An ion analyzer includes: a reaction chamber 2 into which precursor ions derived from a sample component are introduced; a radical generation unit including an insulating tube 551, and a discharge unit 54, 552 configured to generate a discharge inside the insulating tube; a gas supply unit 52, 53 capable of supplying a first gas which is a radical raw material gas, and a second gas which is any of an oxygen gas, an ozone gas, a nitrogen gas, a gas of a compound containing an oxygen atom or a nitrogen atom, and a rare gas to an inside of the insulating tube; an evacuation unit 57 configured to evacuate the inside of the insulating tube; a radical introduction unit 55 configured to introduce radicals into an inside of the reaction chamber; and a control unit 93 configured to perform a first operation of introducing the first gas into the inside of the insulating tube, generating radicals by generating a discharge, and introducing the radicals into the inside of the reaction chamber, and a second operation of introducing the second gas into the inside of the insulating tube.

An apparatus (100, 300, 700) is described, comprising: a linear ion trap (102) comprising two pairs of pole electrodes and a radiofrequency, RF, electrical potential supply (117) configured to apply respective RF waveforms to the pairs of pole electrodes, thereby forming a RF trapping field component to trap analyte ions (116) radially in a trapping region (115) of the linear ion trap for processing of the analyte ions (116) therein; a charged particle source (101) comprising a pulse valve (103), a conduit (106, 107), having an entrance in fluid communication therewith and an exit, wherein the conduit (106, 107) extends in the direction of the trapping region (115), and a discharge device (108) electrically coupled to an electrical potential supply (109) and disposed between the entrance and the exit of the conduit (106, 107), wherein the pulse valve (103) is configured to release a gas pulse from a gas supply into the entrance of the conduit (106, 107) and wherein the electrical potential supply (109) is configured to apply a high voltage to the discharge device (108) to generate a discharge (110) in the gas pulse in the conduit (106, 107), thereby generating charged particles (114) from the gas and accelerating the generated charged particles in the direction of the trapping region (115). A method is also described.

A mass spectrometer system comprises: (a) an ion source; (b) a mass filter or a time-of-flight (TOF) ion separator configured to receive a stream of first-generation ions from the ion source; (c) an ion storage device having an ion inlet configured to receive a stream of filtered ions comprising a plurality of ion species from the mass filter or TOF separator and to accumulate the plurality of ion species therein; (d) an ion mobility cell having an ion inlet configured to receive an accumulated batch of ion species from the ion storage device and an ion outlet configured to release, one at a time, the individual ion species therefrom; and (e) a mass analyzer configured to receive and mass analyze each first-generation ion species or each fragment ion species generated by fragmentation or other reaction of the various first-generation ion species.

A method of mass and/or ion mobility spectrometry is disclosed that includes ionising analyte from a sample so as to generate a plurality of ions, separating precursor ions from first fragment and/or other ions of the plurality of ions, fragmenting or reacting at least some of the precursor ions using a fragmentation, reaction or collision device so as to generate second fragment ions, and then analysing at least some ions that emerge from the fragmentation, reaction or collision device. The sample is classified and/or identified based on the analysis of the second fragment ions.

Systems and methods are disclosed for identifying actual XIC peaks of compounds of interest from samples so that more accurate expected retention times and more accurate expected retention time windows can be calculated. In one system, an actual XIC peak is identified using standard samples. The ratio of the quantity of the compound of interest in any two different samples is known, so this ratios is compared to the intensities of the XIC peak calculated in the two samples to identify an actual XIC peak. In another system, an actual XIC peak is identified using information about other compounds of interest in a plurality of samples. It is known that the XIC peaks of compounds of interest in the same samples have a similar distribution of retention times across those samples, so the distributions of retention times of XIC peaks are compared to identify actual XIC peaks.

The invention provides hybrid mass spectrometric systems which comprise an ion source, a first trapped ion mobility spectrometry (TIMS) analyzer and a mass analyzer, wherein the TIMS analyzer is located and operated in a first vacuum chamber at an elevated pressure above 500 Pa, and methods for operating the hybrid mass spectrometric systems.

A mass spectrometer comprises an orifice plate having an orifice, a first multipole ion guide in a first chamber downstream of said orifice plate, said first multipole ion guide comprising a plurality of rods, and a second multipole ion guide in a second chamber downstream of said first chamber, said second multipole ion guide comprising a plurality of rods. A first ion lens is between the first and the second multipole ion guides. A third multipole ion guide is in a third chamber downstream of the second chamber, the third multipole ion guide comprises a plurality of rods. A second ion lens is between the second and third chambers. A tunable DC voltage source applies a tunable DC offset voltage to at least one of the above ion guide and ion lenses to increase an axial kinetic energy of the ions to cause at least one of declustering and/or fragmentation.

Provided are methods for determining the amount of tamoxifen and its metabolites in a sample by mass spectrometry. In some aspects, the methods provided herein determine the amount of N-Desmethyl Tamoxifen. In some aspects, the methods provided herein determine the amount of N-Desmethyl Tamoxifen and other tamoxifen metabolites. In some aspects, the methods provided herein determine the amount of tamoxifen, N-Desmethyl Tamoxifen, and other tamoxifen metabolites.

A method for determining an isotopic profile for a molecule is provided. The isotopic profile is indicative of an isotopic content for the molecule. The method comprises mass selecting ions of the molecule in a mass window, the mass window excluding a mass for a monoisotopic molecular ion and including a mass for at least one isotopic variant of the monoisotopic molecular ion. The method comprises fragmenting the mass selected ions into fragment ions, performing mass analysis on one or more of the fragment ions to produce a mass spectrum, and determining the isotopic profile for the molecule, the isotopic profile comprising at least one data value. Each data value is calculated for a fragment ion as a function of intensities of multiple peaks in the mass spectrum. A computer program is provided. A mass spectrometry system is provided. A method for identifying a sample is provided.

A method of performing targeted multiplexed mass spectrometry includes performing, at a mass spectrometer, a targeted MS3 analysis of an isobaric tag-labeled target analyte included in a multiplex sample eluting from a column. The targeted MS3 analysis is performed during an acquisition segment scheduled based on an expected retention time of the isobaric tag-labeled target analyte. The method further includes performing, during the acquisition segment, a plurality of MS2 analyses of product ions derived from components included in the multiplex sample and eluting from the column. The method further includes determining, based on MS3 mass spectra acquired by the targeted MS3 analysis and MS2 mass spectra acquired by the plurality of MS2 analyses, a relative quantity of the isobaric tag-labeled target analyte in the multiplex sample.