Abstract: Processes and apparatus are described for the analysis of molecules or fragments thereof, which are capable of carrying multiple charges, by reacting the multiply charged molecules or fragments thereof with other ions using mass spectrometry.

Abstract: A method of inhibiting the reaction between ions of opposite polarity is disclosed. The method includes exposing a population of ions to a resonance excitation frequency during a mass-to-charge altering reaction between a first subpopulation of ions and a second subpopulation of ions, the resonance excitation frequency being tuned to inhibit the mass-to-charge altering reaction between an ion of the first subpopulation of ions having a predetermined mass-to-charge ratio and an ion of the second subpopulation of ions so that when an ion of the first subpopulation of ions attains the predetermined mass-to-charge ratio, the ion having the predetermined mass-to-charge ratio is selectively inhibited from reacting with ions of the second subpopulation of ions.

Abstract: Applicant's present invention comprises an apparatus having a tandem configuration of a three-dimensional or linear RF multipole ion trap, a linear RF multipole device and a time-of-flight mass spectrometer, and the associated method of operation generating an associated product ion mass spectrum and a mass spectrum of residual parent ions wherein the associated product ion mass spectrum is combined with the mass spectrum of the residual parent ions to generate a three-dimensional mass spectrum of parent and associated product ions from a single, stored population of heterogeneous ions.

Abstract: Mass spectrometry is used to identify a protein of interest. The protein is first ionized then fragmented into protein product ion. Masses of the observed product ions are compared to product ion masses calculated in silico for database protein sequences to identify product ion matches within a predetermined mass tolerance. An algorithm that weights the product ion to matches based upon one or more factors such as product ion abundance, favored cleavage sites, product ion type, precursor ion charge state and polarity is used to score the possible matches to database proteins in order to identify the protein of interest. The invention represents a “top down” approach and is particularly well-suited for identification of a protein in a complex mixture.

Abstract: The methods of the invention exploit the mass-to-charge ratio dependent motion of ions in an electrodynamic ion traps in synergy with a charge quenching process. In an electrodynamic ion trap, each mass-to-charge ratio is characterized by a unique set of frequencies of motion. Accordingly, by tailoring the time-varying electrical potential of the ion trap the invention controls which ions are allowed or retained in the ion trap and which ions are subjected to charge quenching reactions. Control of ion retention and charge quenching is used to improve sample throughput, dynamic mass range and signal discrimination in the mass spectrometry of multiply charged ions.

Abstract: The methods of the invention exploit the mass-to-charge ratio dependent motion of ions in an electrodynamic ion traps in synergy with a charge quenching process. In an electrodynamic ion trap, each mass-to-charge ratio is characterized by a unique set of frequencies of motion. Accordingly, by tailoring the time-varying electrical potential of the ion trap the invention controls which ions are allowed or retained in the ion trap and which ions are subjected to charge quenching reactions. Control of ion retention and charge quenching is used to improve sample throughput, dynamic mass range and signal discrimination in the mass spectrometry of multiply charged ions.