A Simple and Highly Successful C-terminal Sequence Analysis of Proteins by Mass Spectrometry

Introduction

Protein identification via Peptide Mass Fingerprinting (PMF) is conducted by enzymatically digesting the protein and analyzing the resulting digest using mass spectrometry. A database search is then applied to the list of peaks obtained from this analysis. However, assignment of the N and C terminal sequences is not always easily accomplished with a database search because 1) the protein N and C terminals are often changed due to processing and post-translational modification, and 2) a portion of the protein sequence may not be detectable by the mass spectrometer due to the ion suppression effect. The protein N-terminal amino acid sequence can be determined using a protein sequencer (PPSQ- 31A/33A) or a protein N-terminal sequencing kit (ORFinder-NB^TM). However, in the case of the C- terminal, there has been a need for a technique importance of protein terminal amino acid sequence analysis is becoming more important than ever. Here we introduce an example of mass spectrometric analysis of a sample consisting of selectively collected protein C-termini, demonstrating a newly developed, successful method of amino acid sequencing.

June 29, 2010 GMT