SEQUENCE TAG IDENTIFICATION OF INTACT PROTEINS BY MATCHING TANDEM MASS-SPECTRAL DATA AGAINST SEQUENCE DATA-BASES

Molecular and fragment ion data of intact 8- to 43-kDa proteins from e lectrospray Fourier-transform tandem mass spectrometry are matched aga inst the corresponding data in sequence data bases. Extending the sequ ence tag concept of Mann and Wilm for matching peptides, a partial ami no acid sequence in the unknown is first identified from the mass diff erences of a series of fragment ions, and the mass position of this se quence is defined from molecular weight and the fragment ion masses, F or three studied proteins, a single sequence tag retrieved only the co rrect protein from the data base; a fourth protein required the input of two sequence tags. However, three of the data base proteins differe d by having an extra methionine or by missing an acetyl or heme substi tution. The positions of these modifications in the protein examined w ere greatly restricted by the mass differences of its molecular and fr agment ions versus those of the data base, To characterize the primary structure of an unknown represented in the data base, this method is fast and specific and does not require prior enzymatic or chemical deg radation.