A method of mass spectrometry is provided. The method comprises eluting a sample from a chromatography system, and calculating a desired maximum scan duration for the sample eluting from the chromatographic system based on a duration of a chromatographic peak of the sample as it elutes from the chromatography system, and a minimum number of scans per chromatographic peak to be performed. A maximum accumulation duration is calculated based on the desired maximum scan duration. The sample is ionised to produce sample ions using an ion source. The sample ions are directed along an ion path from the ion source to a mass analyser. A first set of mass analysis scans are performed. Each of the first set of mass analysis scans comprises: accumulating a portion of sample ions at a point along the ion path, wherein the portion of sample ions are accumulated for a duration not exceeding the maximum accumulation duration, and mass analysing the portion of sample ions using the mass analyser. The mass analyser is a Fourier Transform mass analyser or a Time of Flight mass analyser.

A data independent acquisition method of mass spectrometry for analyzing a sample within a mass range of interest as it elutes from a chromatography system. The method comprises selecting precursor ions within a mass range of interest to be analyzed, performing at least one MS1 scan of the precursor ions using a first, high-resolution mass analyzer and performing a set of MS2 scans by segmenting the precursor ions into a plurality of precursor mass segments, each precursor mass segment having a mass range of no greater than 5 amu, and for each precursor mass segment fragmenting the precursor ions within that precursor mass segment and performing an MS2 scan of the fragmented ions using a time of flight mass analyzer.

A system and method of mass spectrometry is provided. Ions from an ion source are stored in a first ion storage device and in a second ion storage device. Ions are ejected from the first ion storage device to a first mass analysis device during a first ejection time period, for analysis during a first analysis time period. Ions are ejected from the second ion storage device to a second mass analysis device during a second ejection time period. The ion storage devices are connected in series such that an ion transport aperture of the first ion storage device is in communication with an ion transport aperture of the second ion storage device. The first analysis time period and the second ejection time period at least partly overlap.

A method of producing a mass spectrum from a time-varying transient signal detected in a mass spectrometer, the method comprising: performing a Fourier transform of the transient signal to produce a first set of complex amplitudes wherein each of the complex amplitudes corresponds to a respective frequency of a first set of frequencies; generating a second set of complex amplitudes, wherein each of the complex amplitudes corresponds to a respective frequency of a second set of frequencies with a minimum spacing less than the inverse of the duration of the transient signal; optimizing the second set of complex amplitudes to produce an improved second set; generating a mass spectrum from at least some of the improved second set of complex amplitudes; wherein optimizing the second set of complex amplitudes to produce an improved second set of complex amplitudes is based on an objective function subject to some phase constraints.

A data independent acquisition method of mass spectrometry for analysing a sample as it elutes from a chromatography system is disclosed. The method comprises selecting a precursor mass range, and performing a plurality of MS1 scans and sets of MS2 scans across the precursor mass range. Each of the MS1 scans uses a mass analyser operated at a first, relatively higher resolution, for identification and/or quantitation of the sample in the MS1 domain. The set of MS2 scans comprises performing MS2 scans of fragmented mass range segments performed with the mass analyser, operated at a second, relatively lower resolution. In the method, the MS1 scans are interleaved throughout the performing of the set of MS2 scans such that the MS1 scans provide a mass chromatogram of the sample. The ratio of the number of MS1 scans to sets of MS2 scans performed across the chromatographic peak width is at least 3:1.

An electrostatic trap such as an orbitrap is disclosed, with an electrode structure. An electrostatic trapping field of the form U(r, , z) is generated to trap ions within the trap so that they undergo isochronous oscillations. The trapping field U(r, , z) is the result of a perturbation W to an ideal field U(r, , z) which, for example, is hyperlogarithmic in the case of an orbitrap. The perturbation W may be introduced in various ways, such as by distorting the geometry of the trap so that it no longer follows an equipotential of the ideal field U(r, , z), or by adding a distortion field (either electric or magnetic). The magnitude of the perturbation is such that at least some of the trapped ions have an absolute phase spread of more than zero but less than 2 radians over an ion detection period T.sub.m.

A system comprises an electrostatic trapping mass analyzer and an information processor configured to receive a transient signal from the electrostatic trapping mass analyzer at a maximum resolution, the information processor comprising instructions operable to: partition the transient signal into segments and, while a quality metric is either less than a pre-determined minimum threshold or greater than a pre-determined maximum threshold value, to perform the steps of: (i) defining a test transient as being equal to either a first one of the segments or a previously defined transient with an appended signal segment; (ii) generating a spectrum of component frequencies by calculating a mathematical transform of the test transient; and (iii) determining the quality metric from the spectrum of component frequencies; and set an instrumental resolution to be employed for subsequent mass spectral data acquisitions in accordance with a length of the most-recently-defined test transient.

A data independent acquisition method of mass spectrometry for analyzing a sample within a mass range of interest as it elutes from a chromatography system. The method comprises selecting precursor ions within a mass range of interest to be analyzed, performing at least one MS1 scan of the precursor ions using a Fourier Transform mass analyser and performing a set of MS2 scans by segmenting the precursor ions into a plurality of precursor mass segments, each precursor mass segment having a mass range of no greater than 5 amu, and for each precursor mass segment fragmenting the precursor ions within that precursor mass segment and performing an MS2 scan of the fragmented ions.

A system comprises an electrostatic trapping mass analyzer and an information processor configured to receive a transient signal from the electrostatic trapping mass analyzer at a maximum resolution, the information processor comprising instructions operable to: partition the transient signal into segments and, while a quality metric is either less than a pre-determined minimum threshold or greater than a pre-determined maximum threshold value, to perform the steps of: (i) defining a test transient as being equal to either a first one of the segments or a previously defined transient with an appended signal segment; (ii) generating a spectrum of component frequencies by calculating a mathematical transform of the test transient; and (iii) determining the quality metric from the spectrum of component frequencies; and set an instrumental resolution to be employed for subsequent mass spectral data acquisitions in accordance with a length of the most-recently-defined test transient.

A data independent acquisition method of mass spectrometry for analysing a sample as it elutes from a chromatography system is disclosed. The method comprises the steps of: ionising the sample to produce precursor ions, selecting a precursor mass range for the sample to be analysed, performing a plurality of MS1 scans and performing at most two sets of MS2 scans. Each of the MS1 scans uses a mass analyser operated at a first, relatively higher resolution, for identification and/or quantitation of the sample in the MS1 domain across the precursor mass range. The set of MS2 scans comprises performing MS2 scans of fragmented mass range segments performed with the mass analyser, operated at a second, relatively lower resolution. In the method, the MS1 scans are interleaved throughout the performing of the set of MS2 scans such that the MS1 scans provide a mass chromatogram of the sample.