A mass spectrometer is operated to simultaneously measure precursor and production data over a number of acquisitions. For each acquisition, the following steps are performed. Ion transfer optics inject ions from an ion beam into an ELIT causing the ions to oscillate axially between two electric fields produced by two the sets of reflectrons. The ELIT measures a time domain image current of the oscillating ions from ion injection to a total acquisition time, Tacq1, and fragments the oscillating ions at one or both turning points of the oscillating ions adding product ions to the oscillating ions. The fragmentation is performed at a delay time relative to the ion injection that is increased by a time increment in each subsequent acquisition making the fragmentation dependent on ion position. The measured time domain image current is stored as a row or column of a two-dimensional matrix.

A charge detection mass spectrometer may include an electrostatic linear ion trap (ELIT) or an orbitrap, an ion source to supply ions thereto, at least one amplifier operatively coupled to the ELIT or orbitrap, a processor coupled to ELIT or orbitrap and to the amplifier(s), and processor programmed to control the ELIT or orbitrap as part of a trapping event to attempt to trap therein a single ion supplied by the ion source, to record ion measurement information based on output signals produced by the amplifier(s) over a duration of the trapping event, to determine, based on the measurement information, whether the control of the ELIT or orbitrap resulted in trapping of a single ion, no ion or multiple ions, and to compute an ion mass or mass-to-charge ratio from the measurement information only if a single ion was trapped during the trapping event.

Apparatus and methods for performing charge detection mass spectrometry are disclosed. An analyte ion is injected into an electrostatic trap, which has electrodes shaped and arranged to establish a trapping field that causes the analyte ion to undergo harmonic motion along a longitudinal axis. A time-varying signal is generated by a detector representative of the harmonic motion. A data system processes the time-varying signal to derive the frequency of ion motion and the amplitude at the harmonic motion frequency, and determines the mass-to-charge ratio (m/z) of the ion based on the derived frequency and the charge from the derived amplitude. The product of the experimentally determined m/z and charge yields the mass of the analyte ion. The electrodes preferably include an elongated inner electrode surrounded by an outer electrode, forming an orbital or non-orbital electrostatic trap.

There is disclosed a method for eliminating an added crosstalk signal from a measured data signal, which is generated by an image current. There is further disclosed a signal processing unit for carrying out the method. There is still further disclosed a mass spectrometer and a mass analyser comprising the signal processing unit for carrying out the method. There is yet still further disclosed a Fourier transform mass spectrometer configured to eliminate the added crosstalk signal from a measured data signal.

Methods for confirming charged-particle generation in an instrument are provided. A method to confirm charged-particle generation in an instrument includes providing electrical connections to a charged-particle optics system of the instrument while the charged-particle optics system is in a chamber. The method includes coupling an electrical component having an impedance to charged-particle current generated in the chamber. Moreover, the method includes measuring an electrical response by the electrical component to the charged-particle current. Related instruments are also provided.

An apparatus configured to produce an image charge/current signal representative of trapped ions undergoing oscillatory motion. The apparatus includes: an electrostatic ion trap configured to trap ions such that the trapped ions undergo oscillatory motion in the electrostatic ion trap; an image charge/current detector configured to obtain an image charge/current signal representative of trapped ions undergoing oscillatory motion in the electrostatic ion trap, wherein the electrostatic ion trap configured to trap ions such that the image charge/current signal in the time domain repeats, for ions of a given mass/charge ratio m, at a frequency f.sub.sig(m) [Hz] with a signal period T.sub.sig(m) [s]. The image charge/current detector includes one or more pickup electrodes configured to obtain the image charge/current signal. The one or more pickup electrodes are arranged to detect two signal pulses caused by ions having the given mass/charge ratio m within each signal period T.sub.sig(m). The one or more pickup electrodes are further arranged such that the time separation t.sub.sep(m) between the two signal pulses caused by ions having the given mass/charge ratio m within each signal period T.sub.sig(m) is approximately equal to 2p+1/2.n.f.sub.sig(m) so as to suppress a predetermined nth harmonic within the image charge/current signal, where n is an integer that is 1 or more, and where p is an integer that is 0 or more.

One or more ions are received along a central axis through a first set of reflectron plates of an ELIT. Voltages are applied to the first set of plates and to a second set of reflectron plates in order to trap and oscillate the one or more ions. A first induced current is measured from a cylindrical pickup electrode between the first set of reflectron plates and the second set of reflectron plates. A second induced current is measured from one or more plates of the first set of reflectron plates. A third induced current is measured from one or more plates of the second set of reflectron plates. The first measured induced current, second measured induced current and third measured induced current are combined to reduce higher order frequency harmonics of the induced current.

Disclosed herein are various methods and apparatus for performing charge detection mass spectrometry (CDMS). In particular, techniques are disclosed for monitoring a detector signal from a CDMS device to determine how many ions are present in the ion trap (10) of the CDMS device. For example, if no ions are present the measurement can then be terminated early. Similarly, if more than one ion is present, the measurement can be terminated early, or ions can be removed from the trap (10) until only a single ion remains. Techniques are also provided for increasing the probability of there being a single ion in the trap (10). A technique for attenuating an ion beam is also provided.

A quadrupole ion trap apparatus includes a main electrode, a first end-cap electrode, a second end-cap electrode, and a phase-controlled waveform synthesizer. The phase-controlled waveform synthesizer generates a main RE waveform for the main electrode. The main RE waveform includes a plurality of sinuous waveform segments each of which is a part of a sine wave, and a plurality of phase conjunction segments each of which is non-sinuous. Each of the sinuous waveform segments is bridged to another sinuous waveform segment via one of the phase conjunction segments, so as to perform ordering of micro motions of sample ions trapped by the electrodes.

An ion intensity array is computed for each mass spectrum forming a mass spectrum array. For each ion intensity array, a plurality of indices ae showing a plurality of characteristics of the mass spectrum as a whole are computed. Based on the plurality of indices, a plurality of index distribution images are computed. A plurality of index distribution images may alternatively be computed based on a mass image array generated from the mass spectrum array.