Abstract: In one aspect, a method of performing MRM mass spectrometry is disclosed, which includes identifying a plurality of precursor ions expected to arrive at an ion guide positioned upstream of a mass filter during a predefined time period subsequent to MRM analysis of a current precursor ion selected by the mass filter, determining a bandpass window for application to said ion guide based on a maximum m/z difference between an m/z of the current precursor ion and m/z ratios of said plurality of precursor ions to be analyzed in said subsequent time period, and configuring the ion guide to provide said bandpass window.

Abstract: Systems and methods are provided for predicting the mass spectrum of an unknown compound. An experimental mass spectrum of a known compound is obtained. One or more mass peaks of the experimental mass spectrum corresponding to a substructure of the known compound are annotated with at least one modification an unknown compound is predicted to include. An in-silico mass spectrum is created for the unknown compound from the experimental mass spectrum and the annotated one or more mass peaks. The unknown compound is then identified from a sample by mass analyzing the sample, producing an unknown experimental mass spectrum, and comparing the unknown experimental mass spectrum to the in-silico mass spectrum.

Abstract: A first analysis of a mass range of a first sample is performed using a separation coupled mass spectrometer, producing a first set of multivariate data that includes both retention time and mass spectral data. A second analysis of a mass range of a second sample is performed using a separation coupled mass spectrometer, producing a second set of multivariate data that includes both retention time and mass spectral data. Each of the first set and the second set is divided into two or more subsets corresponding to two or m/z sub-ranges of the mass range. One or more chromatographic peaks in each of the two or more subsets of the first set are independently aligned with one or more chromatographic peaks in each corresponding subset of the two or more subsets of the second set using an alignment method.

Abstract: A mass spectrometry system comprises a detector configured to detect a plurality of signals corresponding to a plurality of compounds in a sample; and an analyzer module configured to receiving, from the detector, signal data corresponding to the plurality of signals; performing an analysis of a signal of the plurality of signals corresponding to a compound of the plurality of compounds to detect an onset of an increase in the signal, wherein the analysis is different from comparing an intensity of the signal with a threshold; and increasing a dwell time for the compound in response to detecting the onset. In some embodiments, the analyzer module is further configured to determine an onset probability as the probability of occurrence for the onset; and utilize the onset probability in detecting the onset.

Abstract: A method of performing liquid chromatography (LC) with an LC system including an LC column and an analyzer includes delivering a transport liquid to an open port interface (OPI) of a sample receiving circuit, wherein the sample receiving circuit includes a sample transfer chamber. A sample is ejected from a sample holder into the OPI with a non-contact ejector. The transport liquid and the sample are received in the sample transfer chamber. The sample transfer chamber is decoupled from the sample receiving circuit. A solvent is delivered to the analysis circuit. The sample is pushed from the sample transfer chamber with the solvent. The sample and the solvent is passed through the LC column to produce an eluent. The eluent is analyzed with the analyzer.

Abstract: A method and system of data acquisition in an acoustic ejection mass spectrometer including a plurality of reservoirs, each reservoir containing a sample, the method including scheduling a plurality of ejection events for the plurality of reservoirs, setting an analysis method for each ejection event, ejecting a first sample at a first ejection time, starting a first analysis method of the ejected first sample at a first start time, ejecting a second sample at a second ejection time, and starting a second analysis method of the ejected second sample at a second start time, the second start time being or equal to or earlier than the first end time. For example, before starting the first analysis method, it is determined whether an ejection of the first sample has occurred, and if the ejection of the first sample is determined not to have occurred, the second sample is ejected.

Abstract: A measured mass spectrum and intensity data provided as a function of m/z and at least one additional dimension are received. Peaks of the measured spectrum are compared to peaks of each of a plurality of library mass spectra. A set of library mass spectra is identified using a fit score. For each spectrum of the set, a group of related peaks of the measured spectrum calculated using a deconvolution algorithm is recalculated. The recalculation lowers a threshold for selection in the group if a matching peak of the library spectrum contributed to the fit score. A group of related peaks of the measured spectrum is produced for each library spectrum. For each spectrum of the set, peaks of the group are compared to peaks of the library spectrum and a purity score is calculated. At least one library spectrum of the set with the highest purity score is identified.

Abstract: An analytical instrument produces intensity versus time measurements or intensity versus m/z measurements for each acquisition of n acquisitions using m instrument parameter values for each acquisition of n acquisitions, wherein n is a number greater than or equal to two and m is a number equal to or greater than one. For each acquisition of the n acquisitions, the instrument stores a data file that includes m one or more instrument parameter values applied to the instrument, producing n data files. A first data file of the n data files for a first acquisition is retrieved. A next data file of the n data files of a next acquisition is retrieved. The m corresponding parameter values of the first data file and the next data file are compared. If any corresponding parameter values differ between the first data file and the next data file, a notification of an instrument parameter difference corresponding to a name of the next data file is displayed.

Abstract: A method for measuring a concentration of an analyte in a sample includes: sampling, from a first sample, a first one or more droplets for mass analysis, wherein the first sample includes the sample; performing mass analysis on the first one or more droplets to determine a first intensity of an analyte in the first one or more droplets; sampling, from a second sample, a second one or more droplets for mass analysis, wherein the sec-ond sample includes the sample and a first spike of the analyte; performing mass analysis on the second one or more droplets to determine a second intensity of the analyte in the second one or more droplets; fitting a curve to the first intensity and the second intensity; and based on the fitted curve, calculating an analyte concentration for the sample.

Abstract: The technology relates to systems and methods for performing mass spectrometry analysis of a sample. An example method may include receiving, as input via an input device, a target mass-to-charge (m/z) ratio for a fragment ion of interest; setting a target m/z range based on the target m/z ratio; ionizing the sample to generate precursor ions; fragmenting the precursor ions to generate fragment ions having a range of mass-to-charge ratios larger than the target m/z range; accelerating the fragment ions to a detector such that fragment ions inside and outside of the target m/z ratio are detected; summing a count of fragment ions within the target m/z range without storing ion counts for fragment ions outside of the target m/z range; and storing the summed ion count as corresponding with the target mass-to-charge ratio.

Abstract: A method of performing liquid chromatography (LC) with an LC system including an LC column and an analyzer includes delivering a transport liquid to an open port interface (OPI) of a sample receiving circuit, wherein the sample receiving circuit includes a sample transfer chamber. A sample is ejected from a sample holder into the OPI with a non-contact ejector. The transport liquid and the sample are received in the sample transfer chamber. The sample transfer chamber is decoupled from the sample receiving circuit. A solvent is delivered to the analysis circuit. The sample is pushed from the sample transfer chamber with the solvent. The sample and the solvent is passed through the LC column to produce an eluent. The eluent is analyzed with the analyzer.

Abstract: The resolution of a TOF mass analyzer is maintained despite a loss of resolution in one or more channels of a multichannel ion detection system by selecting the highest resolution channels for qualitative analysis. Ion packets that impact a multichannel detector are converted into multiplied electrons and emitted from two or more segmented electrodes that correspond to impacts in different regions across a length of the detector. The electrons received by each electrode of the two or more segmented electrodes for each ion packet are converted into digital values in a channel of a multichannel digitizer, producing digital values for at least two or more channels. Qualitative information about the ion packets is calculated using digital values of a predetermined subset of one or more channels of the at least two or more channels known to provide the highest resolution.

Abstract: An operational condition of a liquid chromatography (LC) system (2110) is detected and displayed without user intervention. A plurality of pressure measurements over time are received from a pressure sensor (2119) of the LC system. A processor (2140) calculates values from the measurements for six parameters including a beginning pressure (PB), an ending pressure (PE), an average pressure (T1) for a first half of the separation, an average pressure (T2) for a second half of the separation, a ratio T1/PB, and a ratio T2/PB. The values of the six parameters are classified as one of one or more operational conditions of the LC system using a machine learning model. The machine learning model is created from values of the six parameters calculated from known separations for each of the one or more operational conditions. The operational condition found from the classification is displayed on a display device (2141).

Abstract: The resolution of a TOF mass analyzer is maintained despite a loss of resolution in one or more channels of a multichannel ion detection system by selecting the highest resolution channels for qualitative analysis. Ion packets that impact a multichannel detector are converted into multiplied electrons and emitted from two or more segmented electrodes that correspond to impacts in different regions across a length of the detector. The electrons received by each electrode of the two or more segmented electrodes for each ion packet are converted into digital values in a channel of a multichannel digitizer, producing digital values for at least two or more channels Qualitative information about the ion packets is calculated using digital values of a predetermined subset of one or more channels of the at least two or more channels known to provide the highest resolution.

Abstract: One or more known compounds of a sample are ionized using an ion source, producing an ion beam of precursor ions. A tandem mass spectrometer receives the ion beam from the ion source, selects one or more precursor ions from the ion beam using a precursor ion mass selection window, fragments precursor ions within the precursor ion mass selection window, and mass analyzes the resulting product ions, producing an unknown product ion mass spectrum. A library product ion mass spectrum for a known compound is retrieved from a memory. Each peak of the unknown spectrum is analyzed for a potential non-halogen isotopic peak using a processor, and if a potential non-halogen isotopic peak is found, it is removed if it does not have a corresponding peak in the library spectrum.

Abstract: One or more known compounds of a sample are ionized using an ion source, producing an ion beam of precursor ions. A tandem mass spectrometer receives the ion beam from the ion source, selects one or more precursor ions from the ion beam using a precursor ion mass selection window, fragments precursor ions within the precursor ion mass selection window, and mass analyzes the resulting product ions, producing an unknown product ion mass spectrum. A library product ion mass spectrum for a known compound is retrieved from a memory. Each peak of the unknown spectrum is analyzed for a potential non-halogen isotopic peak using a processor, and if a potential non-halogen isotopic peak is found, it is removed if it does not have a corresponding peak in the library spectrum.

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: 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: 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: Systems and methods are provided for interlacing ramped mass spectrometer parameter values during data acquisition. Ions from a sample are acquired within a cycle time, Ct, using a mass spectrometer. Within each Ct, two or more scans of the acquired ions are performed using two or more ramped values for a parameter of the mass spectrometer. When it is determined that scans for a desired range of ramped parameter values cannot be performed within Ct, the desired range of ramped values is divided into at least two interlaced groups of ramped values. The mass spectrometer is instructed to perform scans for each of the interlaced groups within two or more cycle times. Spectra from the scans for each of the at least two interlaced groups are combined. The ramped parameter values of the combined spectra have the desired range and the desired effective step size.