The present invention comprises novel methods of continuously monitoring the performance of an atmospheric pressure ionization (API) system. The methods of the invention allow for improved quality monitoring of the processes that leads to the formation of ions at atmospheric pressure. The methods of the invention further allow for continuously monitoring for the quality of the ion formation process in API without the addition of extraneous material (such as labelled compounds or control known compounds) to the system being monitored.

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.

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.

The user specifies regions of interest (ROIs) such as a region where a large amount of compound to be identified is estimated to be included and a region where the compound is overlapped with another compound on one or more specific MS images, and specifies addition or subtraction of the ROIs. For each of the specified ROIs, an average MS/MS spectrum is calculated from MS/MS spectrum data at measurement points in the regions, and the average MS/MS spectra at the ROIs are subjected to addition or subtraction, to obtain an MS/MS spectrum. By addition between the ROIs, the intensity of peak derived from the target compound can be increased. By subtraction between the ROIs, a peak derived from the other compound overlapped with the target compound can be removed. When the MS/MS spectrum after addition or subtraction is subjected to library search for identification, a score indicating the similarity of the spectrum is higher than the conventional score, and the identification accuracy can be improved.

The present invention relates to a method and device for measuring m/z ratios of ions in ion cyclotron resonance (ICR) mass spectrometry. The described ion traps for ICR mass spectrometry are distinct from the previous configurations by having one or many narrow aperture (flat) detection electrodes that could be moved radially inward the ICR trap, for example on the plane where radiofrequency excitation potential is minimal, closer to the post-excitation ion trajectories.

A method for analyzing charged particles may include generating, in or into an ion source region, charged particles from a sample of particles, causing the charged particles to enter a mass spectrometer from the ion source region at each of a plurality of differing physical and/or chemical conditions in a range of physical and/or chemical conditions in which the sample particles undergo structural changes, controlling the mass spectrometer to measure at least the charge magnitudes of the generated charged particles at each of the plurality of differing physical and/or chemical conditions, determining, with a processor, an average charge magnitude of the generated charged particles at each of the plurality of differing physical and/or chemical conditions based on the measured charge magnitudes, and determining, with the processor, an average charge magnitude profile over the range of physical and/or chemical conditions based on the determined average charge magnitudes.

A method of processing an image charge/current signal representative of trapped ions undergoing oscillatory motion. The method includes: identifying a plurality of fundamental frequencies potentially present in the image charge/current signal based on an analysis of peaks in a frequency spectrum corresponding to the image charge/current signal in the frequency domain, wherein each candidate fundamental frequency falls in a frequency range of interest; deriving a basis signal for each candidate fundamental frequency using a calibration signal; and estimating relative abundances of ions corresponding to the candidate fundamental frequencies by mapping the basis signals to the image charge/current signal. At least one candidate fundamental frequency is calculated using a frequency associated with a peak that falls outside the frequency range of interest and that has been determined as representing a second or higher order harmonic of the candidate fundamental frequency.

A method of processing an image-charge/current signal representative of one or more ions undergoing oscillatory motion within an ion analyser apparatus, the method comprising obtaining a recording of the image-charge/current signal generated by the ion analyser apparatus in the time domain. By a signal processing unit, the method includes selecting N (where N is an integer>1) separate values (OP.sub.n, where n=1 to N; N?M) of the frequency-domain spectrum of the image-charge/current signal each from amongst a plurality of spectral peaks which include a harmonic peak associated with a target ion. By solving a system of equations:

[00001]${\mathrm{OP}}_n=\underset{m=1}{\overset{N}{.Math.}}{?}_{nm}?{\mathrm{TP}}_m,$$\mathrm{for}n=1\mathrm{to}N;$$N?M$ where ?.sub.nm are coefficients and TP.sub.m are corrected values of the spectrum, the charge of the target ion is determined based on a magnitude of a corrected value(s) (TP.sub.m) associated with that ion.

Systems and methods described herein provide for the injection of ions into an ELIT at a variety of kinetic energies such that the ions turn around at various locations. In certain aspects, such systems and methods for operating an ELIT may reduce ion density at the turning points to reduce the impact of the space charge effect. Various aspects of the present teachings also provide for the design or optimization of the ELIT electrode spacing and/or injection potentials to reduce the impact of the space charge effect. In some related aspects, the ELIT may additionally provide time-focusing of the various ion groups at the detector as they oscillate along their respective path lengths.