An example system includes an electron ionization ion source and a mass analyzer. The electron ion source is configured, during operation of the system, to create from sample molecules a beam of ions extending along an ion beam axis. The system also includes a collision cooling chamber comprising a gas manifold and an electric field generator. The cooling chamber defines an entrance aperture and an exit aperture on respective opposing ends of the cooling chamber, the entrance aperture of the cooling chamber being in axial alignment with the ion beam axis. The cooling chamber is configured, during operation of the system, to generate a radio frequency (RF) field within the cooling chamber using the electric field generator, and receive collision gas through the gas manifold to pressurize the cooling chamber.

In some examples, an ion funnel-based collision cell may include an ion funnel entrance section formed by a plurality of adjacently disposed entrance members. Each entrance member of at least one pair of the adjacently disposed entrance members may include a successively larger opening to form a tapered or profiled entrance for ions entering the ion funnel-based collision cell. An insulation material may be disposed adjacent to or in contact with each entrance member of the at least one pair of the adjacently disposed entrance members to prevent, outside of each successively larger opening, flow of gas between each entrance member of the at least one pair of the adjacently disposed entrance members.

A method for analyzing a plurality of molecules with cryogenic vibrational spectroscopy including the steps of providing a packet of molecules in a ionized form, injecting the packet into an ion mobility section, spatially separating the ions of the packet into subpackets according to their collisional cross section (CCS), recompressing the subpackets, by removing an empty space between them, loading the ions into a cryogenic ion trap by keeping subpackets with different collisional cross section in a respective separate compartment, cooling the ions in collisions with a buffer gas, tagging the ions by attaching a messenger molecule, sending a pulse to the trap to excite vibrations of the cold, trapped, and messenger-tagged ions, and separately ejecting ion subpacket from the trap into an extraction region of a time-of-flight mass spectrometer and measuring the number of remaining messenger-tagged ions and untagged ions for each subpacket.

A method, system, and computer-readable medium for identifying and creating a database of isomers and isobars of molecules including the steps of performing isomer or isobar separation on molecules to obtain separate isomeric or isobaric molecules, measuring mass-to-charge ratios (m/z) to obtain IR fingerprints of the separate isomeric or isobaric molecules, and storing first data on the mass-to-charge ratios (m/z) and/or the IR fingerprints of the separate isomeric or isobaric molecules to a database.

The ion trap comprises a multipole electrode assembly, a first confining electrode, and a second confining electrode. The multipole electrode assembly is configured to confine ions of the first polarity to an ion channel extending in an axial direction of the multipole electrode assembly. The first confining electrode is provided adjacent to the multipole electrode assembly and extends in the axial direction of the multipole electrode assembly. The second confining electrode is provided adjacent to the multipole electrode assembly and extends in the axial direction of the multipole electrode assembly aligned with the first confining electrode. The first and second confining electrodes are spaced apart in the axial direction in order to define an ion confining region of the ion channel between the first and second confining electrodes. The first and second confining electrodes are configured to receive a DC potential of the first polarity to further confine ions within the ion channel in the ion confining region.

A method for analyzing a plurality of molecules with cryogenic vibrational spectroscopy including the steps of providing a packet of molecules in a ionized form, injecting the packet into an ion mobility section, spatially separating the ions of the packet into subpackets according to their collisional cross section (CCS), recompressing the subpackets, by removing an empty space between them, loading the ions into a cryogenic ion trap by keeping subpackets with different collisional cross section in a respective separate compartment, cooling the ions in collisions with a buffer gas, tagging the ions by attaching a messenger molecule, sending a pulse to the trap to excite vibrations of the cold, trapped, and messenger-tagged ions, and separately ejecting ion subpacket from the trap into an extraction region of a time-of-flight mass spectrometer and measuring the number of remaining messenger-tagged ions and untagged ions for each subpacket.

An ion transport device of a mass spectrometer includes a plurality of pole rod arranged in first and second parallel rows and a controller. The controller is configured to apply voltages in a repeating voltage pattern to the pole rods of the first row and apply a common voltage to the pole rods of the second row thereby creating a plurality of potential wells capable of capturing ions, wherein each ion transport cell receives the same pattern of voltages; move the repeating voltage pattern along the pole rods of the first row to move captured ions within and between the plurality of ion transport cells along the ion transport device; and apply at least one ejection voltage to one or more electrodes to cause ions to be ejected from the ion transport device.

A method for operating a mass spectrometer comprises: generating a stream of ions by an ion source; directing the stream of ions into a first one of a pair of ion storage locations and trapping a first portion of the ions therein; directing a packet of ions from the other one of the pair of ion storage locations into an ion cooling cell that damps the kinetic energy of the ions comprising the packet of ions; directing the packet of ions to a mass analyzer of the mass spectrometer for mass analysis thereby; directing the first portion of ions from the first one of the pair of ion storage locations into the ion cooling cell; and directing the first portion of ions to the mass analyzer for mass analysis thereby.

An example system includes an electron ionization ion source and a mass analyzer. The electron ion source is configured, during operation of the system, to create from sample molecules a beam of ions extending along an ion beam axis. The system also includes a collision cooling chamber comprising a gas manifold and an electric field generator. The cooling chamber defines an entrance aperture and an exit aperture on respective opposing ends of the cooling chamber, the entrance aperture of the cooling chamber being in axial alignment with the ion beam axis. The cooling chamber is configured, during operation of the system, to generate a radio frequency (RF) field within the cooling chamber using the electric field generator, and receive collision gas through the gas manifold to pressurize the cooling chamber.

The invention provides a mass spectrometer that comprises a collision cell having an axial electric field that enhances transmission of light ions, especially elemental ions, through the collision cell, relative to heavier ions. The invention also provides methods of mass spectrometry that employ an axial electric field that is provided in a collision cell.