Abstract: The present invention discloses methods for deconvolving and converting 1D mass spectra to 2D mass spectrum in order to obtain migration time centers and total intensities of the neutral mass envelopes of 2D spectra. The present invention also discloses devices that include a preparation/separation unit coupled to a mass spectrometer unit, and a computer unit capable of deconvolving mass spectra and calculating neutral mass envelopes.

Abstract: Methods and apparatus for mass filtering based on a-priori biomarker knowledge and elution time intervals for selected ion species from a separation device. A sample may be screened for biomarker patterns based on distinct elutions times for selected ions or peptides. A mass spectrum for species of interest can be tailored by filtering out undesired ions by measuring corresponding elution times and determining a priori selected elution time intervals for desired ion species only. The invention assists in the identification of biomarkers having known mass spectral peaks corresponding to known proteins or ions of interest that are known to elute from a separation device within a pre-defined elution time window.

Abstract: An automated electrospray ionization (ESI) device and related methods to optimize electrospray interface conditions for mass spectrometric analysis. The optimization process can be performed with calibration or optimization solutions that produce expected ESI parameters such as an ESI signal or an ion current. The ESI device may include an input/output (I/O) controller that is coupled to an electrospray assembly including an XYZ stage for positioning an electrospray emitter relative to a mass spectrometer orifice. The I/O controller may be connected to a power supply for applying an adjustable electrospray ionization voltage, and an adjustable flow regulator that alters the flow of solution by modifying applied voltage and/or pressure. A central processing unit instructs the I/O controller to control selectively the electrospray assembly based on the resultant signals from the mass spectrometer or the ion currents within the mass spectrometer in accordance with a predetermined optimization algorithm.

Abstract: Microfluidic devices provide substances to a mass spectrometer. The microfluidic devices include first and second surfaces, at least one microchannel formed by the surfaces, and an outlet at an edge of the surfaces. Some embodiments also include a tip surface with one or more surface features for helping guide substances from the outlet of the device toward a mass spectrometer. In some embodiments, the surface feature(s) includes a groove, which may be hydrophilic along all or part of its length. Hydrophilic surfaces and/or hydrophobic surfaces may also help guide substances out of the outlet and/or toward the mass spectrometer. In some embodiments, the outlet and/or the tip surface is recessed back from an adjacent portion of the edge. A source of electrical potential can help move substances through the microchannel, separate substances and/or provide electrospray ionization.

Abstract: A mass spectrometer and associated methods analyze an ion beam by accumulating ions for a sequence of time periods, and driving the accumulated ions in pulses. Differing quantities of ions can be accumulated in the sequential pulses according to a pseudo-random sequence, and the slower ions are overtaken by the faster ions of a subsequent pulse. A mass spectrum may be reconstructed from an overlapping ion detector signal using an inverse of a weighted simplex matrix or inverse Hadamard transform techniques.

Abstract: Methods and apparatuses are disclosed that model the lineshapes of mass spectrometry data. Ions can be modeled with an initial distribution that models molecules as having multiple positions and/or energies prior to traveling in the mass spectrometer. These initial distributions can be pushed forward by time of flight functions. Fitting can be performed between the modeled lineshapes and empirical data. Filtering can greatly reduce dimensions of the empirical data, remove noise, compress the data, recover lost and/or damaged data.

Abstract: Systems for customization of assays. The method includes steps of collecting case samples representing a clinical phenotypic state and control samples representing patients without said clinical phenotypic state. Preferably the system uses a mass spectrometry platform system to identify patterns of polypeptides in said case samples and in the control samples without regard to the specific identity of at least some of said polypeptides. Based on identified representative patterns of the state, the system performs optimized assays for greater sensitivity, specificity, and/or cost effectiveness.

Abstract: A business method for use in classifying patient samples. The method includes steps of collecting case samples representing a clinical phenotypic state and control samples representing patients without said clinical phenotypic state. Preferably the system uses a mass spectrometry platform system to identify patterns of polypeptides in said case samples and in the control samples without regard to the specific identity of at least some of said polypeptides. Based on identified representative patterns of the state, the business method provides for the marketing of diagnostic products using representative patterns.

Abstract: Microfluidic devices provide substances to a mass spectrometer. The microfluidic devices include first and second surfaces, at least one microchannel formed by the surfaces, and an outlet at an edge of the surfaces which is recessed back from an adjacent portion of the edge. Hydrophilic surfaces and/or hydrophobic surfaces guide substances out of the outlet. A source of electrical potential can help move substances through the microchannel, separate substances and/or provide electrospray ionization.

Abstract: A mass spectrometer and associated methods analyze an ion beam by accumulating ions for a sequence of time periods, and driving the accumulated ions in pulses. Differing quantities of ions can be accumulated in the sequential pulses according to a pseudo-random sequence, and the slower ions are overtaken by the faster ions of a subsequent pulse. A mass spectrum may be reconstructed from an overlapping ion detector signal using an inverse of a weighted simplex matrix or inverse Hadamard transform techniques.

Abstract: A microfluidic chip formed with multiple fluid channels terminating at a common electrospray ionization tip for mass spectrometric analysis. The fluid channels may be formed within a substrate plate that are in fluid communication with corresponding reservoirs. The electrospray tip can be formed along a defined portion of the substrate plate, wherein the electrospray tip includes an open-tip region at which the fluid channels converge. A top laminate plate may substantially enclose most portions of the fluid channels formed in the bottom polymer plate except for the open-tip region. Another aspect of the invention provides methods for conducting mass spectrometric analysis of multiple samples flowing through individual fluid channels in a single microfluidic chip that is formed with a convergent electrospray tip. The convergent electrospray tip includes an open or exposed distal pointed tip region.

Abstract: An improved mass spectrometer makes use of flexible circuit-board technology for directing charged particles through an interface from an ionization source to an analyzer of a mass spectrometer. A heated focusing structure may reduce or eliminate the use alternative desolvation techniques, such as use of heated capillaries and/or drying gas, to desolvate ions.