Abstract: Techniques and apparatus for analyzing mass spectrometry data are described. In one embodiment, for example, an apparatus may include logic to access a product ion data set generated via mass analyzing a sample comprising a target precursor, access precursor composition information for elements of the target precursor that includes nominal mass and mass defect information, determine nominal mass (NM)-mass defect (MD) relationship information for ion fragments associated with the target precursor based on the precursor composition information, determine one or more fragment upper boundaries and one or more fragment lower boundaries, extract candidate ion fragments from the ion fragments via applying the one or more fragment upper boundaries and the one or more fragment lower boundaries to the NM-MD relationship information, and determine target ion fragments from the plurality of candidate ion fragments based on fragmentation efficiency information associated with the candidate ion fragments.

Abstract: Exemplary embodiments of the present disclosure are directed to manipulating pressure-related hysteresis in a pressurized flow system by setting the pressure of the system to a predetermined location in the hysteresis band to advantageously minimize an effect of the pressure related hysteresis on the pressure of the system or to advantageously benefit from the effects of the hysteresis on the pressure of the system.

Abstract: Described is a method for vacuum degassing of a liquid such as a solvent for a liquid chromatography system. The method includes modulating application of a vacuum to a fluid channel of a degasser so that each volume of a liquid drawn from the degasser experiences a residence time that is equal to the residence times of the other volumes. The residence time is determined as a time that the volume resides in the fluid channel under application of the vacuum and to a magnitude of the applied vacuum. The method is advantageous for use with liquid chromatography systems where differences in the diffusion rates of solvents into the degasser vacuum can otherwise introduce error into the composition gradient of a mobile phase.

Abstract: A method of mass spectrometry comprises ionizing a sample and obtaining mass spectral data relating to a plurality of ion detection events. The method then comprises applying match tolerances for mass to charge ratio (m/z), chromatographic retention time (tr), and ion mobility drift time (td), to the ion detection events in order to determine possible charge state connections. The method also comprises constructing a tentative isotope chain and querying ion detection events for a match to the tentative isotope chain.

Abstract: Systems and methods for operating a stepper motor of a pump at a desired low velocity include memory for storing information corresponding to an intake velocity profile. The intake velocity profile represents an optimized acceleration curve for operating the stepper motor over a range of motor velocities during an intake cycle. A processor of a system controller dynamically accesses the memory during the intake cycle to acquire the information representing the intake velocity profile and issues a series of pulses to the stepper motor based on this information. In response to the pulses, the stepper motor accelerates in accordance with the optimized acceleration curve represented by the intake velocity profile. The optimized acceleration curve is based on the available torque of the stepper motor across a range of motor velocities and enables the motor to operate with greater torque utilization and less margin than traditional linear acceleration profiles.

Abstract: A method of mass spectrometry is disclosed comprising mass analysing an eluent from a chromatography device and obtaining parent ion data sets and corresponding product ion data sets, and determining whether, in a first product ion data set, one or more product ions are present that are related to one or more parent ions in a corresponding first parent ion data set, based on the mass or mass to charge ratio and/or intensity of the one or more product ions and the one or more parent ions. If it is determined that the one or more product ions are present, the method further comprises removing the one or more product ions from one or more second product ion data sets to produce one or more second modified product ion data sets and/or removing ions other than the one or more product ions from the first product ion data set to produce a first modified product ion data set.

Abstract: A method of mass spectrometry comprises ionising a sample eluting from a separation device in order to generate a plurality of parent ions. The method further comprises generating a target list of ions, which includes a predicted mass to charge ratio, a predicted chromatographic retention or elution time, and a predicted ion mobility drift time, derived from a model. Multiple cycles of operation are then performed as the sample elutes from the separation device. Each cycle of operation includes mass filtering the parent ions so that selected ions having mass to charge ratios within a first mass to charge ratio range are onwardly transmitted to a fragmentation or reaction device. The target list is then checked and the model is updated accordingly. The first mass to charge ratio range can then be adjusted in response to the updated model.

Abstract: A method of mass spectrometry comprises ionising a sample and obtaining mass spectral data relating to a plurality of ion detection events. The method then comprises applying match tolerances for mass to charge ratio (m/z), chromatographic retention time (tr), and ion mobility drift time (td), to the ion detection events in order to determine possible charge state connections. The method also comprises constructing a tentative isotope chain and querying ion detection events for a match to the tentative isotope chain.

Abstract: A method of mass spectrometry comprises ionising a sample eluting from a separation device in order to generate a plurality of parent ions. Multiple cycles of operation are performed as the sample elutes from the separation device. Each cycle of operation comprises mass analysing the parent ions to obtain parent ion mass spectral data, and mass analysing fragment or product ions derived from the parent ion to obtain fragment or product ion mass spectral data. Each cycle of operation also comprises mass analysing fragment or product ions derived from parent ions having mass to charge ratios within a first range to obtain first fragment or product ion mass spectral data, and mass analysing fragment or product ions derived from parent ions having mass to charge ratios within a second different range to obtain second fragment or product ion mass spectral data. The method can provide a hybrid data independent acquisition (DIA) and data dependent acquisition (DDA) approach.

Abstract: A solvent delivery subsystem for a chromatography device performs relatively low pressure, high flow mixing of solvents to form a gradient and subsequent high pressure, low flow delivery of the gradient to the separation column. The mixing of the gradient is independent and does not interfere with the gradient delivery. To form the gradient, the outputs of an aqueous pump and an organic pump are mixed to fill a storage capillary while a downstream point from the storage capillary is vented to atmosphere. After gradient formation, the vent to atmosphere is closed, the solvent delivery system rises to high pressure, and only the aqueous pump runs for gradient delivery. To maintain integrity of the fluid stream, the solvent delivery system uses feed forward compensation and controls at least one parameter selected from the group consisting of pressure and flow in the conduit means to follow a gradual ramp.

Abstract: Described is a method for vacuum degassing of a liquid such as a solvent for a liquid chromatography system. The method includes modulating application of a vacuum to a fluid channel of a degasser so that each volume of a liquid drawn from the degasser experiences a residence time that is equal to the residence times of the other volumes. The residence time is determined as a time that the volume resides in the fluid channel under application of the vacuum and to a magnitude of the applied vacuum. The method is advantageous for use with liquid chromatography systems where differences in the diffusion rates of solvents into the degasser vacuum can otherwise introduce error into the composition gradient of a mobile phase.

Abstract: Described is a method of reducing liquid composition errors in a low-pressure mixing pump system. Packets representing the switching intervals of each component of the desired fluid mixture are provided to an intake of the mixing pump system. For each packet, a switching time associated with at least one of the components in the packet is modulated. Modulated switching times are based on time offsets that are specifically selected according to the undesirable frequency characteristic of an intake response of the mixing pump system. The average of the volumes contributed by the packets thus modulated is equal to a component volume that achieves a desired proportion of the component in the output flow of the mixing pump system. Modulated switching times enable the reduction or elimination of composition error in the output flow of the mixing pump system.

Abstract: A solvent delivery subsystem for a chromatography device performs relatively low pressure, high flow mixing of solvents to form a gradient and subsequent high pressure, low flow delivery of the gradient to the separation column. The mixing of the gradient is independent and does not interfere with the gradient delivery. To form the gradient, the outputs of an aqueous pump and an organic pump are mixed to fill a storage capillary while a downstream point from the storage capillary is vented to atmosphere. After gradient formation, the vent to atmosphere is closed, the solvent delivery system rises to high pressure, and only the aqueous pump runs for gradient delivery. To maintain integrity of the fluid stream, the solvent delivery system uses feed forward compensation and controls at least one parameter selected from the group consisting of pressure and flow in the conduit means to follow a gradual ramp.

Abstract: A sample manager of a liquid chromatography system implements a thermal system that uses a dual-loop feedback control system to control temperature within a thermal chamber. The sample manager includes an external heatsink disposed externally to the thermal chamber, an internal heatsink disposed within the thermal chamber, and one or more thermoelectric devices thermally coupled to the external and internal heatsinks to transfer heat therebetween in response to a pulse-width modulated power signal. A first temperature sensor disposed within the thermal chamber continuously measures a chamber temperature. A second temperature sensor coupled to the internal heatsink within the thermal chamber continuously measures temperature at the internal heatsink. A feedback control system controls a duty cycle of the pulse-width modulated power signal in response to a target chamber temperature and real-time temperature measurements produced by the first and second temperature sensors.

Abstract: A method of analyzing a complex sample includes performing a sequential chromatographic-IMS-MS analysis of a sample to obtain a plurality of experimental mass spectra having isotopic clusters, wherein each spectrum of the plurality of spectra is associated with a chromatographic retention time and an ion-mobility drift time. The method also includes calculating a model isotopic cluster of a precursor or product ion associated with a candidate compound in the sample, in correspondence to the natural isotopic-abundance ratios of elements composing the compound. The method further includes comparing peaks of the model isotopic cluster to corresponding peaks of an isotopic cluster of one of the experimental mass spectra to extract one or more saturated or interfered peaks of the experimental isotopic cluster, wherein at least one of the peaks of the experimental isotopic cluster is un-saturated and un-interfered.

Abstract: Described is a method of reducing liquid composition errors in a low-pressure mixing pump system. Packets representing the switching intervals of each component of the desired fluid mixture are provided to an intake of the mixing pump system. For each packet, a switching time associated with at least one of the components in the packet is modulated. Modulated switching times are based on time offsets that are specifically selected according to the undesirable frequency characteristic of an intake response of the mixing pump system. The average of the volumes contributed by the packets thus modulated is equal to a component volume that achieves a desired proportion of the component in the output flow of the mixing pump system. Modulated switching times enable the reduction or elimination of composition error in the output flow of the mixing pump system.

Abstract: Exemplary embodiments of the present disclosure are directed to manipulating pressure-related hysteresis in a pressurized flow system by setting the pressure of the system to a predetermined location in the hysteresis band to advantageously minimize an effect of the pressure related hysteresis on the pressure of the system or to advantageously benefit from the effects of the hysteresis on the pressure of the system.

Abstract: Systems and methods for operating a stepper motor of a pump at a desired low velocity include memory for storing information corresponding to an intake velocity profile. The intake velocity profile represents an optimized acceleration curve for operating the stepper motor over a range of motor velocities during an intake cycle. A processor of a system controller dynamically accesses the memory during the intake cycle to acquire the information representing the intake velocity profile and issues a series of pulses to the stepper motor based on this information. In response to the pulses, the stepper motor accelerates in accordance with the optimized acceleration curve represented by the intake velocity profile. The optimized acceleration curve is based on the available torque of the stepper motor across a range of motor velocities and enables the motor to operate with greater torque utilization and less margin than traditional linear acceleration profiles.

Abstract: Described is a method of reducing liquid composition errors in a low-pressure mixing pump system. Packets representing the switching intervals of each component of the desired fluid mixture are provided to an intake of the mixing pump system. For each packet, a switching time associated with at least one of the components in the packet is modulated. Modulated switching times are based on time offsets that are specifically selected according to the undesirable frequency characteristic of an intake response of the mixing pump system. The average of the volumes contributed by the packets thus modulated is equal to a component volume that achieves a desired proportion of the component in the output flow of the mixing pump system. Modulated switching times enable the reduction or elimination of composition error in the output flow of the mixing pump system.

Abstract: Systems and methods for operating a stepper motor of a pump at a desired low velocity include memory for storing information corresponding to an intake velocity profile. The intake velocity profile represents an optimized acceleration curve for operating the stepper motor over a range of motor velocities during an intake cycle. A processor of a system controller dynamically accesses the memory during the intake cycle to acquire the information representing the intake velocity profile and issues a series of pulses to the stepper motor based on this information. In response to the pulses, the stepper motor accelerates in accordance with the optimized acceleration curve represented by the intake velocity profile. The optimized acceleration curve is based on the available torque of the stepper motor across a range of motor velocities and enables the motor to operate with greater torque utilization and less margin than traditional linear acceleration profiles.