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: An RF voltage is applied across each electrode of a first array of evenly spaced, parallel, and coplanar electrodes and its corresponding electrode of a second array of evenly spaced, parallel, and coplanar electrodes. The RF voltage varies in amplitude according to an RF voltage amplitude gradient. The RF voltage produces an array of different quadrupole RF electric fields in a uniform gap between the first array and the second array. A DC voltage is superimposed on each electrode of the first array and its corresponding electrode of the second array. The DC voltage varies according to a DC voltage gradient in order to produce a DC electric field in the uniform gap. When ions are introduced in the uniform gap, the DC electric field causes the ions to drift toward quadrupole RF electric fields with increasing RF voltage amplitudes where the ions are trapped according to their m/z.

Abstract: Systems and methods for identifying precursor ions of product ions from combined product ion spectra are provided. N precursor ions are selected. N groups of the N precursor ions are created. The tandem mass spectrometer is instructed to perform multiplexed precursor ion selection on the continuous beam of ions, fragment each of the N?1 precursor ions, and measure the intensities of the product ions, producing N product ion spectra. A heat map is plotted, producing N heat maps. The N product ion spectra are combined into a combined product ion spectrum. A corresponding precursor ion of a peak is identified by finding a heat map of the N heat maps that does not have data for the mass of the peak and determining that a precursor ion of the N precursor ions that is not included in a group that produced the heat map is the corresponding precursor ion.

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.

Abstract: Systems and methods are provided for enabling or disabling a DMS device during an IDA method. Each cycle of the method includes a survey scan step, producing a precursor ion mass spectrum, and an MS/MS scan step. During the MS/MS scan step, one or more user-defined MS/MS scans are performed that correspond to compounds of interest found in the precursor ion mass spectrum. With each user-defined MS/MS scan, a DMS enable parameter that determines if the DMS device is enabled or disabled and one or more DMS parameters necessary to enable the DMS device for the corresponding compound of interest are received. During the MS/MS scan step, for each user-defined MS/MS scan, the DMS device is enabled or disabled according to the DMS enable parameter and one or more parameters of the DMS device are set according to the one or more DMS parameters.

Abstract: Apparatus, systems, and methods for reducing or eliminating crosstalk in ion mobility spectrometers are provided. In some aspects, the apparatus, systems, and methods can reduce or eliminate crosstalk without significantly increasing the overall capacitive load of the ion mobility system. In accordance with various aspects of the applicant's teachings, cross talk compensation circuits are disclosed herein that address resulting issues in RF pickup and/or crosstalk in ion mobility spectrometers used with high-sensitivity downstream mass spectrometers such as mass spectrometers having high velocity gas interfaces that can be coupled to the ion mobility spectrometer.

Abstract: Methods and systems are provided for reducing the occurrence of unwanted electrical discharge when operating an electrospray ion source to generate ions for mass spectrometric analysis. In accordance with various aspects of the applicant's teachings, the methods and systems described herein can provide for controlling the ion emission current so as to limit the onset of avalanche of electrical discharge between the electrospray electrode and the counter electrode under ionization conditions that typically tend to increase the likelihood of such discharge (arcing), while nonetheless providing for maximal ionization efficiency.

Abstract: Systems and methods are provided for multiplexed precursor ion selection using a filtered noise field (FNF). Two or more different precursor ions are selected using a processor. The processor calculates an FNF waveform. The calculated FNF waveform is applied to a continuous beam of ions using the processor. The processors sends information to a mass spectrometer, which includes an ion source that provides the continuous beam of ions and a first quadrupole that receives the continuous beam of ions, so that the first quadrupole applies the calculated FNF waveform to the continuous beam of ions. The first quadrupole applies the calculated FNF waveform to the continuous beam of ions by applying the calculated FNF waveform between pairs of rods or between pairs of auxiliary electrodes placed between rods.

Abstract: An m/z range of an ion beam is divided into two or more precursor ion mass selection windows. A pattern of two or more different window m/z ranges to be used during two or more successive cycles for at least one precursor ion mass selection window is determined. The pattern includes an initial window m/z range and one or more successively different window m/z ranges. Each of the one or more successively different window m/z ranges includes at least a portion of the initial window m/z range. A tandem mass spectrometer is instructed to select and fragment the two or more precursor ion mass selection windows during each cycle of a plurality of cycles and to repeatedly use the pattern for each group of two or more successive cycles of the plurality of cycles for the selection and fragmentation of the at least one precursor ion mass selection window.

Abstract: A static magnetic field is applied in the same direction using a first magnet and a second magnet. The magnetic field is applied to a gap of uniform thickness between the first and second magnets. Voltages are applied to three or more electrodes located in the gap using a switchable voltage source. The voltages are applied to create a static electric field perpendicular to the static magnetic field in an input channel and at least one channel of two or more output channels. The channels are defined by gaps between the three or more electrodes. The simultaneous application of the static magnetic field and the static electric field causes ions from an ion beam of a mass spectrometer to move into and through the input channel and through at least one channel of the two or more output channels to another location in the mass spectrometer.

Abstract: Systems and methods are provided for identifying a precursor ion without using any a priori precursor ion information. In one method, a sample is analyzed using a tandem mass spectrometer, producing at least one measured product ion spectrum from a precursor mass-to-charge ratio range. The at least one measured product ion spectrum are received. A subset of measured product ions is selected from the at least one measured product ion spectrum. A list of candidate compounds is created by searching a dictionary of potential compounds that includes one or more predicted product ions for each of the potential compounds using the subset of measured product ions. A candidate compound on the list is selected as the identified compound. In another method, the measured product ions are assumed to correspond to shortened forms of the peptide and a protein database is searched for shortened forms of the peptide.

Abstract: Systems and methods prevent potentially convolved precursor ion peaks from being excluded in subsequent cycles of an IDA experiment so that additional product ion data is collected. A sample is ionized producing an ion beam. A plurality of cycles of an IDA experiment are performed on the ion beam. During each cycle of the IDA experiment and for each precursor ion peak on a filtered peak list produced in the filtering step of each cycle, several steps are performed. The precursor ion peak is identified in the precursor ion spectrum produced in the MS survey scan step of the cycle. It is determined if the precursor ion peak in the precursor ion spectrum includes a feature of convolution. If the precursor ion peak includes a feature of convolution, the precursor ion peak is prevented from being excluded in a filtering step of one or more subsequent cycles.

Abstract: One or more known compounds of a sample are ionized. At least one precursor ion corresponding to a compound of the one or more known compounds is selected and fragmented, producing a product ion mass spectrum for the precursor ion. An m/z tolerance probability function that varies from 1 to 0 with increasing values of an m/z difference between two mass peaks and that includes one or more values between 1 and 0 is received. A library product ion mass spectrum for the at least one compound is retrieved from a memory. An m/z difference between at least one experimental product ion mass peak in the product ion mass spectrum and at least one library product ion mass peak in the library product ion mass spectrum is calculated. An m/z tolerance probability that determines if the two peaks are corresponding peaks is calculated from the m/z difference using the probability function.

Abstract: Methods and systems for delivering a liquid sample to an ion source for the generation of ions and subsequent analysis by mass spectrometry are provided herein. In accordance with various aspects of the present teachings, MS-based systems and methods are provided in which a desorption solvent utilized in a sampling interface to desorb one or more analyte species from an SPME device is fluidly coupled to an ion source for ionizing the one or more analyte species desorbed into the desorption solvent for subsequent mass spectrometric analysis (e.g., without a liquid chromatography (LC) column between the sampling interface and the ion source).

Abstract: Systems and methods for filtering a continuous beam of ions are provided. An acceleration electric field is applied to a continuous beam of ions using an accelerator to produce an accelerated beam of ions. A field is applied to the accelerated beam to separate ions in time and space using a deflector producing a separated beam of ions. The field applied by the deflector is a rotating field or a circulant rastering field. The rotating field can be a rotating magnetic or electric field. Only accept those ions from the separated beam whose m/z values lie within a range centered around a target m/z value using an aperture. The aperture can include a pinhole aperture in a rotating disk or an annular aperture in a first stationary disk, a second deflector, and a pinhole aperture in the center of a second stationary disk.