Abstract: Polymorphic forms of deoxycytidine and methods for preparing the same are provided herein. Also provided are compositions comprising polymorphic forms of deoxycytidine and at least one residual solvent, as well as methods of treating mitochondrial diseases using said compositions.

Abstract: Deoxynucleotide prodrugs for treatment of diseases characterized by unbalanced nucleotide pools are provided herein.

Abstract: In various embodiments, provided are ion optics systems comprising an even number of ion mirrors arranged in pairs such that a trajectory of an ion exiting the ion optics system can be provided that intersects a surface substantially parallel to an image focal surface of the ion optics system at a position that is substantially independent of the kinetic energy the ion had on entering the ion optics system. In various embodiments, provided are ion optics systems comprising an even number of ion mirrors arranged in pairs where the first member and second member of each pair are disposed on opposite sides of a first plane such that the first member of the pair has a position that is substantially mirror-symmetric about the first plane relative to the position of the second member of the pair.

Abstract: Systems and methods for analyzing compounds in a sample. In one embodiment, the present technology is directed towards a method of analyzing a sample, comprising: emitting ions from the sample; selectively filtering the emitted ions for at least one designated trigger ion; fragmenting the designated trigger ions; scanning for a designated trigger ion fragment; and upon detecting the designated trigger ion fragment, scanning for at least one confirmatory ion fragment.

Abstract: A mass spectrometer system including a differential mobility spectrometer and a mass spectrometer at least partially sealed to, and in fluid communication, with, the differential mobility spectrometer, together with a related method, are provided. The mass spectrometer system can be operable to, and method can comprise, a) maintaining the differential mobility spectrometer at an internal operating pressure; b) providing ions to the differential mobility spectrometer; c) maintaining the mass spectrometer at a vacuum pressure lower than the internal operating pressure to draw a gas flow including the ions through the differential mobility spectrometer and into the vacuum chamber; and, d) modifying the gas flow between the differential mobility spectrometer and the mass spectrometer to change a gas flow rate through the differential mobility spectrometer.

Abstract: A mass analysis system including a low pressure dissociation region and a differential mobility spectrometer. The differential mobility spectrometer including at least one pair of filter electrodes defining an ion flow path where the filter electrodes generate an electric field for passing through a selected portion of the sample ions based on the mobility characteristics of the sample ions. The differential mobility spectrometer also includes a voltage source that provides DC and RF voltages to at least one of the filter electrodes to generate the electric field, an ion inlet that receives sample ions that have passed through the low pressure dissociation region, and an ion outlet that outputs the selected portion of the sample ions. A mass spectrometer receives some or all of the selected portion of the sample ions.

Abstract: Methods for cooling ions retained in an ion trap are described. In various embodiments, a cooling gas is delivered into a linear ion trap causing a non-steady state pressure elevation in at least a portion of the trap above about 8×10?5 Torr for a duration less than the ion-retention time. In various embodiments, the duration of pressure elevation can be based upon a period of time required for an ion to lose a desired amount of its kinetic energy.

Abstract: Ion trap apparatus and methods for efficiently addressing the effects of charge space caused by ion trap overfilling, useful in linear ion traps of mass spectrometers.

Abstract: A method of processing multiple precursor ions in a tandem mass spectrometer includes generating a plurality of precursor ions with an ion source. At least some of the plurality of precursor ions is trapped in an ion trap. At least two precursor ions of interest are isolated from the plurality of precursor ions with a filtered noise field. Precursor ions of interest are sequentially ejected toward a collision cell. The sequentially ejected precursor ions of interest are fragmented in a collision cell. The mass-to-charge ratio spectra of the fragmented ions are then determined with a mass spectrometer.

Abstract: A mass spectrometer system and a method of operating a mass spectrometer are provided. An RF field is produced between the plurality of rods to radially confine the ions in the rod set. The RF field has a resolving DC component field. The resolving DC component field is varied along at least a portion of a length of the rod set to provide a DC axial force acting on the ions.

Abstract: A method of operating a mass spectrometer having an elongated rod set and a set of auxiliary electrodes is provided, the rod set having an entrance end and an exit end and a longitudinal axis. The method comprises a) admitting ions into the entrance end of the rod set; b) trapping at least some of the ions in the rod set by producing a barrier field at an exit member adjacent to the exit end of the rod set and by producing an RF field between the rods of the rod set; and, c) providing an auxiliary AC excitement voltage to the set of auxiliary electrodes to energize a first group of ions of a selected mass to charge.

Abstract: In various aspects, provided are methods for identification of the presence of modified peptides using at least in part mass spectrometric signals from metastable ions that are formed in the field free region of the analyzer. For example, in various embodiments where the modified peptides are phosphopeptides, such metastable ions can appear approximately 95 u lower than the precursor ion m/z value from which they were formed when the peptide contains a phosphate group. In various embodiments, detection of such metastable ions in a MALDI-TOF mass spectrum can identify the modified peptide. In various aspects, provided are methods for identification of the presence of modified peptides using at least in part MS/MS data from two or more of modified peptides, de-modified peptides and non-modified peptides by comparing the sequence and/or site of modification information for two or more of these three forms of a peptide.

Abstract: A method and apparatus for multiplexing ions in an MSn mass spectrometer is provided. Ion are filtered to produce a group of ions of interest, the group of ions below a space charge limit of the MSn mass spectrometer. At least a portion of the group of ions are fragmented to form a fragmented group of ions. At least a portion of the fragmented group are stored such that a plurality of portions of the fragmented group can be sequentially selected for mass spectrometry analysis. Each of the plurality of portions of the fragmented group are sequentially selected and re-fragmented prior to mass spectrometry analysis. Each of the plurality of portions of the fragmented group are analyzed, via mass spectrometry, once each of the plurality of portions of the fragmented group has been fragmented.

Abstract: A method for introducing samples through a boundary member partially defining a chamber at an entrance point coaxial to a sampling inlet of a mass spectrometer is described. Field-free conditions can be established in at least one region of the chamber. The sample can be introduced adjacent to the sampling inlet, and introducing at least a second sample can be introduced through at least one other entrance point in the chamber not adjacent to the sampling inlet. An apparatus having a sampling inlet and a boundary member partially defining a chamber is also described. Field-free conditions can be established in at least one region of the chamber, and there can be a first aperture in the boundary member through which a source emits sample. Related devices, uses and mass spectrometers are also described.

Abstract: The present teachings relate to a method of filtering mass spectrometer data using a variable filter window. The width of the window can depend on the mass itself and the mass defects for a family of compounds. The teachings can be used with a plurality of compounds including but not limited to peptides and can be utilized on a brood range of mass spectrometers.

Abstract: A mass spectrometer having an elongated rod set, the rod set having a first end, a second end, a plurality of rods and a central longitudinal axis is described as is a method operating same.

Abstract: A mass spectrometer system including a differential mobility spectrometer and a mass spectrometer at least partially sealed to, and in fluid communication, with, the differential mobility spectrometer, together with a related method, are provided. The mass spectrometer system can be operable to, and method can comprise, a) maintaining the differential mobility spectrometer at an internal operating pressure; b) providing ions to the differential mobility spectrometer; c) maintaining the mass spectrometer at a vacuum pressure lower than the internal operating pressure to draw a gas flow including the ions through the differential mobility spectrometer and into the vacuum chamber; and, d) modifying the gas flow between the differential mobility spectrometer and the mass spectrometer to change a gas flow rate through the differential mobility spectrometer.

Abstract: A system including a differential mobility spectrometer is described as is a method of operating the system including the differential mobility spectrometer.

Abstract: In various aspects, the present teachings provide systems and methods for reducing chemical noise in a mass spectrometry instrument that use a neutral chemical reagent and one or more mass filters to reduce interfering chemical background ion signals that are generated by ionization sources of mass spectrometers. In various embodiments, the neutral chemical reagent belongs to the class of organic chemical species containing a disulfide functionality.

Abstract: A method of operating a mass spectrometer having a rod set is provided. The rod set has a first end, a second end opposite to the first end, and a longitudinal axis extending between the first end and the second end.