Identification of Proteins by LC-MALDI System

Introduction

Peptide Mass Fingerprinting (PMF) is a powerful protein identification method that can rapidly identify a protein. The unknown protein is enzymatic digested into smaller peptides whose masses can be accurately measured with a mass spectrometer and the masses are in silico compared to either a database containing known protein sequences or even the genome. Proteins can be identified quickly and easily with mass spectrometer. Therefore PMF is used very widely for proteomics researchers. However, there are not many fragments from enzymatic digest of low molecular weight proteins, so it is very difficult to identify these proteins by PMF. And low abundance proteins result in limited numbers of fragments, then it is hard that they are not identified by PMF. Furthermore, post- translational modified proteins generally result in matches to the native, unmodified proteins.In these case, we try MS/MS ion search as the next move to make. This application note introduces that protein identification by MS/MS ion search using an LC- MALDI system which combines a nano-LC system (Prominence nano-AccuSpot-AXIMA Performance).

February 6, 2009 GMT