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Top-down mass spectrometry is an emerging approach for the analysis of intact proteins. The term was coined as a contrast with the better-established, bottom-up strategy for analysis of peptide fragments derived from digestion, either enzymatically or chemically, of intact proteins. Although the term top-down originates from proteomics, it can also be applied to mass spectrometric analysis of intact large biomolecules that are constituents of protein assemblies or complexes. Traditionally, mass spectrometry has usually started with intact molecules, and in this regard, top-down approaches reflect the spirit of mass spectrometry. This article provides an overview of the methodologies in top-down mass spectrometry and then reviews applications covering protein posttranslational modifications, protein biophysics, DNAs/RNAs, and protein assemblies. Finally, challenges and future directions are discussed.

Connexin43 (Cx43) is a major cardiac gap junction channel protein required for normal electrical and contractile activity. Gap junction channel assembly, function, and turnover are regulated by phosphorylation under both normal and disease conditions. The carboxyl terminus (CT) of Cx43 contains numerous amino acid residues that are phosphorylated by protein kinases. However, our knowledge of the specific residues and kinases involved is incomplete. The objective of this study was to identify amino acid residues in the Cx43-CT that are targets of the multifunctional protein kinase, Ca(2+)/calmodulin protein kinase II (CaMKII), an enzyme known to play critical roles in Ca(2+) homeostasis, transcription, apoptosis, and ischemic heart disease. We subjected fusion protein containing the Cx43-CT to phosphorylation by CaMKII in vitro, digestion with Lys-C and trypsin followed by enrichment for phosphorylated peptides using TiO(2), and analysis in an LTQ XL Orbitrap with collision-induced dissociation and electron transfer dissociation. We deduced the sites of modification by interpreting tandem spectra from these "orthogonal" methods of gas phase peptide fragmentation. We have identified 15 serine residues, including one novel site, in the Cx43-CT that are phosphorylated by CaMKII, the activity of which may be important in regulating Cx43 in normal and diseased hearts.

The mechanism of the multiple charging of macromolecules in elecirospray ionization (ESI) continues to inspire debate and controversy. Recently, we proposed that the number of charges on a macromolecule is determined by the emission of small charge carriers from macromolecule-containing nanodroplets and that, after solvent evaporation, the remaining charge is transferred to the macromolecule. In this study, we tested the applicability of this new theory for macromolecular, positive-ion ESI mass spectrometry by measuring the mean charge states and charge distributions of globular proteins under nondenaturing and denaturing conditions. Predictions of protein mean charge states for native state proteins are in excellent agreement with mass spectrometric measurements, giving strong credence to the proposed theory. Theoretical predictions are also in good agreement with mean charge states measured for proteins in basic solutions (pH = 11.5). For some proteins in acidic solutions (pH = 2.1), the measured mean charge states are anomalously higher than the Rayleigh limit of a water droplet with a volume equivalent to that of the protein. We propose that some macromolecules that are highly charged in solution may desorb from charged droplets of the same polarity in a similar manner to that whereby charge carriers emit from nanodroplets, leading to "super-charged" macromolecular ions. Examination of rate expressions for solvent evaporation and charge-carrier emission demonstrates that the newly proposed model for ESI is consistent with previously reported ion-emission kinetics. Overall, we obtained additional experimental evidence for the charge carrier emission model for macromolecular charging, suggesting opportunities for understanding and applying ESI-MS. [ABSTRACT FROM AUTHOR]