A method of operating a mass spectrometer that allows for high-speed operation is disclosed. The method consists in separating the various steps needed to produce a mass spectrum into three or more conceptual stages in a pipeline, such that the instrument is performing steps to process more than two precursor-ion species simultaneously. In general, the number of stages in the pipeline should at least one more and, preferably, at least two more than the number of buffering storage devices in the instrument. The presently-taught methods and apparatus allow for nearly 100% duty cycle of ion accumulation for precursors of interest.

A system and method is described for characterizing glycopeptides which includes a first quadrupole mass filter, a multipole rod set of an ion guide, a lens electrode, an ExD device and a mass analyzer. The multipole rod set is adapted to receive a radial radio frequency (RF) trapping voltage and a radial dipole direct current (DC) voltage The lens electrode is adapted to receive an axial trapping alternating current (AC) voltage and a DC voltage. The ExD device performs electron capture dissociation or electron transfer dissociation, the ExD device being positioned so that an entrance of the ExD device is disposed on the other side of the lens electrode opposite the multipole rod set. The mass analyzer is positioned at an exit of the ExD device for receiving ions from the ExD device.

Certain configurations described herein are directed to mass spectrometer systems that can use a gas mixture to select and/or detect ions. In some instances, the gas mixture can be used in both a collision mode and in a reaction mode to provide improved detection limits using the same gas mixture.

An ionising apparatus for ionising a sample of gaseous fluid. The ionising apparatus comprises an ioniser configured to provide reactant ions; an ion modifier configured to modify the reactant ions, and a reaction region arranged to receive the modified reactant ions and a sample and to combine the sample with the modified reactant ions to ionise the sample for analysis by a detector configured to identify a substance of interest in the sample.

A mass spectrometer including: a reaction chamber into which a precursor ion derived from a sample molecule is introduced; a collision gas supply part configured to supply collision gas to the reaction chamber; a radical supply part configured to supply hydrogen radicals, oxygen radicals, nitrogen radicals, or hydroxyl radicals to the reaction chamber; a dissociation operation control part configured to control operations of the collision gas supply part and the radical supply part to generate the product ions by collision-induced dissociation and radical attachment dissociation of the precursor ion inside the reaction chamber, an ion detection part configured to mass-separate and detect ions ejected from the reaction chamber, and a spectrum data generation part configured to generate spectrum data based on a detection result by the ion detection part.

A method for parallel accumulation and serial fragmentation of ions, wherein ions are injected into a device capable of serial ejection using a pseudopotential barrier created by an RF voltage. In all instances, the ions may be filtered prior to accumulation in the device capable of serial ejection. In some cases this filtering may take the form of discrete isolation windows using isolation waveforms with multiple notches. In some cases these waveforms may be applied to a quadrupole mass filter. Following accumulation of the precursor ions, the initial population may be serially ejected using a pseudopotential barrier created by an RF voltage. Following serial ejection, the individual precursor ion populations are analyzed. In some cases, this analysis might involve additional rounds of ion isolation and manipulation (e.g., MSn, CID, ETD, etc.).

The present disclosure provides a method of analyzing the structure of a glycan sample, the method including: receiving data indicative of one or more spectra of mass-to-charge ratio (m/z) versus relative abundance of the glycan sample from a mass spectrometer (MS) instrument; generating a ratio according to the following Equation:

[00001]$\frac{a}{a+b}$

wherein a is a magnitude of one or more first peaks in the one or more spectra and b is the magnitude of one or more second peaks in the one or more spectra; determining that the ratio is within a range of a predetermined ratio; based on determining that the ratio is within the range of the predetermined ratio, determining that a predetermined structural characteristic is present in the glycan sample; and outputting an indication of the predetermined structural characteristic in the glycan sample.

An ion analyzer includes a reaction chamber into which precursor ions derived from a sample component are introduced, a radical irradiation unit that generates and emits a predetermined type of radicals, a standard substance supply unit that individually supplies kinds of standard substances to the reaction chamber, where activation energy of radical addition reaction is known for each of the kinds of standard substances, and the activation energies are different in magnitude, an ion measurement unit that measures an amount of predetermined product ions generated from precursor ions derived from the standard substance by irradiation with the radicals, and a radical temperature calculation unit that obtains an amount of radicals that caused the radical addition reaction from the amount of the predetermined product ions and obtains a radical temperature based on a relationship between the amount of the radicals obtained for each kind of standard substance and activation energy.

Methods and systems are provided herein for selectively removing product ions resulting from an ECD dissociation event from the interaction region of an ECD reaction cell, while other precursor peptide ions continue to undergo ECD within the interaction region, thereby reducing or preventing the occurrence of multiple electron capture events by the product ions. In some aspects, the preferential extraction of product ions from the interaction region during the ECD reaction can occur without an auxiliary AC field being generated within the interaction region. Additionally, in some aspects, the methods and systems disclosed herein can subject the various product ions to a non-dissociative charge reduction via exposure to reagent ions of the opposite polarity so as to selectively concentrate product ions to a lower charge state.

A method comprises: (1) making an extract of a biological sample; (2) repeatedly: (a) choosing a respective one of a plurality of pre-determined protein or polypeptide analyte compounds; (b) introducing a portion of the extract into an electrospray ionization source, thereby generating positive ions comprising a plurality of ion species; (c) isolating a plurality of subsets of the ion species comprising respective mass-to-charge (m/z) ratio ranges, each range including an m/z ratio corresponding to a respective protonation state of the chosen compound; (d) reacting the isolated plurality of subsets of first-generation ion species with proton transfer reaction reagent anions for a pre-determined time duration; (e) generating a mass spectrum of the product ion species; and (g) identifying either the presence or absence of the compound based on the mass spectrum; and (3) identifying the presence or absence of the microorganism within the sample based on analytes present.