INSTABILITY OF SIDE-CHAIN PROTECTING GROUPS DURING MALDI-TOF MASS-SPECTROMETRY OF PEPTIDE-FRAGMENTS

Matrix-assisted laser desorption and ionization time-of-flight mass sp ectrometry (MALDI-TOF MS), a well-suited method for the characterizati on of peptides and proteins, was used for analysis of protected peptid e fragments. It is shown that acidic matrices, e.g. 2,5-dihydroxybenzo ic acid, frequently used in MALDI-TOF MS of peptides, causes partial c leavage of acid-labile side-chain protecting groups. Because this effe ct is strongly related to the matrix used, the observed deprotection c an be avoided by choosing an appropriate matrix such as 2,4,6-trihydro xyacetophenone or 2-amino-5-nitropyridine. The advantage of neutral ma trix compounds for MALDI-TOF analysis of protected peptides is clearly demonstrated, confirming the potential of MALDI-TOF mass spectrometry .