondary protein list comprising proteins from the secondary protein database identified by the sequence searching software as matching the one or more protein samples; vi) selecting protein isoforms of proteins from the primary protein list made in the above step iii) from a third database containing various isoforms of protein sequences and then grouping the selected proteins to construct a fourth protein database, followed by recording the fourth protein database and sequence information of the fourth database proteins on a recording system of a computer; vii) screening tandem mass spectra of a specific sample obtained by a mass spectrometer using sequence searching software with the fourth protein database and then preparing a third protein list comprising proteins from the fourth protein database identified by the sequence searching software as matching the specific sample; viii) screening tandem mass spectra of the specific sample obtained by the mass spectrometer using sequence searching software containing modification conditions with the fourth protein database and then preparing a fourth protein list comprising modified proteins from the fourth protein database identified by the sequence searching software as matching the specific sample; and ix) preparing a list of identified proteins comprising all the proteins from the primary protein list, secondary protein list, third protein list and fourth protein list, and printing the identified protein list using an output unit of a computer.