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. be an important complement to other approaches for defining protein modifications and their changes resulting from physiological processes or environmental perturbations. Mass 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) 33419-42-0 supplier 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 proteinCprotein complexes and proteinCnucleic 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 prokaryotes and eukaryotes and are responsible for cellular protein and 33419-42-0 supplier polypeptide synthesis (translation) (11). This key biological process requires a vast investment of cellular resources, including the production of ribosomal RNA, ribosomal proteins, and accessory factors, with the result that this ribosomes are among the most abundant structures found in the cell (12). Recent structural studies of ribosomes indicate that nascent peptide bond formation is accomplished by a ribozyme core (13) and that the associated ribosomal proteins serve to maintain ribosomal structure, regulate ribosomal activity, and cotranslationally modify the nascent peptide as it exits the ribosome complex (10, 14C16). Cytoplasmic ribosomes are composed of the large and small subunits that are synthesized separately in a multistage process (17). The mature large and small subunits are assembled on cytosolic messenger RNAs and interact with many additional factors to undertake protein synthesis. Although considerably larger and more complex than prokaryotic ribosomes, the overall structure and functional regions of yeast cytosolic ribosomes are highly conserved (18). The yeast ribosome is also useful as a model system for the study of translation in higher eukaryotes, as yeast and mammalian ribosomes have high homology in gross structure, active site structure, and subunit interactions (19) and share a complete set of homologous proteins, except for rat L28 that has no apparent yeast equivalent (20). There are currently 137 established ribosomal protein genes in (29, 30). Thawed lysate was diluted with 3 vol lysis buffer + 5 mM DTT, then centrifuged to remove aggregated material (JA-20 rotor, 18,000 values by using an appropriate calibration function (34). Although a recent report on external calibration, which uses the calibration equation with matching total ion currents, has shown to provide low ppm MMA (35), its use requires accurate control of trapped ion population. LRP8 antibody This approach is especially problematic for LC/MS analysis where the population of trapped ions varies significantly and nonsystematically from spectrum to spectrum. Internal calibration should thus provide a more straightforward accounting for the frequency shifts and more accurate mass measurements. Hannis and Muddiman (36) have recently demonstrated the use of an alternating dual ESI with an external accumulation that provided high MMA, achieving 1.1 ppm for 15-mer oligonucleotide (= 929.9664) that typically appeared in the middle of charge state envelopes of most proteins investigated. Achieving high MMAs for high mass species is subject to mass resolution limitations of the measured ion spectra. Larger errors in MMA of ions with higher molecular masses may occur because of the uncertainty in determination 33419-42-0 supplier of the most abundant isotopic peak. We have estimated the MMA for two standard proteins: bovine myoglobin [monoisotopic 33419-42-0 supplier mass 16940.9642 atomic mass units (amu); average mass 16951.6116 amu] and carbonic anhydrase II (monoisotopic mass 29138.8909 amu; average mass 29157.1198 amu). MMA measured with myoglobin, where isotopically resolved distributions were obtained, was 1.0 ppm (SD of 0.8 ppm) for the 10 spectra with various relative intensities of the standard peptide.