A method of spectrometric analysis comprises obtaining one or more sample spectra for an aerosol, smoke or vapour sample. The one or more sample spectra are subjected to pre-processing and then multivariate and/or library based analysis so as to classify the aerosol, smoke or vapour sample. The results of the analysis are used for various surgical or non-surgical applications.

A composition of a focused portion corresponding to a portion of a molecular ion is estimated as a partial composition based on a mass of the focused portion. An initial composition search range is modified based on the partial composition. A composition of the molecular ion is estimated as an overall composition based on a mass of the molecular ion under a modified composition search range. A way of modifying the composition search range may include a method for modifying a lower limit to a range of the number of atoms and a method for adding a new range of the number of atoms associated with a new chemical element.

A composition estimation target peak is selected from a mass spectrum of a sample, and a group of measured isotope peaks related to the composition estimation target peak is selected. A composition candidate for the sample is estimated based on the composition estimation target peak. A distribution of a theoretical isotope peak corresponding to the composition candidate is calculated. Presence or absence of an adduct ion or a desorbed ion in the sample is determined based on a first mass difference between isotopes in a distribution of the measured isotope peaks and a second mass difference between isotopes in the distribution of the theoretical isotope peak.

Exemplary embodiments relate to the calibration of mass spectrometry data, and may be especially useful for calibrating collision cross sectional data. These techniques apply assisted (rather than automated) calibration techniques. Context-sensitive user interfaces are presented that allow a user to review matches made by a calibration algorithm, and to override prior selections to improve the fit of a model used to make a calibrating adjustment. The calibrating adjustment can then be applied to past or future data coming from the device in order to normalize it and allow it to be compared to other data.

A method of gain calibration for an ion detector operating at a detector voltage is described. The method includes steps of: generating single ions; determining a parameter of a first relationship between a detector output of an ion detector and a number of ions for a first detector voltage; detecting an ion peak at the ion detector using the first detector voltage; adjusting the detector voltage; and determining a parameter of a second relationship between the detector output and the number of ions for the second detector voltage. A system including a mass spectrometer arrangement and a controller configured to operate the mass spectrometer arrangement in accordance with this method is also described.

The present invention provides methods and systems using gas-phase separation with mass spectrometry analysis instead of liquid chromatography, thereby enabling faster peptide, proteome, and multi-omic analysis. Also provided are improved methods and software for data independent acquisition. One embodiment referred to as Direct Infusion—Shotgun Proteome Analysis (DI-SPA) used with data-independent acquisition mass spectrometry (DIA-MS), resulted in targeted quantification of over 500 proteins within minutes of MS data collection (˜3.5 proteins/second). Enabling fast, unbiased protein and proteome quantification without liquid chromatography, DI-SPA offers a new approach to boosting throughput critical to drug and biomarker discovery studies that require analysis of thousands of proteomes. This invention is also able to perform complex multi-omic analysis of proteomes, lipidomes, and metabolomes on a single platform.

A method includes obtaining a first mass spectrum; selecting a first peak of the first mass spectrum; fragmenting and analyzing ions of the first peak to obtain a second mass spectrum; performing a real-time spectral search for compounds corresponding to peaks in the second mass spectrum; identifying fragments for the compounds identified based on the real-time spectral search; adding mass-to-charge ratios for the fragments to an exclusion list; selecting a second peak present in the first mass spectrum and not on the exclusion list; and fragmenting and analyzing ions of the second peak to obtain a third mass spectrum.

The disclosure features mass spectrometry systems and methods that include an ion source, an ion trap, a detector subsystem featuring first and second detector elements, and a controller electrically connected to the ion source, the ion trap, and the detector subsystem and configured so that during operation of the system, the controller: applies an electrical signal to the ion source to generate positively and negatively charged particles from sample particles in the system; applies an electrical signal to the ion trap to eject a plurality of particles from the ion trap through a common aperture of the ion trap, and determines information about the sample particles based on first and second electrical signals generated by the ejected particles.

Before each sample of a series of batch samples is introduced into a liquid sample delivery device, an ion source device receives aqueous mobile phase solution from the liquid sample delivery device and ionizes its compounds, producing an ion beam. A tandem mass spectrometer performs a neutral loss or precursor ion scan on the ion beam to measure intensities of two or more precursor ions corresponding to a known aqueous mobile phase solution compound. Intensity measurements for each of the two or more different precursor ions are compared to previously stored intensities to determine the threshold times at which these measurements indicate orifice contamination. A threshold time is then predicted for a known compound of interest of the batch samples based on the m/z value of the known compound of interest and the m/z value and the threshold time of each of the two or more different precursor ions.

An analysis device collects data by performing a predetermined analysis on each specimen and processes the data. The analysis device includes an analysis processing unit (23) configured to execute multivariate analysis processing based on collected data for analysis of a difference between a plurality of measurement targets or classification of the plurality of measurement targets, a feature extraction unit (24) configured to extract a characteristic parameter or element estimated to be mainly related to a difference or classification from a multivariate analysis result according to a predetermined criterion, an image creation unit (25) configured to create an image of a predetermined two-dimensional range corresponding to the parameter or element extracted by the feature extraction unit, and a display processing unit (26) configured to assign a same visual aspect to the characteristic parameter or element extracted on the multivariate analysis result and the image created correspondingly and display the multivariate analysis result and the image on a display unit (4).