We present a technique for improving fragmentation in tandem mass spectrometry (MS/MS) of arginine-containing peptides by derivatising the N-termini with the tris(2,4,6-trimethoxyphenyl) phosphonium acetyl group (TMPP-Ac), followed by the conversion of arginine to citrulline with peptidyl arginine deiminase. Owing to the use of enzyme reaction, the deimination occurred specifically at arginine residues and proceeded under mild conditions (at 55 degrees C and pH 7.4, for 3 h). Although the TMPP-Ac-tagged arginine-containing peptides undergo fragmentation to give spectra not informative enough to obtain sequence data, the deimination to yield the corresponding citrulline-containing peptides has greatly enhanced the performance of matrix assisted laser desorption/ionization (MALDI) MS/MS by limiting the observation of fragment peaks to those of a-type ions. Additional information available to interpret the fragment patterns for sequencing includes the subsidiary but characteristic appearance of peaks due to the -17 Da and -43 Da neutral losses of ammonia and isocyanic acid, respectively, from a-type ions.