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 method for examining a gas by mass spectrometry includes: ionizing the gas for producing ions; and storing, exciting and detecting at least some of the produced ions in an FT ion trap. Producing and storing the ions in the FT ion trap and/or exciting the ions prior to the detection of the ions in the FT ion trap includes at least one selective IFT excitation, such as a SWIFT excitation, which is dependent on the mass-to-charge ratio of the ions. The disclosure further relates to a mass spectrometer. A mass spectrometer includes: an FT ion trap; and an excitation device for storing, exciting, and detecting ions in the FT ion trap.

A variable data dependent acquisition/dynamic exclusion (vDDA/DE) method selects target m/z range utilizing a MS1 precursor topography map over the most recently acquired MS spectrum to identify the precursor m/z values and MS/MS acquisition parameters to improve the selection of the next data-dependent MS/MS acquisition. The topography used to define the next set of DDA scan events is defined by previous tandem MS scan events defined by precursor quadrupole isolation windows as well as all detected compounds contained within the specific tandem MS events. At least some of the parameters used for MS/MS data acquisition are dynamic so as to exhaustively sample the user specified MS mass range with MS/MS information. These parameters include the quadrupole MS isolation width and symmetry around the targeted m/z value. Using this approach, a greater proportion of the precursor m/z space is effectively and efficiently sampled per chromatographic peak width.

A method and corresponding apparatus are disclosed for analysis of a peptide-containing sample. The sample is prepared by adding isotopically-labeled peptides corresponding to endogenous peptides of interest, and the prepared sample is analyzed by liquid chromatography-mass spectrometry (LCMS). Detection in a high-resolution, accurate mass (HRAM) MS1 spectrum of a precursor ion matching an isotopically-labeled peptide triggers acquisition of an MS/MS spectrum (preferably acquired in an ion trap or other fast mass analyzer) to determine if a product ion is present matching a characteristic product ion (e.g., the y.sub.1 ion) of the isotopically-labeled peptide. If the characteristic product ion is present, then a HRAM MS/MS spectrum is acquired for detection and quantitation of the corresponding endogenous peptide.

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.

An ion spectrometer is provided, comprising: an ion source, arranged to generate ions continuously with a first range of mass to charge ratios; and an ion trap, arranged to receive ions from the ion source along an axis, and to eject ions with a second range of mass to charge ratios orthogonally to that axis, the second range of mass to charge ratios being narrower than the first range of mass to charge ratios. In some embodiments, ions generated by the ion source continuously flow into the ion trap. Additionally or alternatively, ion optics receive ions ejected from the ion trap and cool the ions without substantial fragmentation. An ion analyser receives ions ejected from the ion trap or ion optics and separates the ions in accordance with at least one characteristic of the ions.

A method of identifying tobacco carbonyl components using non-targeted mass spectrometry is disclosed, which includes the following steps: (1) preparing a tobacco sample extract; (2) derivatizing (part of) the sample/extract with 2,4-dinitrophenylhydrazine (DNPH); (3) derivatizing (another part of) the sample/extract with DNPH-d.sub.3; (4) mixing the derivatized tobacco samples; (5) preparing blank samples; (6) performing ultra performance liquid chromatography (UPLC) and ion trap (Orbitrap) high resolution mass spectrometry (HRMS) on the (derivatized) tobacco samples; (7) processing the LC-MS data; (8) filtering the mass spectrometric characteristic data to retain final chromatographic peaks; and (9) structurally annotating or identifying the retained final chromatographic peaks to obtain the tobacco carbonyl components. The method quickly removes noise or interfering components in the original data set by multiple filtering of the mass spectrometry characteristic data, and enables obtaining composition information of aldehyde and ketone chemical components in cigarettes.

A method for identifying components of a sample includes providing a sample to an ion source and generating a plurality of ions from constituent components of the sample, applying a first RF waveform at a first RF amplitude to an ion trap with field resonances while directing the plurality of ions into the ion trap, and applying a second RF waveform at a second RF amplitude to the ion trap while focusing the plurality of ions towards the center of the ion trap along the longitudinal axis. The method further includes ejecting the plurality of ions from the ion trap into a mass analyzer, and using the mass analyzer to determine the mass-to-charge ratio of the ions.

A method and corresponding apparatus are disclosed for analysis of a peptide-containing sample. The sample is prepared by adding isotopically-labeled peptides corresponding to endogenous peptides of interest, and the prepared sample is analyzed by liquid chromatography-mass spectrometry (LCMS). Detection in a high-resolution, accurate mass (HRAM) MS1 spectrum of a precursor ion matching an isotopically-labeled peptide triggers acquisition of an MS/MS spectrum (preferably acquired in an ion trap or other fast mass analyzer) to determine if a product ion is present matching a characteristic product ion (e.g., the y.sub.1 ion) of the isotopically-labeled peptide. If the characteristic product ion is present, then a HRAM MS/MS spectrum is acquired for detection and quantitation of the corresponding endogenous peptide.

Described herein are examples of systems and methods for integrating IMS and MS systems. In certain examples, systems and methods for decoding double multiplexed data are described. The systems and methods can also perform multiple refining procedures in order to minimize the demultiplexing artifacts. The systems and methods can be used, for example, for the analysis of proteomic and petroleum samples, where the integration of IMS and high mass resolution are used for accurate assignment of molecular formulae.