Abstract: Improvements to a side-on Penning trap include methods to stabilize ions in the trap. The ions are stabilized by injecting ions in the focusing region of the non-uniform DC fields produced by the pad electrodes of the trap. Ions are injected along an injection axis shifted from the central axis of a gap between a positively biased electrode pad and negatively biased electrode pad of the trap. Improvements also include methods to compensate for the Lorentz force that is produced when ions are injected into a side-on Penning trap. Electrodes of an ion injection device are DC biased so that the electrodes produce an electric field along the axis of the device that compensates for the Lorentz force. Finally, methods are provided to increase the m/z range of ions injected into a side-on Penning trap by pre-trapping ions just before injection of the ions into the trap.

Abstract: The present teachings relate to methods, systems, and kits for analyzing a sample containing a glycopeptide of interest that can subject the glycopeptide of interest to a plurality of parallel deglycosylation reactions that differentially cleave the glycan, with the various products resulting from the deglycosylation reactions being differentially labeled (e.g., with isobaric and/or isomeric labeling reagents) to thereby produce labeled glycopeptides or labeled fragments of the glycopeptides. The products of the various deglycosylation reactions can then be mixed together and subject to LC-MS/MS using a single injection of the mixture. In accordance with various aspects, by associating the resulting mass spectral data with a particular deglycosylation reaction (e.g., based on the presence in the MS/MS data of product reporter ions associated with the particular differential labels), the methods and systems described herein can aid in the identification of the glycan structure.

Abstract: 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.

Abstract: Protein confidence values are calculated in proteomic analysis. A protein database is searched for proteins matching peptides found from mass spectrometry of a sample producing a set of proteins and a corresponding set of peptides. Peptide confidence values for the set of peptides are determined. Protein confidence values are calculated for the set of proteins based on the peptide confidence values. A protein is selected from the set of proteins with a largest protein confidence value, the largest protein confidence value is saved for the protein, the protein is removed from the set of proteins, and one or more peptides corresponding to the protein are removed from the set of peptides. Protein confidence values are recalculated for the set of proteins based on the peptide confidence values and an effect of removing the one or more peptides from the set of peptides.

Abstract: Methods and systems for processing fluids utilizing a digital microfluidic device and transferring droplets from the digital microfluidic device to a downstream analyzer are described herein. Methods and systems in accordance with the present teachings can allow for the withdrawal of fluid from a digital microfluidic device, and can in some aspects enable the integration of a digital microfluidic device as a direct, in-line sample processing platform from which a droplet can be transferred to a downstream analyzer.

Abstract: A mass spectrometer is provided having an ion source for generating ions from a sample in a high pressure region, a first vacuum chamber having an inlet aperture, and an exit aperture. The at least one ion guide can be between the inlet and exit apertures and can include an entrance end and an exit end. The at least one ion guide can have a plurality of electrodes arranged around a central axis defining an ion channel, each of the plurality of electrodes being tapered, a planar surface of each of the plurality of tapered electrodes facing the interior of the at least one ion guide, and the surface gradually being narrowed and tilted inward to provide a smaller inscribed radius at the exit; and a power supply for providing an RF voltage to the at least one ion guide.

Abstract: A quadrupole is filled with ions and the ions are cooled by applying a pressure and gas flow within the quadrupole. Ions are trapped in the quadrupole by applying a DC voltage and an RF voltage to quadrupole rods of the quadrupole, one or more DC voltages to a plurality of auxiliary electrodes of the quadrupole, and a DC voltage and an RF voltage to an exit lens at the end of the quadrupole. The ions are coherently oscillated after the filling and cooling by applying a coherent excitation between at least two rods of the quadrupole rods. The coherently oscillating ions are axially ejected through the exit lens and to a destructive detector for detection by changing one or more voltages of the one or more DC voltages of the plurality of auxiliary electrodes and changing the DC voltage of the exit lens.

Abstract: Systems and methods are provided for compound identification using multiple spectra that are a function of a variable instrument parameter that affects the intensity of fragment ions. A plurality of acquired fragment ion spectra that are a function of a variable instrument parameter for at least one ion are received from a mass spectrometer using a processor. The at least one ion is identified by comparing rates of change of mass intensity, with respect to the variable instrument parameter, for acquired and known fragment ions using the processor. Specifically, one or more acquired rates of change calculated for acquired fragment ions from the plurality of acquired fragment ion spectra are compared with one or more known rates of change calculated for one or more stored fragment ions of one or more known compounds in a database of known compounds.

Abstract: Systems and methods described herein utilize an ion guide for use in mass spectrometer systems, which ion guide can receive ions from an ion source for transmission to downstream mass analyzers, while preventing debris (e.g., unsolvated droplets, neutral molecules, heavy charged clusters) from being transmitted into a high-vacuum chamber of the mass spectrometer system. In various aspects, systems and methods in accordance with the present teachings can increase throughput, improve the robustness of the system, and/or decrease the downtime typically required to disassemble/clean sensitive components within the high-vacuum portions of the mass spectrometer system.

Abstract: At least one product ion mass spectrum produced by a tandem mass spectrometer is received. A chemical structure of a compound that corresponds to the at least one product ion mass spectrum is received. One or more elemental compositions are assigned to at least one peak in the at least one product ion spectrum based on the chemical structure using the processor. At least one elemental composition of the one or more assigned elemental compositions is selected for the at least one peak using the processor. The mass of the at least one peak is converted to the mass of the selected at least one elemental composition using the processor, producing a product ion mass spectrum with higher mass accuracy.

Abstract: A linear ion trap includes a quadrupole having four substantially parallel conductive rods that are substantially coextensive in the axial direction. The rods include two diagonally arranged pairs including one continuous, rod pair and one pair of rods that are segmented such that the two segments in a rod are capacitively coupled to facilitate an RF drop when an RF signal is applied to one longer segment and capacitively provided to the other shorter segment. An RF signal is provided to the continuous rods and tire longer segment of the segmented rods.

Abstract: Methods and systems are provided herein for varying the CoV about a nominal CoV-apex while monitoring the ion of interest corresponding to the nominal CoV-apex as it is transmitted by a DMS. In various aspects, the CoV can be swept or stepped across a series of values during the injection of ions into the DMS such that a composite spectra of the ion of interest transmitted by the DMS (or its product ions following one or more stages of fragmentation) can be generated so as to include the transmission of the particular ion at a CoV with optimum sensitivity (i.e., if distinct from the CoV-apex), thereby improving the robustness, accuracy, and/or selectivity during experimental conditions relative to known DMS techniques, which typically used a fixed CoV value for each ion of interest.

Abstract: Improvements to a side-on Penning trap include a feedback system for stabilizing the magnetic field. This system includes a magnetic sensor that measures the magnetic field and a solenoid coil that in response to the magnetic field measurements increases or decreases the overall magnetic field. Improvements also include a number of different configurations of the two sets of PCB electrodes used to produce the quadrupole electric field. Dimensions of the PCB electrodes are optimized, an equipotential surface electrode is added, and additional ring electrodes are added to produce a purer quadrupole field. A central disk electrode is segmented to direct charged particles to the trap center to make the trap useful for applications other than mass spectrometry. Finally, outer ring electrodes are segmented to increase the path of charged particles, thereby increasing sensitivity.

Abstract: Systems and methods are provided for providing a DMS precursor ion survey scan. An ion source configured to receive a sample is instructed to ionize the sample using a processor. A DMS device configured to receive ions from the ion source is instructed to separate precursor ions received from the ion source and transmit precursor ions using two or more CoVs using the processor. A mass analyzer configured to receive transmitted precursor ions from the DMS device is instructed to measure the m/z intensities of the transmitted precursor ions across an m/z range at each CoV of the two or more CoVs using the processor. The measured m/z intensities of the transmitted precursor ions received from the mass analyzer are stored as a function of m/z value and CoV using the processor. This produces a stored two-dimensional mapping of m/z intensities of the precursor ions of the sample.

Abstract: A system and method are provided for loading a sample into an analytical instrument using acoustic droplet ejection (“ADE”) in combination with a continuous flow sampling probe. An acoustic droplet ejector is used to eject small droplets of a fluid sample containing an analyte into the sampling tip of a continuous flow sampling probe, where the acoustically ejected droplet combines with a continuous, circulating flow stream of solvent within the flow probe. Fluid circulation within the probe transports the sample through a sample transport capillary to an outlet that directs the analyte away from the probe to an analytical instrument, e.g., a device that detects the presence, concentration quantity, and/or identity of the analyte. When the analytical instrument is a mass spectrometer or other type of device requiring the analyte to be in ionized form, the exiting droplets pass through an ionization region, e.g.

Abstract: Systems and methods are provided to perform sequential windowed acquisition of mass spectrometry data. A mass range and a mass window width parameter are received for a sample. A plurality of ions from the sample that are within the mass range are collected in an ion trap of a mass spectrometer. Two or more mass adjacent or overlapping windows are calculated to span the mass range using the mass window width parameter. Ions within each mass window are ejected from the ion trap. A mass spectrum is then detected from the ejected ions of the each mass window with a mass analyzer of the mass spectrometer, producing a collection of mass spectra for the mass range. The two or more mass windows can all have the same width, can all have different widths, or can have at least two mass windows with different widths.

Abstract: Methods and systems for analyzing ions in a magnetic ion trap are provided herein. In accordance with various aspects of the present teachings, the methods and systems described herein enable Fourier transform ion cyclotron resonance mass spectrometry across relatively narrow gap magnetic fields substantially perpendicular to the axis along which the ions are injected into the ion trap. As a result, smaller, less expensive magnets can be used to produce the high-intensity, uniform magnetic fields utilized in high performance FT-ICR/MS applications. Accordingly, the present teachings enable permanent magnets (as well as electromagnets) to generate these magnetic fields, potentially reducing the cost, size, and/or complexity of the systems described herein relative to conventional FT-ICR systems.

Abstract: Methods and systems are provided herein for on-line preparation of a sample for mass spectrometry. In accordance with various aspects of applicant's teachings, the methods and systems can provide for the reduction of a polypeptide, for example, on a liquid chromatography column and can reduce or eliminate the need to incubate the reducing agent with the polypeptide and/or expose the reduced polypeptide to an alkylating agent.

Abstract: Systems and methods are provided for microbial identification using cleavable tags. Control information is sent to a mass spectrometer to select a peptide labeled with a first tag of a known microbe, fragment the labeled peptide of the known microbe, and monitor for an intensity of the first tag in an MRM method using a processor. An ion source provides a beam of ions from a sample that includes peptides labeled with the first tag. The first tag binds to a peptide of a known microbe and is cleaved from the peptide of the known microbe during mass spectrometry. The mass spectrometer receives the beam of ions and is adapted to perform the MRM method on the beam of ions. If the intensity of the first tag received from the mass spectrometer exceeds a threshold value, the known microbe is identified in the sample using the processor.

Abstract: A multipole rod set of an ion guide is adapted to receive a radial RF trapping voltage and a radial dipole direct current DC voltage. A lens electrode of the ion guide is positioned at one end of the multipole rod set to extract ions from the multipole rod set and adapted to receive an axial trapping AC voltage and a DC voltage. A radial dipole DC voltage is applied to the multipole rod set and an axial trapping AC voltage is simultaneously applied to a lens electrode in order to extract a bandpass mass range of ions trapped in the multipole rod set. Alternatively, a radial RF trapping voltage amplitude is applied to the multipole rod set and an axial trapping AC voltage is simultaneously applied to the lens electrode in order to extract a bandpass mass range of ions trapped in the multipole rod set.