Methods and systems for performing ionization, including applying radio frequency energy to a chemical compound so that at least one ion of the compound or of a compound fragment is generated, and detecting at least one such ion.

Systems and methods for measuring cross-modal similarity between mass spectra and peptides are provided. A deep learning network can be used and, by training on a variety of labeled spectra, the network can embed both spectra and peptides onto a Euclidean subspace where the similarity is measured by the L2 distance between different points. The network can be trained on a novel loss function, which can calculate the gradients from sextuplets of data points.

A mass spectrometer is disclosed wherein highly charged fragment ions resulting from Electron Transfer Dissociation fragmentation of parent ions are reduced in charge state within a Proton Transfer Reaction cell by reacting the fragment ions with a neutral superbase reagent gas such as Octahydropyrimidolazepine.

A mass spectrometer is disclosed wherein highly charged fragment ions resulting from Electron Transfer Dissociation fragmentation of parent ions are reduced in charge state within a Proton Transfer Reaction cell by reacting the fragment ions with a neutral superbase reagent gas such as Octahydropyrimidolazepine.

A focusing ion guiding apparatus includes at least one ion guiding inlet and ion guiding outlet connected to each other via a transport axial line; at least one group of focusing electrode structures comprising at least one smooth and non-concave focusing electrode or focusing electrode array to which a focusing voltage is applied, the focusing electrode structure causing the ions transported in the apparatus to be radially focused for many times under the action of a focusing electric field formed by the focusing electrode structure; and a neutral gas flow transported in the axial direction, a diffusion path of the gas flow in an at least partially radial direction relative to the axial direction being blocked by the focusing electrode or its bearing substrate to increase a transport velocity of the gas flow in the axial direction and reduce retention or turbulence of the transported ions.

A focusing ion guiding apparatus includes at least one ion guiding inlet and ion guiding outlet connected to each other via a transport axial line; at least one group of focusing electrode structures comprising at least one smooth and non-concave focusing electrode or focusing electrode array to which a focusing voltage is applied, the focusing electrode structure causing the ions transported in the apparatus to be radially focused for many times under the action of a focusing electric field formed by the focusing electrode structure; and a neutral gas flow transported in the axial direction, a diffusion path of the gas flow in an at least partially radial direction relative to the axial direction being blocked by the focusing electrode or its bearing substrate to increase a transport velocity of the gas flow in the axial direction and reduce retention or turbulence of the transported ions.

A mass spectrometry imaging system includes an ionization source located at a first location configured to produce ions from a surface of a sample at the first location; a mass spectrometer located at a second location configured to perform mass spectrometry analysis by analyzing the produced ions based on mass to charge ratio of the ions; and an ion transfer device configured to transfer the ions from the first location to the second location such that the ion transfer device includes a plurality of electrodes, the plurality of electrodes configured to be flexible or flexibly connected to each other, and the ion transfer device is configured to be flexible or re-configurable while transferring the ions.

A mass spectrometry imaging system includes an ionization source located at a first location configured to produce ions from a surface of a sample at the first location; a mass spectrometer located at a second location configured to perform mass spectrometry analysis by analyzing the produced ions based on mass to charge ratio of the ions; and an ion transfer device configured to transfer the ions from the first location to the second location such that the ion transfer device includes a plurality of electrodes, the plurality of electrodes configured to be flexible or flexibly connected to each other, and the ion transfer device is configured to be flexible or re-configurable while transferring the ions.

An ion guide may comprise a set of plate electrodes, each plate electrode having a plurality of apertures formed therethrough. The set of plate electrodes are spatially arranged such that a relative positioning of each plurality of apertures of a respective plate electrode of the set of plate electrodes and respective adjacent plate electrodes of the set of plate electrodes defines a continuous ion flight path through the respective plurality of apertures of each plate electrode of the set of plate electrodes. The continuous ion flight path has a helical-based and/or spiral-based shape.

An ion guide may comprise a set of plate electrodes, each plate electrode having a plurality of apertures formed therethrough. The set of plate electrodes are spatially arranged such that a relative positioning of each plurality of apertures of a respective plate electrode of the set of plate electrodes and respective adjacent plate electrodes of the set of plate electrodes defines a continuous ion flight path through the respective plurality of apertures of each plate electrode of the set of plate electrodes. The continuous ion flight path has a helical-based and/or spiral-based shape.