Protein identification using mass spectrometry: a method overview.

With the introduction of soft ionization techniques such as Matrix Assisted Laser Desorption Ionization (MALDI), and Electrospray Ionization (ESI), proteins have become accessible to mass spectrometric analyses. Since then, mass spectrometry has become the method of choice for sensitive, reliable and inexpensive protein and peptide identification. With the increasing number of full genome sequences for a variety of organisms and the numerous protein databases constructed thereof, all the tools necessary for the high-throughput protein identification with mass spectrometry are in place. This chapter highlights the different mass spectrometric techniques currently applied in proteome research by giving a brief overview of methods for identification of posttranslational modifications and discussing their suitability of strategies for automated data analysis.