Abstract: A method of ion detection comprises: (a) setting electrical potentials of a dynode and a scintillator electrode of a Daly detector and of a focusing lens disposed at an ion inlet of the Daly detector so as to detect negatively charged ions received from a mass analyzer or mass filter; (b) transferring the negatively charged ions from the mass analyzer or mass filter to the Daly detector through the lens and detecting said negatively charged ions by a photodetector of the Daly detector; (c) setting electrical potentials of the dynode, the scintillator electrode and the focusing lens of the Daly detector so as to detect positively charged ions received from the mass analyzer or mass filter; and (d) transferring the positively charged ions from the mass analyzer or mass filter to the Daly detector through the lens and detecting said positively charged ions by the photodetector.

Abstract: A mass spectrometer support apparatus includes a deconvolution logic and a centroider logic. The deconvolution logic is configured to deconvolve a mass spectrum measured by a mass spectrometer using an approximate peak shape. The centroider logic is configured to integrate the deconvolved spectrum and populate a sparse vector of peak locations.

Abstract: The present disclosure relates to novel and improved methods of analyzing proteins, peptides and polypeptides by mass spectrometry using ion-ion reactions. More specifically the disclosure relates to improved methods for implementing the m/z selective arresting of ion-ion reactions within the ion-ion reaction cell of a mass spectrometer system during a period where ion-ion reactions are performed.

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 method is provided that includes receiving a first plurality of experiment parameters for a first experiment to be performed by a scientific instrument on a first sample, the first plurality of experiment parameters including a list, and storing the list. The method further includes receiving a second plurality of experiment parameters for a second experiment to be performed by the scientific instrument, the second plurality of experiment parameters including a selection, within a graphical user interface, of the list from the first experiment to reuse for the second experiment. The method further includes receiving experiment data relating to the second experiment and analyzing the experiment data based on the list from the first experiment to determine a result of the second experiment.

Abstract: Aspects of systems, methods, algorithms, and non-transitory media storing computer-readable instructions for segmenting data processing workflows are provided. In a first aspect, a computer-implemented method for segmenting data processing workflows includes determining a configuration of an instrument system. The instrument system can include an analytical instrument coupled with an instrument PC (IPC). The IPC can be configured to receive raw data from the analytical instrument, to process the raw data, and to communicate with a client computing device coupled with the instrument system. The method can also include segmenting a data process workflow based at least in part on the configuration, attributing at least a subset of constituent operations of the data process workflow to the client computing device or the IPC.

Abstract: A mass spectrometer support apparatus includes a peak shape logic to determine one or more peak shapes using a calibration mass spectrum and known peak locations; and a tuning logic to adjust instrument parameters to achieve a selected peak width. A method for tuning a quadrupole-based mass spectrometer includes determining one or more peak shapes using a calibration mass spectrum and known peak locations; and adjusting instrument parameters to achieve a selected peak width.

Abstract: A needle receiving assembly includes a fluid conducting element housing, a sealing element configured to receive a needle, and a fluid conducting element. The needle receiving assembly is configured to connect to a needle of a needle assembly. The fluid conducting element housing comprises an aligning component configured to contact a needle housing of the needle assembly and to increase alignment between the needle and the needle receiving assembly. The fluid conducting element housing comprises a lateral protruding portion including an inner lateral surface that laterally surrounds a cavity of the fluid conducting element housing and a central protruding portion protruding beyond a base of the fluid conducting element housing and the central protruding portion. The aligning component comprises an aligning inner surface formed by a portion of the inner lateral surface of the lateral protruding portion.

Abstract: A method of generating an inclusion list for targeted mass spectrometric analysis is disclosed. Experimentally-acquired data for a plurality of isobarically-labeled peptides derived by proteolytic digestion of a corresponding protein. The data includes, for each of the isobarically-labeled peptides, a mass-to-charge (m/z) ratio, a charge state, and a chromatographic retention time (RT). The method includes determining a hydrophobicity index (HI) of an unlabeled peptide corresponding to the isobarically-labeled peptide. If the determined HI is less than a threshold value, a substitute unlabeled peptide is selected in accordance with predetermined criteria and predicted properties for the substitute peptide are determined and stored on an inclusion list. If the determined HI for the unlabeled peptide is at least as great as the threshold value, predicted properties for the unlabeled peptide are determined and stored on an inclusion list.

Abstract: A system may control a mass spectrometer to acquire, during a plurality of acquisitions constituting an acquisition cycle, a set of mass spectra of product ions derived from precursor ions isolated based on a parallel isolation window successively positioned throughout a precursor mass-to-charge ratio (m/z) range. The precursor m/z range is divided into a plurality of isolation window units. The parallel isolation window includes, for each acquisition of the acquisition cycle, a set of isolation sub-windows corresponding to a distinct set of isolation window units of the precursor m/z range. At least two adjacent isolation sub-windows of the parallel isolation window are non-contiguous. Each isolation window unit of the precursor m/z range is analyzed at least twice during the acquisition cycle. A mass spectrum for the precursor m/z range may be generated based on the set of mass spectra acquired during the acquisition cycle.

Abstract: A computer-implemented method of training a machine learning model comprises: accessing an elution profile comprising a plurality of detection points representing intensity of ions derived from components eluting from a chromatography column and detected by a mass analyzer as a function of time; generating, based on the elution profile, training data comprising a plurality of training examples, a training example of the plurality of training examples comprising a set of detection points and a target next detection point, the target next detection point comprising a detection point of the plurality of detection points following the set of detection points; and training, using the training data, the machine learning model to determine a predicted next detection point, the predicted next detection point following the set of detection points.

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: 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: Gas is flowed through a gas chromatography column at a first flow rate to cause a first change in pressure defining a first pressure differential. The first pressure differential and/or a first time duration for the first change in pressure is measured. At least one closed exhaust path is opened and a second flow rate through each of the at least one open exhaust paths is set. Gas is flowed through the column at a third flow rate and each of the at least one open exhaust paths at the second flow rate, causing a second change in pressure defining a second pressure differential. The second pressure differential and/or a second time duration for the second change in pressure is measured. A leak is determined based on one or more of measured first pressure differential and/or first time duration and measured second pressure differential and/or second time duration.

Abstract: A method of processing mass spectral data is provided. The mass spectral data includes a plurality of MS1 mass spectra and a plurality of MSN mass spectra each having a respective associated retention time. A group of features is detected in the plurality of MS1 mass spectra, each feature of the group having a respective mass, and the features of the group having corresponding retention times. The method includes, for each of one or more features of the group: submitting a corresponding MSN mass spectrum to a mass spectral search engine in order to obtain an identification result for that feature, and determining a candidate ion type for the feature based on a mass difference between the mass associated with the feature and an expected mass from the identification result. The method also includes identifying one or more compounds based on the group of features and the candidate ion type(s).

Abstract: A sample support for polymer-spray mass spectrometry includes a support substrate comprising a polymer. The support substrate is configured to support a sample on a surface of the support substrate. The sample support also includes a reservoir formed on the surface of the support substrate. The reservoir is configured to hold a spray solvent.

Abstract: It is proposed to improve transmission of ions along the curved path of an ion guide by changing the separation between adjacent multipole rods in the plane of curvature. As the separation increases along the length of the device, the ion confinement in the plane of curvature decreases. At the same time, the external field penetration from the electrodes outside of the main ion guide increases which can be used to create additional DC field gradients to facilitate ion confinement and motion through the ion guide.

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 support apparatus for a scientific instrument comprises first, second, and third logics. The first logic is configured to acquire a first data file via detectors of the instrument. The second logic is configured to convert the first data file into a plurality of second data files stored in an object storage. Each of the second files is named using a suitable file naming convention. The third logic is configured to process a request for a data portion of the first data file and to provide the data portion by accessing one or more of a first memory cache, a second memory cache, and the object storage to obtain a corresponding portion of a corresponding one of the second data files identified based on the file naming convention.

Abstract: A method of performing mass spectrometry includes obtaining, based on a series of mass spectra of detected ions derived from components eluting from a chromatography column, a plurality of extracted ion chromatograms (XICs), each XIC comprising a plurality of detection points representing detected intensity for a distinct selected m/z as a function of time; detecting, based on the series of mass spectra, precursor ions of each distinct selected m/z of the plurality of XICs; and determining, for each XIC based on a set of detection points of the XIC, a predicted next detection point to be obtained based on a next mass spectrum to be acquired.

Abstract: A system for collecting multiple compensation voltage fractions includes a field asymmetric-waveform ion-mobility spectrometry (FAIMS) device which receives ions generated from a sample, such as a biological sample. A mass spectrometer injection gate is configured to inject, when in an open state, ions transmitted by the FAIMS device into a mass analyzer of the mass spectrometer. A controller circuit is configured to open the injection gate and apply a dynamic compensation voltage (CV) to an electrode of the FAIMS device while the injection gate is open. The dynamic CV can have a waveform in the shape of a ramp, triangle, wavelet, sinusoid, or another shape. The dynamic CV includes CVs associated with multiple adjacent CV fractions, and the FAIMS device is configured to transmit the multiple adjacent CV fractions into the mass analyzer via the open injection gate to be scanned together by the mass analyzer in a single experiment.

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.