Characterization of E. coli Ribosomal Particles: Combined Analysis of Whole Proteins by Mass Spectrometry and of Proteolytic Digests by Liquid Chromat

This chapter describes the purification of ribosomal particles from a mutant strain of Escherichia coli using sucrose gradients and the characterization of their protein composition by a combination of mass spectrometry (MS) techniques. The main objective is to identify the ribosomal proteins that are missing in an aberrant ribosomal particle corresponding to a defective large subunit. To address this question, the tryptic digests of the purified ribosomal particles are analyzed by the coupling between liquid chromatography and tandem MS. The presence or absence of a given ribosomal protein in the defective particle is determined by comparing the MS intensities of its identified tryptic peptides with that of the mature large subunit. These analyses also allow identification of proteins copurifying with the ribosomal particles. To detect low-mass proteins escaping identification by the above method, intact proteins are also analyzed by matrix-assisted laser desorption ionization time of flight (MALDI-TOF) and nano-ESI-QqTOF MS.