Abstract: Apparatus and methods for charge detection mass spectrometry cause an ion of interest to undergo harmonic oscillatory movement in the trapping field of an electrostatic trap, such that an image current detector generates a time-varying signal representative of the ion's oscillatory movement. This time-varying signal (transient) is processed (e.g., via a Fourier transform) to derive the ion's frequency and consequently determine the ion's mass-to-charge ratio (m/z). Ion charge is determined by construction of a Selective Temporal Overview of Resonant Ion (STORI) plot, which tracks the temporal evolution of signals attributable to the ion of interest, and where the slope of the STORI plot is related to the charge. The STORI plot may also be employed to identify ion decay events during transient acquisition and/or the presence of multiple ions of the same mass or non-resolvable ions.

Abstract: A process for charge detection mass spectrometry includes acquiring a time-varying signal representative of a current induced on a detector by oscillatory motion of an ion within a trapping region; processing the time-varying signal to derive a frequency of the oscillatory motion; generating, based on the amplitude of the time-varying signal and the derived frequency of the oscillatory motion, Selective Temporal Overview of Resonant Ion (STORI) data representing STORIreal values versus time and STORIimag values versus time; regenerating the STORI data based on a variation of the frequency of the oscillatory motion over time; and determining a charge state of the ion based on the regenerated STORI data.

Abstract: Apparatus and methods for performing charge detection mass spectrometry for measurement of the mass of a single ion of interest are disclosed. The ion of interest is caused to undergo harmonic oscillatory movement in the trapping field of an electrostatic trap, such that an image current detector generates a time-varying signal representative of the ion's oscillatory movement. This time-varying signal (transient) is processed (e.g., via a Fourier transform) to derive the ion's frequency and consequently determine the ion's mass-to-charge ratio (m/z). Ion charge is determined by construction of a Selective Temporal Overview of Resonant Ion (STORI) plot, which tracks the temporal evolution of signals attributable to the ion of interest, and where the slope of the STORI plot is related to the charge. The STORI plot may also be employed to identify ion decay events during transient acquisition and/or the presence of multiple ions of the same mass or non-resolvable ions.

Abstract: A system for performing dynamic DIA directs a mass spectrometer to acquire, based on an acquisition schedule that schedules a plurality of acquisition cycles, MS2 spectra of product ions derived from analytes included in a sample as the analytes elute from a separation system. The acquisition schedule specifies, for each acquisition cycle included in the plurality of acquisition cycles, a dynamic precursor m/z range based on an expected elution time of the analytes. The product ions are produced from precursor ions isolated using an isolation window successively positioned throughout the dynamic precursor m/z range during each acquisition cycle. The system detects an elution time shift in the elution time of the analytes as the analytes elute and adjusts the acquisition schedule based on the detected elution time shift.

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: Mass Spectrometry has been widely used to identify microbes present in a sample. However, rapid analysis (e.g. 1-5 minutes) of spectral data to identify microbes has proven to be very challenging due to the high level of processing required and complexity associated with identification from a large pool of candidate microbes. Disclosed herein are methods and systems for rapidly identifying microbes present in a sample through the application of conditional likelihoods that certain proteoforms are particularly indicative of a candidate microbe.

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 system comprises: (1) a central location comprising: (a) computer storage media having one or more databases thereon; and (b) one or more computers configured to communicate with the computer storage media: and (2) a plurality of sites, each site comprising: (a) an analytical apparatus; and (b) a site computer system comprising program instructions operable to generate a collection of apparatus signatures, each apparatus signature comprising a collection of data relating to the operation of the analytical apparatus at a time when said signature is generated, wherein the one or more computers at the central location are configured to store each collection of signatures in the one or more databases. In embodiments, each site computer system stores the plurality of apparatus signatures generated at the respective site and transmits the stored apparatus signatures to the one or more computers at the central location.

Abstract: Apparatus and methods for performing charge detection mass spectrometry for measurement of the mass of a single ion of interest are disclosed. The ion of interest is caused to undergo harmonic oscillatory movement in the trapping field of an electrostatic trap, such that an image current detector generates a time-varying signal representative of the ion's oscillatory movement. This time-varying signal (transient) is processed (e.g., via a Fourier transform) to derive the ion's frequency and consequently determine the ion's mass-to-charge ratio (m/z). Ion charge is determined by construction of a Selective Temporal Overview of Resonant Ion (STORI) plot, which tracks the temporal evolution of signals attributable to the ion of interest, and where the slope of the STORI plot is related to the charge. The STORI plot may also be employed to identify ion decay events during transient acquisition and/or the presence of multiple ions of the same mass or non-resolvable 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 system and method for processing long scan data from a mass spectrometer is described. The long scan data is broken into multiple discrete subsets and each of the multiple subsets are padded by adding additional strings of data on either end of the subset. Each of the multiple subsets is deconvolved and overhang errors are corrected for on each deconvolved subset.

Abstract: A system and method for processing long scan data from a mass spectrometer is described. The long scan data is broken into multiple discrete subsets and each of the multiple subsets are padded by adding additional strings of data on either end of the subset. Each of the multiple subsets is deconvolved and overhang errors are corrected for on each deconvolved subset. A deconvolved full data set is then assembled from the deconvolved subsets.

Abstract: Methods are provided for predicting the presence, subtype and stage of ovarian cancer, as well as for assessing the therapeutic efficacy of a cancer treatment and determining whether a subject potentially is developing cancer. Associated test kits, computer and analytical systems as well as software and diagnostic models are also provided.

Abstract: Methods are provided for predicting the presence, subtype and stage of ovarian cancer, as well as for assessing the therapeutic efficacy of a cancer treatment and determining whether a subject potentially is developing cancer. Associated test kits, computer and analytical systems as well as software and diagnostic models are also provided.

Abstract: The present disclosure establishes new dissociation parameters that may be used to determine the collision energy (CE) needed to achieve a desired extent of dissociation for a given analyte precursor ion using collision cell type collision-induced dissociation. This selection is based solely on the analyte precursor ion's molecular weight, MW, and charge state, z. Metrics are proposed that may be used as a parameter for the “extent of dissociation”, and then predictive models are developed of the CEs required to achieve a range of values for each metric. Each model is a simple smooth function of only MW and z of the precursor ion. Coupled with a real-time spectral deconvolution (m/z to mass) algorithm, methods in accordance with the invention enable control over the extent of dissociation through automated, real-time selection of collision energy in a precursor-dependent manner.

Abstract: An embodiment of a method for real time material identification is described that comprises determining an approximate mass value for an unknown material from spectral information derived from mass spectral analysis of the unknown material; retrieving profile models that correspond to a known material from a data structure using the approximate mass value; fitting a sample profile for the unknown material from the spectral information to the profile models to generate a fit score for each fit, wherein the lowest fit score corresponds to the best fit; calculating a mass value from the best fitting profile model and the sample profile.

Abstract: A method for mass spectral analysis of a sample containing a plurality of intact protein molecule species comprises: (a) mass analyzing a plurality of ion species generated from a sample portion; (b) automatically recognizing, for each of at least one intact protein molecule species, a respective subset of m/z ratios corresponding to ion species generated from the each intact protein molecule species; and (c) storing or reporting to a user information relating to each subset of the m/z ratios, wherein step (b) comprises: automatically assigning a tentative charge state to each above-threshold m/z ratio; automatically adjusting the tentative charge to achieve a set of self-consistent assigned charge states; and decomposing the assigned charge states into analyte-specific clusters, each analyte-specific cluster being a one of the subsets of the m/z ratios.

Abstract: Applications of ion-ion reaction chemistry are disclosed in which proton transfer reactions (PTR) and real-time data analysis methods are used to (1) simplify complex mixture analysis of samples introduced into a mass spectrometer, and (2) improve resolution and sensitivity for the analysis of large proteins in excess of 50 kDa by removing charge and reducing the collisional cross section.

Abstract: A method for mass spectral analysis of a sample containing a plurality of biomolecule species comprises: (a) mass analyzing a plurality of first-generation ion species generated from a sample portion; (b) automatically recognizing, for each of at least one biomolecule species, a respective subset of m/z ratios corresponding to respective first-generation ion species generated from the each biomolecule species; (c) selecting, from each recognized subset, a single representative m/z ratio; (d) isolating a sub-population of ions having each representative m/z ratio from ions having other m/z ratios; and (e) fragmenting each isolated sub-population of ions so as to generate second-generation ion species.

Abstract: Applications of ion-ion reaction chemistry are disclosed in which proton transfer reactions (PTR) and real-time data analysis methods are used to (1) simplify complex mixture analysis of samples introduced into a mass spectrometer, and (2) improve resolution and sensitivity for the analysis of large proteins in excess of 50 kDa by removing charge and reducing the collisional cross section.