Matrix assisted laser desorption ionization-time of flight (MALDI-ToF) has evolved into a powerful method for structural analysis of biomolecules. The paper reports a very simple and efficient method of sequencing of long peptides using long polyglutamine stretches with and without interruptions as model peptides, using MALDI-ToF in a linear mode. The method does not require any enzymatic or proteolytic digestions and very long synthetic polyglutamine sequences can be sequenced efficiently just by incremental variation of laser power. The data also reveal whenever there is any interruption within a stretch of glutamines it undergoes a very prompt cleavage at that site. Thus, this method provides an alternative tool for validating long polyglutamine stretches which are very often used as models for studying the structure and conformation of proteins associated with a number of neurodegenerative disorders. (C) 2004 Elsevier Inc. All rights reserved.