Direct analysis of protein complexes using mass spectrometry

We describe a rapid, sensitive process for comprehensively identifying prot eins in macromolecular complexes that uses multidimensional liquid chromato graphy (LC) and tandem mass spectrometry (MS/MS) to separate and fragment p eptides. The SEQUEST algorithm, relying upon translated genomic sequences, infers amino acid sequences from the fragment ions. The method was applied to the Saccharomyces cerevisiae ribosome leading to the identification of a novel protein component of the yeast and human 40S subunit. By offering th e ability to identify >100 proteins in a single run, this process enables c omponents in even the largest macromolecular complexes to be analyzed compr ehensively.