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.

A method of removing nuclear isobars from a mass spectrometric technique comprising directing ions, decelerating the ions, neutralizing a first portion of the ions, creating residual ions and a second portion of the ions, reionizing a selective portion of the ions, re-accelerating the selective reionized portion of ions, and directing the reionized portion of ions to a detector. An apparatus to remove nuclear isobars comprising a deceleration lens, an equipotential surface, an electron source to neutralize a portion of the ion beam, a deflector pair, a tunable resonance ionization laser for selective resonant reionization, and an acceleration lens.

A method for correcting mass spectral m/z values comprises: detecting mass spectra for different amounts of sample ions within an ion trapping mass analyzer; evaluating an observable difference of relative m/z shift from the detected mass spectra of at least two of the different amounts of ions induced by space charge; evaluating a visible total charge Q.sub.v and/or the difference of a visible total charge Q.sub.v from the detected mass spectra; determining, from the evaluated observable differences of relative m/z shift and the evaluated visible total charges Q.sub.v and/or differences of the visible total charge Q.sub.v, a slope of a linear correlation between relative m/z shift and visible total charge Q.sub.v; determining a relative m/z shift of sample ions detected in a mass spectrum by multiplying visible total charge Q.sub.v with the determined slope; and correcting the m/z values in the mass spectrum using its determined relative m/z shift.

An ion source assembly for use in a mass spectrometry system comprises a housing defining an ionization chamber disposed in fluid communication with a sampling orifice of a mass spectrometer system. The housing defines a first opening for coupling to a first electrospray probe to discharge a liquid sample at flow rates greater than a nanoflow range along a longitudinal axis that is substantially orthogonal to a central axis of the sampling orifice. An elongate auxiliary electrode assembly extends from the housing to an electrically conductive distal end disposed in the ionization chamber such that the electrically conductive distal end is disposed substantially on the central axis of the sampling orifice. The electrically conductive distal end may be coupled to a power supply to generate an electric field to improve the desolvation of the sample plume and the transport of ions ejected from the sample plume into the sampling orifice.

A method of analysis using mass spectrometry and/or ion mobility spectrometry is disclosed. The method comprises: using a first device to generate smoke, aerosol or vapour from a target comprising or consisting of a microbial population; mass analysing and/or ion mobility analysing said smoke, aerosol or vapour, or ions derived therefrom, in order to obtain spectrometric data; and analysing said spectrometric data in order to analyse said microbial population.

A machine, article, process of using, process of making, products produced thereby and necessary intermediates. Illustratively, there can be a process that includes: ionizing at least some injected gas to form ions; confining, without using magnetic fields, at least some of said ions to produce confined ions; accumulating at least some of said confined ions to produce accumulated ions; cooling at least some of said accumulated ions to produce cooled ions; compressing, without using magnetic fields, at least some of said accumulated ions to produce compressed ions; accelerating at least some of said compressed ions to produce accelerated ions; ejecting at least some of said accelerated ions; and measuring at least one property of said ejected ions.

Disclosed is a method for simultaneous determination of particle size distribution, concentrations of nanoparticulate mercury (Hg-NPs) in natural soils. The method uses sodium pyrophosphate as the extractant, and allows quick extraction of Hg-NPs in the soil without dissolution or aggregation. In combination with spICP-MS determination, the method makes it possible to simultaneously determine the particle size distribution and concentration of Hg-NPs in the complex soil matrix, with accurate determination results.

Systems and methods are disclosed for utilizing an ion mobility cell to improve desolvation prior to interaction with a hydrogen-deuterium exchange reagent, thereby improving the accuracy of the HDX data generated by MS and reducing the effects of conformational changes that can occur with increased temperatures.

A method of mass and/or ion mobility spectrometry is disclosed that comprises accumulating ions for a first period of time (T1) one or more times so as to form one or more first groups of ions, accumulating ions for a second period of time (T2) one or more times so as to form one or more second groups of ions, wherein the second period of time (T2) is less that the first period of time (T1), analysing the one or more first groups of ions to generate one or more first data sets, analysing the one or more second groups of ions to generate one or more second data sets, and determining whether the one or more first data sets comprise saturated and/or distorted data. If it is determined that the one or more first data sets comprise saturated and/or distorted data, then the method further comprises replacing the saturated and/or distorted data from the one or more first data sets with corresponding data from the one or more second data sets.