The dominance of arginine-containing peptides in MALDI-derived tryptic mass fingerprints of proteins

Matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) is a powerful tool for mass fingerprinting of peptide mixtures obtained after enzymatic in-gel digestion of proteins separated by two-dimensional electr ophoresis (2-DE). In the course of a proteome analysis of mycobacteria usin g mass spectrometric identification, it was found that 94% of the most inte nse MALDI-MS peaks denote peptides bearing arginine at the C-terminal end. The effect was demonstrated to be equally prominent using an equimolar mixt ure of the synthetic peptides known to be present in the tryptic digest of the mycobacterial 35 kDa antigen ("synthetic mass map"). In addition, sever al binary mixtures of synthetic peptides differing exclusively at the C ter minus (Arg or Lys) were examined to rationalize the higher sensitivity towa rd arginine-containing peptides. The extent of the effect described depends on the matrix used and may facilitate a more reliable assignment of mass f ingerprint data to protein sequences in databases.