Design and analysis of ABRF-95SEQ, a recombinant protein with sequence heterogeneity

Publisher Summary This chapter summarizes the sequencing results for the current test sample, ABRF-95SEQ that represents the eighth in a series of unknown samples that have been distributed to Amino Acid Analysis Research Committee of the Association of Biomolecular Resource Facilities (ABRF) facilities that perform protein sequencing. The chapter assesses three important aspects of protein sequence analysis that would routinely be encountered in a typical core facility: (1) the length of sequence assignment possible with a low-level sample, (2) the reliability of cysteine and tryptophan identification, and (3) the ability of the members to recognize sample microheterogeneity. Results from ABRF-94SEQ and ABRF-95SEQ suggest that the accuracy of Trp assignments may depend in part on the position of the residue in a sequence, with earlier assignments being more accurate than later ones. Even though there are a number of simple procedures for modifying Cys, most facilities do not routinely use them, resulting in many inaccurate assignments for this residue. Sequence heterogeneity also reduces assignment accuracy but to a lesser extent. Thus, multiple factors play a role in the accuracy of sequence assignments.