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: 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: 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: 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: 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.