An atmospheric pressure electron impact ionization mass spectrometer system includes an atmospheric pressure ionization component operated at an atmospheric pressure. An electron impact ionization mass spectrometer includes an electron ionization source. An atmospheric pressure interface operates below about 10 Torr. The atmospheric pressure interface includes a source block to focus a plurality of molecules and ions from the atmospheric pressure ionization component at the atmospheric pressure into the electron ionization source which operates at a pressure below about 10.sup.?3 Torr.

A linear ion trap includes at least two discrete trapping regions for processing ions and at least one gas pulse valve for applying pulses of gas to dynamically control pressure in the at least two discrete trapping regions. A RF electrical potential generator produces two RF waveforms, each applied to a pair of pole electrodes of the linear ion trap forming a RF trapping field component to trap ions radially. A multi-output DC electrical potential generator produces multiple DC field components superimposed to the RF trapping field component and distributed across the length of the linear ion trap to control ions axially. A control unit is configured to switch the DC electrical potentials and corresponding DC field components collectively forming a first trapping region of the at least two discrete trapping regions that is populated with ions to alter ion potential energy from a first level to a second level, and to enable at least a first ion processing step in at least one of the first and second levels.

The present invention concerns a method for sequencing oligosaccharides, which makes it possible to identify the primary sequence of an oligosaccharide of unknown structure, including its monosaccharide composition, the position (regiochemistry) and configuration (stereochemistry) of glycosidic bonds, the nature and position of functional modifications, and its branched structure, particularly including the identification of the reducing end.

Methods are described for measuring the amount of a vitamin B2 in a sample. More specifically, mass spectrometric methods are described for detecting and quantifying vitamin B2 in a sample utilizing on-line extraction methods coupled with tandem mass spectrometric techniques.

Apparatus is provided and an IDA method is modified to detect and separately dissociate alkali-metal adducts of a compound. An ion source device ionizes one or more compounds of a sample, producing an ion beam. A mass filter selects a mass range of precursor ions from the ion beam, a mass analyzer measures intensities and m/z values of the precursor ions, and one or more of the precursor ions are selected for a peak list. For each pair of precursor ions of the peak list, if an m/z difference between the pair corresponds to an m/z difference between an alkali metal ion and another alkali metal ion or a proton, an ExD device is used to dissociate one precursor ion or both precursor ions of the pair using the processor. A CID device is used to dissociate all other precursor ions of the peak list.

In one aspect, an electron capture dissociation (ECD) device for use in a mass spectrometer is disclosed, which is configured to trap precursor ions and cause the trapped precursor ions (or a portion thereof) to exit the ion trap, via radial excitation thereof by a resonant AC voltage, such that the released precursor ions can enter an ion-electron interaction region in which at least a portion of the precursor ions undergo fragmentation via interaction with an electron beam. The fragment ions are trapped and prevented from undergoing multiple dissociations. Once the fragmentation of the precursor ions is completed and/or after a predefined period, the fragment ions are released from the ECD to be received by downstream components of the mass spectrometer in which the ECD device is incorporated.

Reflectron-electromagnetostatic cells for use in mass spectrometers are provided herein that cause ion packets to pass through the cell a plurality of times during fragmentation.

According to an embodiment, a mass spectrometry apparatus includes a beam irradiator, a laser irradiator, a mass spectrometer and a controller. The beam irradiator irradiates a sample with an ion beam. The laser irradiator irradiates a space above the sample with laser light. The mass spectrometer performs mass spectrometry of an ionized particle. The controller controls at least one of the laser irradiator and the mass spectrometer on the basis of an analysis result of the mass spectrometer.

When, in performing MS/MS analysis on a multivalent ion originated from a target component, an analyzing operator inputs at least two values of a mass value m.sub.Loss of an eliminated fragment, a valence z.sub.Loss of the eliminated fragment, a valence z.sub.Prec of a precursor ion and a valence z.sub.Prod of a product ion by an inputting unit, a valence calculating unit calculates an uninput valence z.sub.Prec or z.sub.Prod based on the relation, z.sub.Prec=z.sub.Prod+z.sub.Loss. Upon the start of the MS/MS analysis, a precursor ion m/z setting unit sets m/z=M.sub.Prec of an ion that passes through a front-stage quadrupole mass filter , and a passed product ion m/z calculating unit calculates m/z=M.sub.Prod of the product ion that passes through a rear-stage quadrupole mass filter by applying M.sub.Prec, m.sub.Loss, z.sub.Prec and z.sub.Prod above to the relational expression, M.sub.Prod=(M.sub.Precz.sub.Precm.sub.Loss)/z.sub.Prod.

This invention discloses a method for constructing a set of database of one or more saccharides, a logical procedure for automatic determination of sequential mass spectra, and a method, program and system for determination the structures of oligosaccharides and glycoconjugates by the set of database. In one aspect, the sequential mass spectra measured by the method, program or system of the invention maybe instructed according to the logical procedure automatically or manually determined. By comparing the sequential mass spectra to the set of database, the structure of the carbohydrate comprising linkage position, anomeric configuration, composed monosaccharide and branch location of the carbohydrate sample can be identified. In another aspect, the method, program may be used to control one or more mass spectrometer automatically or manually.