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.

Abstract: Systems and methods are provided for scheduled MS3. A compound of interest is separated from a sample over a known time period using a separation device. A plurality of sMRM experiments are performed over the known time period on the separating compound of interest using a mass spectrometer. An intensity of a product ion of the compound of interest is produced for each of the plurality of sMRM experiments. Each intensity for the product ion for each of the plurality of sMRM experiments is compared to a threshold intensity level using a processor. When an intensity for the product ion of an sMRM experiment of the plurality of sMRM experiments is equal to or exceeds the threshold intensity level, the mass spectrometer is instructed to perform one or more MS3 experiments for the product ion using the processor.

Abstract: Systems and methods are provided for scheduled MS3. A compound of interest is separated from a sample over a known time period using a separation device. A plurality of sMRM experiments are performed over the known time period on the separating compound of interest using a mass spectrometer. An intensity of a product ion of the compound of interest is produced for each of the plurality of sMRM experiments. Each intensity for the product ion for each of the plurality of sMRM experiments is compared to a threshold intensity level using a processor. When an intensity for the product ion of an sMRM experiment of the plurality of sMRM experiments is equal to or exceeds the threshold intensity level, the mass spectrometer is instructed to perform one or more MS3 experiments for the product ion using the processor.

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.

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.