An ion analyzer for analyzing product ions generated by irradiating precursor ions derived from a sample component with radicals, the ion analyzer including a reaction chamber 2, a radical supply unit 5, 6 configured to generate radicals and supply the radicals to the reaction chamber, a radical temperature acquisition unit 911, 912 configured to acquire a temperature of the radicals to be supplied to the reaction chamber, a standard substance supply unit 11 configured to supply a predetermined amount of predetermined precursor ions to the reaction chamber, the predetermined precursor ions being generated from a standard substance whose activation energy of a reaction in which the radicals attach to the standard substance is known, an ion measurement unit 92 configured to measure an amount of predetermined product ions generated from the precursor ions derived from the standard substance by the reaction with the radicals, a reactive radical amount calculation unit 93 configured to obtain an amount of reactive radicals based on the amount of the predetermined product ions, and a radical density calculation unit 94 configured to obtain a radical density based on the temperature of the radicals, the activation energy, and the amount of the reactive radicals.

A mass isolation device selects a precursor ion of a sample that has been digested using a protease. A first fragmentation device fragments the precursor ion using collision-induced dissociation (CID), and the resulting product ions are analyzed using a mass analyzer producing a CID spectrum. A list of theoretical candidate glycopeptide sequences is determined from CID spectrum. The mass isolation device again selects the precursor ion of the sample. A second fragmentation device fragments the precursor ion using electron-based dissociation (ExD), and the resulting product ions are analyzed using the mass analyzer producing a CID spectrum. For each sequence of the list, the sequence is computationally fragmented, producing theoretical fragments, mass-to-charge ratio (m/z) values are calculated for the theoretical fragments, and the sequence is scored using c and z fragment matching rules. The highest scoring sequence is identified as a peptide sequence of a glycopeptide of the sample.

A method of ionising a sample is disclosed comprising nebulising a sample which includes first biomolecules such as bovine insulin comprising one or more disulphide (S—S) bonds. A stream of droplet or charged droplets comprising one or more disulphide (S—S) bonds is directed so as to impact upon a target (106) or electrode so as to cause the breaking of a portion of the disulphide bonds. Alternatively, charged droplets may pass through an electric field region determined by an electrode (106) arranged downstream of a nebuliser or electrospray probe and an ion inlet (104) of a mass spectrometer so as to cause the breaking of a portion of the disulphide bonds.

Systems, methods, and devices to dissociate ions using one or more light emitting diodes (LEDs). A mass spectrometer for ion dissociation includes an ion source for providing ions for dissociation, a mass analyzer, and a photodissociation (PD) device. The PD device includes an ion transport device. The ion transport device is configured perform one or more of: transporting the ions through the PD device, and trapping the ions within a region of the PD device. The PD device also includes one or more LEDs positioned to irradiate the ions in the PD device, resulting in fragmentation of the ions.

The invention generally relates to systems and methods for collision induced dissociation of ions in an ion trap. In certain aspects, the invention provides a system that includes a mass spectrometer having an ion trap, and a central processing unit (CPU). The CPU includes storage coupled to the CPU for storing instructions that when executed by the CPU cause the system to generate one or more signals, and apply the one or more signals to the ion trap in a manner that all ions within the ion trap are fragmented at a same Mathieu q value.

A method of producing ions from a sample is disclosed. The method comprises directing a spray of droplets onto a sample, and causing droplets comprising analyte from the sample to impact upon a surface so as to generate analyte ions.

Devices and methods for surface-induced dissociation (SID) are disclosed. In one aspect, a device for SID is disclosed which, in one embodiment includes a collision surface, a deflector configured to guide precursor ions from a pre-SID region to the collision surface to cause SID, and an ion carpet having applied electrical properties configured to guide product ions resulting from collision with the collision surface to a post-SID region. In another aspect, a method for SID is disclosed which, in one embodiment includes guiding, by a deflector, precursor ions from a pre-SID region to a collision surface to cause SID, and guiding, by an ion carpet having selected applied electrical properties, product ions resulting from collision with the collision surface to a post-SID region.

A mass isolation device selects a precursor ion of a sample that has been digested using a protease. A first fragmentation device fragments the precursor ion using collision-induced dissociation (CID), and the resulting product ions are analyzed using a mass analyzer producing a CID spectrum. A list of theoretical candidate glycopeptide sequences is determined from CID spectrum. The mass isolation device again selects the precursor ion of the sample. A second fragmentation device fragments the precursor ion using electron-based dissociation (ExD), and the resulting product ions are analyzed using the mass analyzer producing a CID spectrum. For each sequence of the list, the sequence is computationally fragmented, producing theoretical fragments, mass-to-charge ratio (m/z) values are calculated for the theoretical fragments, and the sequence is scored using c and z fragment matching rules. The highest scoring sequence is identified as a peptide sequence of a glycopeptide of the sample.

The invention generally relates to systems and methods for collision induced dissociation of ions in an ion trap. In certain aspects, the invention provides a system that includes a mass spectrometer having an ion trap, and a central processing unit (CPU). The CPU includes storage coupled to the CPU for storing instructions that when executed by the CPU cause the system to generate one or more signals, and apply the one or more signals to the ion trap in a manner that all ions within the ion trap are fragmented at a same Mathieu q value.

The disclosure features systems and methods that include: exposing a biological sample to an ion beam that is incident on the sample at a first angle to a plane of the sample by translating a position of the ion beam on the sample in a first direction relative to a projection of a direction of incidence of the ion beam on the sample; after each translation of the ion beam in the first direction, adjusting a focal length of an ion source that generates the ion beam; and measuring and analyzing secondary ions generated from the sample by the ion beam after adjustment of the focal length to determine mass spectral information for the sample, where the sample is labeled with one or more mass tags and the mass spectral information includes populations of the mass tags at locations of the sample.