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Electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry coupled with capillary reverse-phase liquid chromatography was used to characterize intact proteins from the large subunit of the yeast ribosome. High mass measurement accuracy, achieved by ''mass locking'' with an internal standard from a dual electrospray ionization source, allowed identification of ribosomal proteins. Analyses of the intact proteins revealed information on cotranslational and posttranslational modifications of the ribosomal proteins that included loss of the initiating methionine, acetylation, methylation, and proteolytic maturation. High-resolution separations permitted differentiation of protein isoforms having high structural similarity as well as proteins from their modified forms, facilitating unequivocal assignments. The study identified 42 of the 43 core large ribosomal subunit proteins and 58 (of 64 possible) core large subunit protein isoforms having unique masses in a single analysis. These results demonstrate the basis for the high-throughput analyses of complex mixtures of intact proteins, which we believe will be an important complement to other approaches for defining protein modifications and their changes resulting from physiological processes or environmental perturbations.M ass spectrometry has evolved into a powerful tool for analyzing biomolecules because of the development of matrix-assisted laser desorption ionization (1, 2) and electrospray ionization (ESI) (3) and advances in both mass analyzers and data processing capabilities. With these ionization methods, which are amenable to megadalton-size molecules, the broadly useful detection and characterization of biopolymers by mass spectrometric methods are feasible. For example, MS has become a preferred analytical tool for proteome analyses, in which dynamic populations of proteins are identified and quantified. Proteins are now routinely identified by mass spectrometric and tandem mass spectrometric analysis of proteolytic digests of individual protein spots on two-dimensional (2D) PAGE (4). However, the intact protein level analyses of complex protein mixtures, while potentially providing complementary and direct information for protein identification, have been a much greater experimental challenge and only rarely attempted (5, 6).Many pivotal cellular processes are not carried out by individual proteins, but rather by large protein-protein complexes and protein-nucleic acid complexes. The analyses of such complexes have been greatly expanded by improvements in both biological separations and MS. One of the more complicated protein complexes yet studied by MS is the cytosolic ribosome complex. Efforts to define the protein composition (7, 8), modifications (9), and subunit interactions (10) of ribosomes generally have mirrored the development of biomolecular analysis techniques and experimental approaches for the study of noncovalent protein complexes.Ribosomes are the canonical example of ribonucleoprotein complexes in both prokaryot...

A method is described for identifying intact proteins from genomic databases using a combination of accurate molecular mass measurements and partial amino acid content. An initial demonstration was conducted for proteins isolated from Escherichia coli (E. coli) using a multiple auxotrophic strain of K12. Proteins extracted from the organism grown in natural isotopic abundance minimal medium and also minimal medium containing isotopically labeled leucine (Leu-D10), were mixed and analyzed by capillary isoelectric focusing (CIEF) coupled with Fourier transform ion cyclotron resonance mass spectrometry (FTICR). The incorporation of the isotopically labeled Leu residue has no effect on the CIEF separation of the protein, therefore both versions of the protein are observed within the same FTICR spectrum. The difference in the molecular mass of the natural isotopic abundance and Leu-D10 isotopically labeled proteins is used to determine the number of Leu residues present in that particular protein. Knowledge of the molecular mass and number of Leu residues present can be used to unambiguously identify the intact protein. Preliminary results show the efficacy of this method for unambiguously identifying proteins isolated from E. coli.