Abstract: In DM-SWATH a plurality of CoVs and a precursor ion mass range are received. A processor performs an iterative series of steps for each CoV of the plurality of CoVs. For each CoV of the plurality of CoVs, the CoV is applied to the DMS device to select a group of precursor ions. A mass filter is instructed to select precursor ions of the group that are within the precursor ion mass range, producing a subgroup of precursor ions. A fragmentation device is instructed to fragment the subgroup of precursor ions, producing a group of product ions. A mass analyzer is instructed to measure the intensity and m/z of the group of product ions, producing a product ion spectrum for each CoV of the plurality of CoVs. DM-SWATH is further used to validate if a known compound is in a sample.

Abstract: A plurality of measured product ion spectra is produced using a DIA tandem mass spectrometry method. One or more product ions are retrieved from a spectral library of known compounds or one or more theoretical product ions are calculated for the known compounds of a database. For each known or theoretical product ion, an XIC is calculated from the measured product ion spectra. Measured XIC peaks above a threshold intensity are grouped for the known compounds producing a subset of known compounds. Known or theoretical retention times are retrieved or calculated for the subset of known compounds. A regression function is calculated to correct the known or theoretical retention times using the known or theoretical retention times of the subset of known compounds as the independent variables and the measured retention times of the measured XIC peak groups of the subset of known compounds as the dependent variables.

Abstract: A plurality of measured product ion spectra are produced using a DIA tandem mass spectrometry method. One or more product ions are retrieved from a spectral library of known compounds or one or more theoretical product ions are calculated for the known compounds of a database. The one or more product ions or one or more theoretical product ions for each known compound are compared to the measured product ion spectra to identify one or more known compounds in the sample. A database of related known compounds is searched using one or more known compounds, producing one or more matching related compounds and one or more product ions for each related compound. The one or more product ions for each related compound are compared to the measured product ion spectra to identify one or more related compounds in the sample.

Abstract: Methods and systems are provided herein for selectively removing product ions resulting from an ECD dissociation event from the interaction region of an ECD reaction cell, while other precursor peptide ions continue to undergo ECD within the interaction region, thereby reducing or preventing the occurrence of multiple electron capture events by the product ions. In some aspects, the preferential extraction of product ions from the interaction region during the ECD reaction can occur without an auxiliary AC field being generated within the interaction region. Additionally, in some aspects, the methods and systems disclosed herein can subject the various product ions to a non-dissociative charge reduction via exposure to reagent ions of the opposite polarity so as to selectively concentrate product ions to a lower charge state.

Abstract: In one aspect, a method of processing ions in a mass spectrometer is disclosed, which comprises trapping a plurality of ions having different mass-to-charge (m/z) ratios in a collision cell, releasing said ions from the collision cell in a descending order in m/z ratio, and receiving the ions in a mass analyzer having a plurality of rods to at least one of which an RF voltage is applied, where the RF voltage is varied from a first value to a lower second value as the released ions are received by the mass analyzer.

Abstract: An ultrasonic transmitter (95) and detector (e.g., integrated as an ultrasound transducer) utilized in a feedback control system automatically monitors and/or detects surface profile (e.g., shape) of the liquid-air interface and adjusts the flow rate of sampling liquid to ensure that experimental conditions remain consistent at the time of sample introduction during serial samplings. The feedback control can provide for automated adjustment of the surface profile of the liquid-air interface in accordance with changes in desired set point according to an experimental workflow (e.g., automated adjustment between an interface corresponding to a vortex sampling set point and an overflow cleaning set point).

Abstract: Apparatus, systems, and methods in accordance with various aspects of the applicant's teachings provide for improved interfaces for providing a sample flow from a sample conduit (e.g., an analytical conduit or capillary), including those used in sample separation techniques such as CE and HPLC, to an ESI source for ionization thereby.

Abstract: A separation device separates an unknown intact mAb or reduced mAb subunits of a known mAb class from a sample. An ion source device ionizes the mAb. A mass spectrometer fragments the ionized mAb using an ECD device and mass analyzes resulting product ions using a mass analyzer, producing one or more product ion spectra. Theoretical product ion peaks are calculated for one or more constant portions of the mAb class. The theoretical product ion peaks are removed from the one or more product ion spectra, producing one or more difference product ion spectra. De novo sequencing is applied to the one or more difference product ion spectra, producing one or more candidate sequences for one or more variable portions of the mAb. A genome database is searched for matches to the one or more candidate sequences, producing one or more matched sequences for the one or more variable portions.

Abstract: A mass isolation device selects a precursor ion of a sample that has been digested using a protease. A first fragmentation device fragments the precursor ion using collision-induced dissociation (CID), and the resulting product ions are analyzed using a mass analyzer producing a CID spectrum. A list of theoretical candidate glycopeptide sequences is determined from CID spectrum. The mass isolation device again selects the precursor ion of the sample. A second fragmentation device fragments the precursor ion using electron-based dissociation (ExD), and the resulting product ions are analyzed using the mass analyzer producing a CID spectrum. For each sequence of the list, the sequence is computationally fragmented, producing theoretical fragments, mass-to-charge ratio (m/z) values are calculated for the theoretical fragments, and the sequence is scored using c and z fragment matching rules. The highest scoring sequence is identified as a peptide sequence of a glycopeptide of the sample.

Abstract: Systems and methods described herein relate to a mass spectroscopy system having multipole ion guides that can receive ions from an ion source for transmission to downstream mass analyzers, while preventing unwanted ions from being transmitted into the high-vacuum chambers of mass spectrometer systems. At least one ion guide can have two or more auxiliary electrodes that extend along at least a portion of the ion guide. A power supply provides an RF voltage to the poles of the ion guide for radially confining the ions within the internal volume of the ion guide. The auxiliary electrodes are also provided with an auxiliary electrical signal that can selectively radially deflect from the internal volume at least a portion of low m/z ions so as to prevent transmission of undesired low m/z ions into the downstream mass analyzers.

Abstract: A dissociation device fragments a precursor ion, producing at least two different product ions with overlapping m/z values in the dissociation device. The dissociation device applies an AC voltage and a DC voltage creating a pseudopotential that traps ions below a threshold m/z including the at least two product ions. The dissociation device receives a charge reducing reagent that causes the trapped at least two product ions to be charge reduced until their m/z values increase above the threshold m/z set by the AC voltage. The increase in the m/z values of the at least two product ions decreases their overlap. The at least two product ions with increased m/z values are transmitted to another device for subsequent mass analysis by applying the DC voltage to the dissociation device relative to a DC voltage applied to the other device.

Abstract: Mass spectrometer based analytical systems and methods in which a feedback control system can be utilized to control the flow of liquid within a sampling probe to adjust and/or maintain the surface profile (e.g., shape) of the liquid-air interface within an open sampling port of the sampling probe. The feedback control systems can automatically monitor and/or detect the surface profile of the liquid-air interface and adjust the flow rate of the sampling liquid to ensure that experimental conditions remain consistent at the time of sample introduction during serial samplings. These can provide stable and reproducible analyte flows of consistent dilution to the ion source, increasing reproducibility and/or accuracy of data generated by MS analysis. Can be used with a change in the desired set point according to the particular experimental workflow (e.g., automated adjustment between an interface corresponding to a sampling set point and a cleaning set point).

Abstract: Methods and systems for delivering liquid sample to an ion source and subsequent analysis by mass spectrometry. In accordance with various aspects of the present teachings, MS-based systems and methods are provided in which desorption solvent is used in sampling interface to desorb analyte species from an SPME device that is coupled to an ion source to ionize analyte species desorbed into the desorption solvent for MS analysis (e.g., without a liquid chromatography (LC) column between the sampling interface and the ion source). In various aspects of the methods and systems described herein, configuring the sampling interface can be optimized so as to reduce the fluid volume dead space about the fluid inlet so as to concentrate the one or more analyte species desorbed at optimized conditions from the SPME substrate in a decreased volume of the desorption solvent when the SPME device is inserted into sampling interface.

Abstract: Systems and methods are disclosed for analyzing a sample using overlapping precursor isolation windows. A mass analyzer of a tandem mass spectrometer is instructed to select and fragment at least two overlapping precursor isolation windows across a precursor ion mass range of a sample using a processor. The tandem mass spectrometer includes a mass analyzer that allows overlapping precursor isolation windows across the mass range of the sample.

Abstract: Methods and systems for separating, detecting, and/or quantifying sample enantiomers using differential mobility spectrometry (DMS) are provided herein. In accordance with various aspects of the applicant's teachings, the methods and systems can provide for the separation of racemic or non-racemic mixtures of sample enantiomers that may be difficult to separate with conventional techniques, such as mass spectrometry (MS), by reacting the sample enantiomers with an enantiomerically-pure compound to form diastereomers separable by DMS.

Abstract: A system and method are provided for loading a sample into an analytical instrument using acoustic droplet ejection (“ADE”) in combination with a continuous flow sampling probe. An acoustic droplet ejector is used to eject small droplets of a fluid sample containing an analyte into the sampling tip of a continuous flow sampling probe, where the acoustically ejected droplet combines with a continuous, circulating flow stream of solvent within the flow probe. Fluid circulation within the probe transports the sample through a sample transport capillary to an outlet that directs the analyte away from the probe to an analytical instrument, e.g., a device that detects the presence, concentration quantity, and/or identity of the analyte. When the analytical instrument is a mass spectrometer or other type of device requiring the analyte to be in ionized form, the exiting droplets pass through an ionization region, e.g.

Abstract: Systems and methods for atmospheric pressure chemical ionization are provided herein. In various aspects, the APCI apparatus, systems, and methods can provide an asymmetric sample spray into a vaporization chamber asymmetrically (e.g., off axis from the longitudinal axis of the vaporization chamber) so as to increase the interaction of the molecules in the sample spray with the vaporization chamber's sidewalls (and expose more of the molecules to the heat generated thereby), which can thereby result in improved consistency and/or efficiency of ion formation, and/or increased sensitivity relative to conventional APCI techniques.

Abstract: A plurality of product ion spectra measured over plurality of cycles for each precursor ion mass selection window of two or more precursor ion mass selection windows are received from a tandem mass spectrometer. A product ion extracted ion chroatograms (XIC) is calculated for each precursor ion mass selection window of the two or more precursor ion mass selection windows from the plurality of product ion spectra for each precursor ion mass selection window. Two or more product ion XICs are produced. A two-dimensional binary bit matrix is generated to represent each product ion XIC of the two or more product ion XICs. For each XIC of the two or more product ion XICs, the binary bit matrix is separately initialized with binary values calculated from each XIC and the initialized binary bit matrix is compared with stored information about known compounds to identify known compounds of each XIC.

Abstract: A holder that can be used to stand up a PCR tube on a flat surface or held in a user's hand. The holder has a first elongated portion, a second elongated portion and a third elongated portion. The first elongated portion having a magnet, the second elongated portion having a tube holding means and the third elongate portion acting as a stabilizer to allow the holder to standup in an upright position. The third elongate portion can also be used as a gripping surface to be held between fingers of a hand.

Abstract: A mass spectrometer is operated to simultaneously measure precursor and production data over a number of acquisitions. For each acquisition, the following steps are performed. Ion transfer optics inject ions from an ion beam into an ELIT causing the ions to oscillate axially between two electric fields produced by two the sets of reflectrons. The ELIT measures a time domain image current of the oscillating ions from ion injection to a total acquisition time, Tacq1, and fragments the oscillating ions at one or both turning points of the oscillating ions adding product ions to the oscillating ions. The fragmentation is performed at a delay time relative to the ion injection that is increased by a time increment in each subsequent acquisition making the fragmentation dependent on ion position. The measured time domain image current is stored as a row or column of a two-dimensional matrix.