Protein Sequencing Using In-Source Decay

Introduction

The MALDI-TOF mass spectrometer can detect ions that are formed due to fragmentation within the ion source (ISD, In-Source Decay). When ISD occurs in analysis of proteins, primarily it is the c-type ion (Fig. 1) of the N-terminus that is detected. Up to now, 2,5-dihydroxybenzoic acid (DHB) has been used widely as a matrix for inducing ISD, but recently, 1,5-diaminonaphtalene (DAN) has been reported to be a more effective matrix in this regard (see References). Amino acid sequence information is easily acquired by detection of ISD ions using DAN, and highly homologous proteins can be investigated using homology searches. Assignment of c9 – c41 (excluding c34 and c39) was achieved for the amino acid sequence of the BSA N-terminus. The peak assignment (Leu/Ile and Lys/Gln could not be distinguished) operation was conveniently facilitated using the Database Viewer function provided in the AXIMA software.

January 29, 2010 GMT