Abstract: In one aspect, a method of performing mass spectrometry is disclosed, which comprises introducing a plurality of ions into a mass spectrometer, selecting a portion of the precursor ions having m/z ratios within a first desired range to provide a plurality of precursor ions, causing fragmentation of at least a portion of the precursor ions to generate a plurality of product ions, selecting a portion of the product ions having m/z ratios within a second desired range, and performing mass analysis of the selected productions.

Abstract: A known compound and at least one adduct, modified form, or peptide of the known compound are separated from a sample mixture and analyzed. An XIC is calculated for each of M product ions of the known compound and L product ions of the at least one adduct, modified form, or peptide. A first XIC peak group is calculated from the M XICs and a second XIC peak group is calculated from the L XICs using curve subtraction. Representative first and second XIC peaks are selected for the two XIC peak groups. The retention time of the second XIC peak is shifted by an expected retention time difference found from a database. The retention time of the first XIC peak is verified as the retention time of the known compound if the difference of the retention times of the first and second XIC peaks is within a threshold.

Abstract: Each of one or more unknown compounds are separated from a sample over a separation time period. Separated compounds are ionized, producing one or more compound precursor ions for each of the unknown compounds and a plurality of background precursor ions. A precursor ion mass spectrum is measured for the combined compound and background precursor ions at each time step of a plurality of time steps spread across the separation time period, producing a plurality of precursor ion mass spectra. One or more background precursor ions are selected from the plurality of precursor ion mass spectra that have a resolving power in a range below a threshold expected resolving power. A separation time is detected for an unknown compound when a decrease in an intensity measurement of the selected background precursor ions over a time period exceeds a threshold decrease in intensity with respect to time.

Abstract: A method of adjusting a position of an electrode within a nebulizer probe of a mass spectrometry device having an open port interface for receiving a sample includes performing a first analysis of the sample at a first analysis condition including a first position of the electrode and a first flow rate. After performing the first analysis, a second analysis of the sample is performed at a second analysis condition including the first position of the electrode and a second flow rate higher than the first flow rate. Thereafter, a third analysis of the sample is performed at a third analysis condition including a second position of the electrode and the second flow rate.

Abstract: A calibration apparatus for a mass analyzer includes an ion source device and a dual-purpose electron beam generating unit. The ion source device ionizes an analyte of a sample, producing analyte ions. The dual-purpose electron beam generating unit is positioned between the ion source device and the mass analyzer. In a first mode, the dual-purpose electron beam generating unit is used to create fragments of analyte ions of unknown mass-to-charge ratio. In a second mode, the dual-purpose electron beam generating unit is used to create ions of calibration compounds of known mass-to-charge ratio. All ions are subsequently transferred to the mass analyzer.

Abstract: In one aspect, a mass spectrometer is disclosed, which comprises an ion trap having a plurality of electrodes arranged in a multipole configuration so as to provide an inlet for receiving ions along a longitudinal axis into a space between the electrodes, where at least one of the plurality of electrodes comprises a passageway through which ions can be extracted radially from the ion trap. The electrodes are configured for application of one or more RF voltages thereto for providing radial confinement of the ions, and a DC voltage source configured to apply a dipolar DC voltage pulse across said at least one electrode and an opposed electrode for causing radial extraction of at least a portion of said ions from said ion trap through said passageway.

Abstract: A method of adjusting a position of a tip of an electrode relative to an end of a nebulizer nozzle of a mass spectrometry device includes providing a conduit and the electrode connected to the conduit at a first end of the conduit. The electrode tip is disposed at a first position relative to the nebulizer nozzle end. The pressure gauge is connected to a second end of the conduit. A gas ejection is initiated from the nozzle with the electrode tip at the first position. During the gas ejection, the position of the electrode tip is adjusted from the first position towards a second position relative to the nozzle end. Adjusting the position from the first position towards the second position is terminated when the pressure gauge displays a pressure condition. Once adjusting is terminated, the electrode tip is at the second position.

Abstract: A method of sampling an ejection of a sample from a liquid container includes disposing the liquid container adjacent an open port in-terface. The container includes a sampling port. The open port interface en-gages with the sampling port. The sample from the liquid container is eject-ed, through the sampling port, and into the open port interface. The sample is analyzed with a mass spectrometry device.

Abstract: A method of operating a differential mobility spectrometer (DMS) includes providing a heater disposed proximate a ceramic body of a DMS cell. A first control voltage is applied to the heater. A first threshold is detected by a first sensor disposed within a curtain plate that substantially surrounds the DMS cell. A second control voltage is applied to the heater based at least in part on the detected first threshold. During application of the second control voltage, a mass spectrometry analysis of a gas within the DMS cell is performed.

Abstract: In one aspect, a mass analyzer is disclosed, which comprises a quadrupole having an input end for receiving ions and an output end through which ions can exit the quadrupole, said quadrupole having a plurality of rods to at least some of which a drive RF signal and an excitation signal can be applied. A fixed phase relationship is maintained between the drive RF signal and the excitation signal, thereby enhancing the signal-to-noise ratio of the mass detection signal.

Abstract: A method of delivering transport fluid from an open port interface to an outlet via a transfer conduit includes delivering, to the open port interface, a transport liquid at a first flow rate. The open port interface is disposed in a pressure environment having a first pressure. A second pres-sure is applied at the outlet, wherein the second pressure is less than the first pressure. The pressure applied at the outlet generates a motive flow on the transport liquid, thereby drawing into the transfer conduit (a) the transport fluid, wherein the transport fluid is in contact with a wall of the transport conduit, and (b) a gas present in the pressure environment. The gas forms an air core within the drawn transport fluid. The air core extends substantially an entire length of the transfer conduit.

Abstract: An ion source ionizes a compound, producing precursor ions with different m/z values. A reagent source supplies charge reducing reagent. An ion guide is positioned between a mass filter and both the ion source and the reagent source. The ion guide applies an AC voltage and DC voltage to its electrodes that creates a pseudopotential to trap the precursor ions in the ion guide below a threshold m/z. This AC voltage, in turn, causes the trapped precursor ions to be charge reduced by the reagent so that m/z values of the trapped precursor ions increase to a single m/z value above the threshold m/z. The ion guide applies the DC voltage to its electrodes relative to a DC voltage applied to electrodes of the mass filter that causes the precursor ions with m/z values increased to the single m/z value to be continuously transmitted to the mass filter.

Abstract: Methods and systems for conducting affinity selection by mass spectrometry in high throughput assays are disclosed herein. The methods can comprise identifying a set of hit com-pounds having a selected affinity to a binding target immobilized onto a magnetic particle. Methods can comprise forming an assay mixture within an assay vessel comprising a plurality of drug candidates and a binding target immobilized onto a magnetic particle. Methods also can comprise preparing at least a portion of the assay mixture for mass analysis transferring a sample containing the set of hit compounds to an open port sampling interface of a mass spectrometer.

Abstract: A method of ejecting a plurality of samples from a well plate includes receiving a first sample intensity prediction associated with a first sample in a first well of the well plate. A second sample intensity prediction associated with a second sample in a second well is also received. The second sample intensity prediction is less than the first sample intensity prediction. An ejection time delay value for a subsequent analysis of the first sample and the second sample is determined, based at least in part on the second sample intensity prediction. Thereafter, the first sample is acoustically ejected from the first well, and the second sample is acoustically ejected from the second well.

Abstract: In some embodiments, a method for optimizing performance of a mass spectrometer comprises using an ion source to generate ions, collisionally cooling the ions within an ion guide, directing said ions from the ion guide through at least one ion lens to a downstream mass analyzer, ramping a DC voltage applied to the ion lens, performing a mass analysis of the ions within the mass analyzer while the DC voltage applied to the ion lens is ramped, estimating performance of the mass spectrometer by measuring one or more characteristics of at least one of an ion signal and the voltage ramp, and adjusting a DC voltage applied to said at least one lens element based on said measured one or more characteristics of at least one of the ion signal and the voltage ramp so as to enhance performance of the mass spectrometer.

Abstract: Methods and systems for FTMS-based analysis having an improved duty cycle relative to conventional FTMS techniques are provided herein. In various aspects, the methods and systems described herein operate on a continuous ion beam, thereby eliminating the relatively long duration trapping and cooling steps associated with Penning traps or orbitraps of conventional FTMS systems, as well as provide increased resolving power by sequentially interrogating the continuous ion beam under different radially-confining field conditions.

Abstract: The teachings herein provide for a method of analyzing testosterone using mass spectrometry. The method entails combining in a vial or well, a tagging reagent that is reactive with testosterone, an aqueous precipitation agent that precipitate proteins from solution, and an internal standard solution, the internal standard solution containing a known concentration of an isotopically enriched testosterone and then adding to the vial or well, a sample containing or suspected to contain testosterone. The vial can then be mixed to cause simultaneous precipitation of proteins and reaction of any testosterone present with the tagging reagent to form a mixture of a precipitate and a liquid solution. The liquid solution can then be separated from any precipitate and then analyzed for testosterone using liquid chromatography tandem mass spectrometry.

Abstract: A method is disclosed for calculating and recalculating protein confidence values by recalculating peptide confidence values in proteomic analysis. A plurality of scans are performed of a sample that is proteolytically digested into surrogate peptide analytes. A plurality of spectra are obtained, and a plurality of peptides are identified. A protein database is searched for proteins matching peptides from the plurality of peptides. Peptide confidence values are determined for the set of peptides. A protein confidence value is calculated for each protein in the set of proteins. A protein from the set of proteins with a largest protein confidence value is selected, the largest protein confidence value for the protein is saved, the protein from the set of proteins is removed, and peptides corresponding to the protein is removed from the set of peptides. The protein confidence value is recalculated for each protein in the set of proteins.

Abstract: The technology relates to a system for improved mass analysis operation by proactively identifying contamination. The system includes a mass analysis instrument comprising mass analysis hardware components, a processor, and memory storing instructions that, when executed by the processor, cause the system to perform a set of operations. The set of operations include performing, by the mass analysis instrument at a first time, a predefined series of operational tests to produce first mass analysis results for a calibrant; performing, by the mass analysis instrument at a second time, the predefined series of operational tests to produce second mass analysis results for the calibrant; determining an analysis difference between the first mass analysis results and the second mass analysis results; and based on a magnitude of the analysis difference, generating at least one of a contamination indicator or a degradation indicator.

Abstract: A method for processing a fluid sample containing a first target analyte includes introducing a first batch of magnetic particles into a fluid conduit, the fluid conduit having a first open end, a second open end, and a first electromagnetic trap between the first open end and the second open end. The magnetic particles include a first receptor to bind the first target analyte in the fluid sample. The method further includes activating the first electromagnetic trap to trap and mix the magnetic particles within the first electromagnetic trap. A flow of the fluid sample is introduced through the fluid conduit from the first open end to the second open end. Deactivating first electromagnetic trap releases the magnetic particles from the first electromagnetic trap.