A system and method is described for characterizing glycopeptides which includes a first quadrupole mass filter, a multipole rod set of an ion guide, a lens electrode, an ExD device and a mass analyzer. The multipole rod set is adapted to receive a radial radio frequency (RF) trapping voltage and a radial dipole direct current (DC) voltage The lens electrode is adapted to receive an axial trapping alternating current (AC) voltage and a DC voltage. The ExD device performs electron capture dissociation or electron transfer dissociation, the ExD device being positioned so that an entrance of the ExD device is disposed on the other side of the lens electrode opposite the multipole rod set. The mass analyzer is positioned at an exit of the ExD device for receiving ions from the ExD device.

In a tandem mass spectrometer, when the measurement mode is switched between a positive ion measurement mode and a negative ion measurement mode, a DC offset voltage applied to a lens electrode to impart collision energy to an ion is temporarily switched to 0V (S1). After being maintained at 0V for a predetermined waiting time (S2), the voltage is changed to a DC offset voltage corresponding to a measurement mode which is used after the switching operation (S3). By such an operation, the voltage difference between the neighboring plate electrodes among the plate electrodes (171, 172, 173) included in the lens electrode can be decreased as compared to the case where the polarity of the DC offset voltage is immediately switched. Consequently, unintended electric discharge between the neighboring electrodes can be prevented.

A method for mass spectrometry comprises: receiving or generating a respective value of an optimal collision energy for generating each one of a plurality of n product-ion species of interest from at least one precursor-ion species, each optimal collision energy corresponding to a respective maximum fragmentation efficiency; determining a number, m, wherein m<n, of precursor-ion collision energy values required to fragment all of the at least one precursor-ion species such that a fragmentation efficiency of each product-ion species of interest generated by the fragmentation is equal to the respective maximum fragmentation efficiency, within a pre-determined tolerance; and performing a mass spectrometric analysis that includes fragmenting the one or more precursor-ion species in a collision cell by imparting, in sequence, each of and only the m precursor-ion collision energy values to ions received from an ion source.

An apparatus for molecular imaging of biological samples includes a first optical port configured to receive a first pulsed optical beam that is directed in an optical path along an optical axis. A transparent target that include a first surface having an electrically conductive surface that supports a biological sample under analysis and a second surface is positioned in the optical path along the optical axis. A moveable target mount is configured to translate the transparent target to a plurality of predetermined locations. A first optical focusing element is configured to focus the first pulsed optical beam to a first predetermined diameter at the first surface of the transparent target. A second optical port is configured to receive a second pulsed optical beam that is directed in a second optical path along the optical axis. A second optical focusing element is configured to focus the second pulsed optical beam to a second predetermined diameter at the electrically conductive surface on the transparent target. A TOF mass spectrometer comprising an ion accelerator having a central axis that is substantially coaxial with the optic axis so that ions generated by the first and second pulsed optical beams are accelerated by the ion accelerator. A controller instructs the TOF mass spectrometer to acquire mass spectral data at the plurality of predetermined locations, thereby generating a molecular image of the biological sample under analysis.

In an inductively coupled plasma-mass spectrometry (ICP-MS) system, ions are transmitted into a collision/reaction cell. A DC potential is applied at an exit of the cell at a first magnitude to generate a DC potential barrier effective to prevent the ions from exiting the cell. The DC potential barrier is maintained during a confinement period to perform an interaction. After the confinement period, analyte ions or product ions are transmitted to a mass spectrometer by switching the exit DC potential to a second magnitude effective to allow the analyte ions or product ions to pass through the cell exit as a pulse. The analyte ions or product ions are then counted during a measurement period. The interaction may be ion-molecule reactions or ion-molecule collisions.

A mass spectrometer includes a collision cell and a system controller. The collision cell includes a plurality of rod pairs configured to generate pseudopotential well through the application of radio frequency potentials to the rod pairs. The collision cell configured to generate a target fragment from a parent ion by colliding the parent ion with one or more gas molecules. The system controller is configured to set a radio frequency amplitude of the radio frequency potentials to a default amplitude; monitor the production of a target fragment ion while adjusting the collision energy; set the collision energy to optimize the production of the target fragment ion; apply a linear full range ramp to the radio frequency amplitude to determine an optimal radio frequency amplitude; and set the radio frequency amplitude to the optimal radio frequency amplitude for the parent ion, target fragment ion pair.

Methods are described for measuring the amount of C peptide in a sample. More specifically, mass spectrometric methods are described for detecting and quantifying C peptide in a sample utilizing on-line extraction methods coupled with tandem mass spectrometric or high resolution/high accuracy mass spectrometric techniques.

Apparatus and method are proposed for the strong improvement of dynamic range (DR) of detectors and of data systems for time-of-flight mass spectrometers (TOF MS) with periodically repetitive signals. TOF separated ions are converted into secondary particles, primarily electrons, and the flow of secondary particles is controllably attenuated to sustain the data acquisition system in a counting mode above the electronic noise threshold. The acquisition time is split between at least two time segments, characterized by alternated transmission efficiency SE of secondary particles. Using strong electron suppression (SE1) is employed for recording intense ion peak, while counting ions with either ADC, or TDC, or ADC with extracting peak centroids. A longer time segment employs an efficient electron transfer (SE=1) for detecting weak ion species. In another independent aspect, an ion-optical element is provided upstream of the ion detector and is configured to deflect, reflect or retard ions such that ions that have been scattered or fragmented in the time of flight region do not impact on the ion detector.

An ion optical arrangement (1) for use in a mass spectrometer comprises a collision cell defining an ion optical axis along which ions may pass, electrodes comprising a set of parallel poles (11A, 11B, 11C) arranged in the collision cell, and a voltage source for providing voltages to the electrodes to produce electric fields. The ion optical arrangement is arranged for switching between a first operation mode in which the collision cell is pressurized and a second operation mode in which the collision cell is substantially evacuated. The ion optical arrangement is further arranged for producing a radio frequency electric focusing field in the first operation mode and a static electric focusing field in the second operation mode.

Under the control of an analysis control unit (5), a mass spectrometer unit (2) performs a product-ion scan measurement for a target component in a target sample within a time range where the component is introduced. It also performs a scan measurement over an m/z range including the m/z of an ion originating from a standard component within the same segment of time. A mass correction information calculator (42) calculates mass correction information from measured and theoretical values of the m/z of the ion originating from the standard component observed on an MS spectrum obtained by the scan measurement. Using the mass correction information, a mass corrector (43) corrects the m/z of each ion peak originating from the target component observed on an MS/MS spectrum obtained by the product-ion scan measurement performed within the same cycle as the scan measurement concerned. It is possible to consider that the MS measurement and the MS/MS measurement within the same cycle have been almost simultaneously carried out. Accordingly, a mass correction which is almost equivalent to an internal standard method can be achieved.