Introduction

The most widespread method currently in use for high throughput protein identification combines the resolving power of electrophoresis with the fingerprinting capabilities of mass spectrometry. Perhaps the most common format is two-dimensional gel electrophoresis associated with peptide mass spectrometry by Matrix Assisted Laser Desorption/Ionization Time of Flight Mass Spectrometry (MALDI-TOF-MS). Another particularly powerful approach to protein analysis is provided by Nuclear Magnetic Resonance (NMR) methods which can provide information on the structure and the conformation of proteins.

We are using a two-dimensional IR spectroscopy method to identify proteins by their amino acid content. Each different amino acid have different side chains which give potentially different vibrational signatures. We can identify these different features in the 2D spectra and then, by using a internal reference, quantify the relative amount of a given amino acid. This quantification is possible since the signal intensity on resonance with a particular peak is propostional to the square of the number of "oscillators" excited.

The first step of our experiment is to demonstrate the method by measuring spectra of known peptides (Peptides). This method is then applied to known proteins (Proteins) and ultimately to unknown proteins.