Certain embodiments described herein are directed to injector inserts and injector assemblies. In some examples, an injector insert that includes an inlet comprising a substantially inert metal is described. In other examples, an injector that includes a major amount of a substantially inert metal in a fluid flow path is disclosed. Devices and systems using the injectors inserts and injectors are also described.

A method of mass spectrometry is disclosed comprising: performing a plurality of cycles of operation during a single experimental run, wherein each cycle comprises: mass selectively transmitting precursor ions of a single mass, or range of masses, through or out of a mass separator or mass filter at any given time, wherein the mass separator or mass filter is operated such that the single mass or range of masses transmitted therefrom is varied with time; and mass analysing ions.

There is provided a method of guiding ions, comprising providing an ion guide comprising a plurality of electrodes, confining ions radially within said ion guide by applying one or more voltages to said plurality of electrodes, applying an orthogonal DC field along at least a portion of said ion guide in order to control the temperature of ions as they travel through said ion guide, and applying an electrostatic driving potential to said plurality of electrodes to urge ions along the axial length of the ion guide, wherein said electrostatic driving potential is applied in the form of a DC travelling wave potential or other transient DC potential.

A linear ion trap system includes a linear ion trap having at least two discrete trapping regions for processing ions. An RF electrical potential generator produces two RF waveforms applied to a pair of pole electrodes of the linear ion trap forming a RF trapping field component to trap ions radially. A multi-output DC electrical potential generator produces a first set of multiple DC field components superimposed to the RF trapping field component and distributed across the length of the linear ion trap to control ions axially. A control unit is configured to switch the DC electrical potentials and DC field components collectively forming a first trapping region of the at least two discrete trapping regions that is populated with ions to alter ion potential energy from a first level to a second level, and to enable at least a first ion processing step in at least one of the first and second levels.

A method of mass spectrometry is disclosed comprising: performing a plurality of cycles of operation during a single experimental run, wherein each cycle comprises: mass selectively transmitting precursor ions of a single mass, or range of masses, through or out of a mass separator or mass filter at any given time, wherein the mass separator or mass filter is operated such that the single mass or range of masses transmitted therefrom is varied with time; and mass analysing ions.

Provided is a mass spectrometer including: a measurement condition setter (42) configured to set a plurality of measurement conditions which are different from each other in terms of the set value of at least one measurement parameter; a measurement executer (43) configured to acquire a plurality of sets of mass spectrometric data respectively corresponding to the plurality of measurement conditions; a product ion extractor (44) configured to extract product ions detected with intensities exceeding a previously determined reference value; an MRM spectrum element information creator (45) configured to determine the mass-to-charge ratios and measured intensities of the extracted product ions, the mass-to-charge ratio of the precursor ion, as well as the measurement condition, and to create a plurality of pieces of MRM spectrum element information; an MRM spectrum composer (46) configured to compose an MRM spectrum from the mass-to-charge ratios and the measured intensities of the product ions included in the plurality of pieces of MRM spectrum element information; and a library data creator (47) configured to relate the MRM spectrum to information concerning the target compound to create library data for the target compound.

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.

A sampling period of an A/D converter is set in accordance with an ion pulse ejection operation of a collision cell of an accumulation type. Start timing of the sampling period is changed in accordance with a selected m/z of a second mass analysis unit. In addition, end timing of the sampling period may be changed in accordance with the selected m/z of the second mass analysis unit. In place of the sampling period, a data cut-out period may be changed.

A method of injecting ions into an ion storage device, comprising: providing an RF trapping field in the ion storage device that defines a trapping volume in the ion storage device by applying one or more RF voltages to one or more trapping electrodes; providing a gas in the trapping volume; injecting ions into the trapping volume through an aperture in an end electrode located at a first end of the ion storage device, the end electrode having a DC voltage applied thereto; reflecting the injected ions at a second end of the ion storage device, opposite to the first end, thereby returning the ions to the first end; and ramping the DC voltage applied to the end electrode during the period between injecting the ions through the aperture and the return of the ions to the first end, such that by the time the ions return to the first end for a first time a potential barrier is established by the ramped DC voltage that prevents returning ions from striking the end electrode. Also an apparatus for injecting ions into an ion storage device, which comprises a controller for ramping a first DC voltage applied to an end electrode of the device having an entrance aperture during a period between injection of ions through the entrance aperture and a return of the injected ions to the aperture so as to establish a potential barrier that prevents returning ions from striking the end electrode.

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.