Primary structural determination of N-terminally blocked peptides from the bark of Eucommia ulmoides Oliv by mass spectrometric analysis.

Sequencing of N-terminally blocked proteins/peptides is a challenge since these molecules inhibit processing by Edman degradation. By using high accuracy Fourier transform ion cyclotron resonance (FTICR) tandem mass spectrometry and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOFMS), the primary structures of two novel N-terminally blocked antifungal peptides (EAFP1 and EAFP2), purified from the bark of Eucommia ulmoides Oliv, have been determined. The results show that the high mass accuracy provided by FTICR mass spectrometry is effective to determine the N-terminally blocking group, and can simplify the task of spectral interpretation and improve the precision of sequence determination. The combination of MALDI-TOFMS with carboxyl peptidase Y digestion was used to determine the C-terminal 36- and 27-residue sequences of EAFP1 and EAFP2, respectively, to provide the sequence linkage information for tryptic fragments. Compared with traditional peptide chemistry the advantage of mass spectrometric techniques is their simplicity, speed and sensitivity.