Abstract: Control of an amplitude of a signal applied to rods of a quadrupole is described. In one aspect, a mass spectrometer includes an amplifier circuit that causes a radio frequency (RF) signal to be applied to the rods of the quadrupole. A controller circuit can determine that the actual amplitude of the RF signal differs than the expected amplitude and, in response, identify current and past environmental and performance parameters to adjust the amplitude.

Abstract: A Liquid Chromatography Mass Spectrometry system comprises: a chromatograph; a mass spectrometer configured to ionize separated fractions of a sample received from the chromatograph; and a programmable processor operable to repeatedly execute the steps of: (i) causing the mass spectrometer to perform a data-independent analysis of the precursor ion species using a mass analyzer of the mass spectrometer; (ii) calculating one or more degree-of-matching scores that relate to detection of an internal standard; and (iii) if each of the degree-of-matching scores meets a respective degree-of-matching condition, performing a quantitative tandem mass spectrometric analyses of both the internal standard and the analyte; the programmable processor further operable to calculate a quantity of the analyte in the sample by comparison between intensities of one or more mass spectral signals generated by the quantitative tandem mass spectrometric analyses of the analyte and the internal standard.

Abstract: A method of performing mass spectrometry includes accessing a series of mass spectra of detected ions derived from components eluting from a chromatography column; obtaining, based on the series of mass spectra, an elution profile including a plurality of detection points representing intensity of at least a set of the detected ions as a function of time; and determining, based on a set of detection points included in the plurality of detection points, a predicted next detection point of the elution profile to be obtained based on a next mass spectrum to be acquired subsequent to acquisition of the series of mass spectra.

Abstract: A method for preparing a protein-containing sample for analysis by mass spectrometry includes introducing the sample into a reaction vessel. The reaction vessel contains a reagent mixture including pre-measured quantities of an immobilized proteolytic enzyme, a reducing agent and an alkylating agent. The contents of the reaction vessel are activated by heating or by sonication.

Abstract: An electrospray ionization system used in mass spectrometry provides for improved current measurement. The system includes a fluid union, a fluid column coupled with a first port of the fluid union, a power source coupled with the fluid union and configured to apply a voltage potential to the fluid union, and an electrospray emitter coupled with a second port of the fluid union. The power source is coupled with the first port and configured to apply the voltage potential to the first port to restrict current leakage from the fluid union. The current sensing circuit is configured to determine an electrical current flow between the power source and the at least one of the fluid union and the first port.

Abstract: Real-time search (RTS) for mass spectrometry is described. In one aspect, a mass spectrometer can identify a candidate peptide for a product ion spectrum by searching a mass spectral database. While executing the search of the mass spectral database, the elapsed search time can be monitored. If the elapsed search time of the identification of the candidate peptide is completed before reaching a maximum value, then the mass spectrometer can perform further actions.

Abstract: 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.

Abstract: A metal-channel conversion dynode comprises: a wafer comprising a first face and a second face parallel to the first face and having a thickness less than 1000 ?m; and a plurality of channels passing through the wafer from the first face to the second face at an angle to a plane of the first face and a plane of the second face. In some embodiments, each inter-channel distance may be substantially the same as the wafer thickness. In some embodiments, the wafer is fabricated from tungsten. In some other embodiments, the wafer comprises a non-electrically conductive material that is fabricated by three-dimensional (3D) printing or other means and that is coated, on its faces and within its channels, with a metal or suitably conductive coating that produces secondary electrons upon impact by either positive or negative ions.

Abstract: Methods are described for the automatic determination and correction of retention time shift of a MS data set relative to a control data set, to correct for retention time drifts endemic to targeted LCMS analyses. In an embodiment, a 2D grid of periodic MS spectra versus time is collected for a control experiment, and RT windows are determined with an additional set of unscheduled mass spectral analyses. During successive experiments, spectra from periodic MS scans are used to determine the correspondence between the current time and the time in the control experiment. The active set of MSn scans to be acquired by the instrument is then determined as the scans with adjusted retention time windows that bracket the corrected retention time.

Abstract: A method for cleaning an electrospray emitter of a mass spectrometer comprises the steps of: (a) changing a mode of operation of the electrospray emitter from a stable jet mode of operation to a dripping mode or a pulsating mode of operation by lowering a magnitude, |V|, of a voltage applied between a counter electrode and the electrospray emitter; and (b) changing the mode of operation of the electrospray emitter from the dripping mode or the pulsating mode of operation to the stable jet mode of operation by increasing the magnitude, |V|, of the applied voltage; wherein the repetitions are performed at a predetermined frequency that depends on one or more of liquid flow rate, an emitter internal diameter, and liquid properties.

Abstract: A method of performing mass spectrometry includes accessing a series of mass spectra of detected ions derived from components eluting from a chromatography column; obtaining, based on the series of mass spectra, an elution profile including a plurality of detection points representing intensity of at least a set of the detected ions as a function of time; and determining, based on a set of detection points included in the plurality of detection points, a predicted next detection point of the elution profile to be obtained based on a next mass spectrum to be acquired subsequent to acquisition of the series of mass spectra.

Abstract: A mass spectrometry method comprises: introducing a first packet of ions into an electrostatic trap mass analyzer through a set of electrostatic lenses, wherein, during the introducing of the first packet, either the lenses are operated in a first mode of operation or an injection voltage of a first pre-determined magnitude is applied to an electrode of the mass analyzer; mass analyzing the first ion packet using the mass analyzer; introducing a second packet of ions into the mass analyzer through the set of lenses, wherein, during the introducing of the second packet, either the lenses are operated in a second mode of operation or an injection voltage of a second pre-determined magnitude is applied to the electrode of the mass analyzer; and mass analyzing the second packet of ions using the electrostatic trap mass analyzer.

Abstract: Disclosed herein are systems and methods for a mass spectrometer having a multipole configured to pass an ion stream, and a detector configured to detect the properties of the abundance of ions represented by data points. The mass spectrometer also includes a processing system that is configured to obtain a plurality of paired data points (e.g., detector data points and RF amplitude data points), and identify, based on centroiding a portion of the plurality of paired data points, at least one characteristic of a peak and determine, based on the at least one characteristic of the peak, a preferred peak shape.

Abstract: A mass spectrometry system having a simplified control interface includes a processor and a memory. The memory includes instructions that when executed cause the processor to perform the steps of providing a user interface including a plurality of adjustment elements for adjusting at least one results effective parameter and at least one sample descriptive parameter; determining a plurality of instrument control parameters based on the at least one results effective parameter and the at least one sample descriptive parameter; and analyzing a sample while operating according to the plurality of instrument control parameters.

Abstract: Disclosed herein are scientific instrument support systems, as well as related methods, computing devices, and computer-readable media. For example, in some embodiments, a scientific instrument support apparatus includes evaluation logic to identify a first syringe has a bent needle, a bent plunger, a blocked needle, or a stuck plunger; syringe logic to switch from the first syringe to a second syringe; and reporting logic to notify a user of a syringe problem.

Abstract: An optimization control system may receive mass spectra of ions emitted from an ionization emitter toward an inlet of a mass spectrometer and control, based on the mass spectra, an automated motion system to adjust a position of the emitter relative to the inlet.

Abstract: A system for analyzing a sample includes a source configured to generate ions from constituent components of the sample; a mobility separator configured to separate ions received from the source based on the mobility in a gas; a ion storage array configured to store ions from the mobility separator as a plurality of mobility fractions; a mass filter configured to select ions within a mass-to-charge window; a mass analyzer configured to determine the mass-to-charge ratio of the ions; and a controller. The controller is configured to identify an ion mobility fraction and a mass-to-charge window to select for a charge state or ion class; utilize the mass filter to select ions from the ion storage array within the mass-to-charge window corresponding to a charge state or ion class; and analyze the selected ions with the mass analyzer.

Abstract: A method of performing targeted multiplexed mass spectrometry includes performing, at a mass spectrometer, a targeted MS3 analysis of an isobaric tag-labeled target analyte included in a multiplex sample eluting from a column. The targeted MS3 analysis is performed during an acquisition segment scheduled based on an expected retention time of the isobaric tag-labeled target analyte. The method further includes performing, during the acquisition segment, a plurality of MS2 analyses of product ions derived from components included in the multiplex sample and eluting from the column. The method further includes determining, based on MS3 mass spectra acquired by the targeted MS3 analysis and MS2 mass spectra acquired by the plurality of MS2 analyses, a relative quantity of the isobaric tag-labeled target analyte in the multiplex sample.

Abstract: A compression fitting includes a nut with a threaded end for receiving a threaded tube and a receiving end for holding a plunger head; and a plunger with an inner bore for receiving a capillary tube and the plunger head for engaging a ferrule positioned within the receiving end between the plunger head and the threaded tube, the plunger slidingly engaged with the nut to force the ferrule from the nut.

Abstract: A first multipole assembly includes a first plurality of rod electrodes arranged about an axis and configured to confine ions radially about the axis. A second multipole assembly disposed adjacent to the first multipole assembly includes a second plurality of rod electrodes arranged about the axis and configured to confine the ions radially about the axis. An orientation of the first multipole assembly about the axis is rotationally offset relative to an orientation of the second multipole assembly about the axis.