Abstract: The invention provides related apparatus and methods of making an integrated electrospray tip by depositing ionic and/or electronic conductor materials onto a planar substrate. The invention also features methods of forming an electrospray apparatus comprising coupling a first planar substrate to the surface of a second planar substrate, wherein a surface on at least one of the substrates includes one or more microfluidic channels and/or reservoirs which are at least partially or totally enclosed therebetween. The conductive regions of the apparatus do not intersect the microfluidic channels within other portions of the apparatus provided preferably. The invention further provides related apparatus and methods for manufacturing and using microfluidic devices with integrated electrodes for electrospray ionization.

Abstract: The invention provides related apparatus and methods of making an integrated electrospray tip by depositing ionic and/or electronic conductor materials onto a planar substrate. The invention also features methods of forming an electrospray apparatus comprising coupling a first planar substrate to the surface of a second planar substrate, wherein a surface on at least one of the substrates includes one or more microfluidic channels and/or reservoirs which are at least partially or totally enclosed therebetween. The conductive regions of the apparatus do not intersect the microfluidic channels within other portions of the apparatus provided preferably. The invention further provides related apparatus and methods for manufacturing and using microfluidic devices with integrated electrodes for electrospray ionization.

Abstract: The present invention provides methods for diagnosing cancers, such as prostate cancer. Also, methods for evaluating the prostate cancer state of a patient are described herein. These methods involve the detection, analysis, and classification of biological patterns in biological samples. The biological patterns are obtained using, for example, mass spectrometry systems, antibody based techniques, or nucleic acid based techniques. The present invention also includes therapeutic and prophylactic agents that target the biomarkers described herein. Also, the present invention provides methods for the treatment of prostate cancer using the markers described herein or agents that mimic the properties of these markers.

Abstract: A microfluidic chip formed with multiple fluid channels terminating at a tapered electrospray ionization tip for mass spectrometric analysis. The fluid channels may be formed onto a channel plate that are in fluid communication with corresponding reservoirs. The electrospray tip can be formed along a defined distal portion of the channel plate that can include a single or multiple tapered surfaces. The fluid channels may terminate at an open-tip region of the electrospray tip. A covering plate may substantially enclose most portions of the fluid channels formed on the channel 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 tapered electrospray tip having an open-tip region.

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: The invention provides related apparatus and methods of making an integrated electrospray tip by depositing ionic and/or electronic conductor materials onto a planar substrate. The invention also features methods of forming an electrospray apparatus comprising coupling a first planar substrate to the surface of a second planar substrate, wherein a surface on at least one of the substrates includes one or more microfluidic channels and/or reservoirs which are at least partially or totally enclosed therebetween. The conductive regions of the apparatus do not intersect the microfluidic channels within other portions of the apparatus provided preferably. The invention further provides related apparatus and methods for manufacturing and using microfluidic devices with integrated electrodes for electrospray ionization.

Abstract: Methods are disclosed for coating at least a portion of a hydrophobic surface, including the surfaces of plastics or other polymers. Such methods include the use of a first coating layer and/or region that interacts with the hydrophobic surface, although the formation of a chemical bond between the first coating layer and the hydrophobic surface is not required. Subsequent layers may then interact chemically or non-chemically with at least a portion of the first coating layer and/or region. Such coated surfaces may be part of a device or apparatus, including microfluidic devices.

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: Microfluidic devices provide substances to a mass spectrometer. The microfluidic devices include a substrate having at least one microchannel, a cover arranged on a surface of the microchannel, and at least one electrical potential source. Some embodiments include a microchannel widened at an outlet. Other embodiments position the electrical potential source along a surface of the cover. Still other embodiments include a well in which an electrode and a membrane are disposed. The various embodiments provide stable electrospray ionization of substances from a microfluidic device to a mass spectrometer.

Abstract: The present invention provides methods for diagnosing cancers, such as prostate cancer. Also, methods for evaluating the prostate cancer state of a patient are described herein. These methods involve the detection, analysis, and classification of biological patterns in biological samples. The biological patterns are obtained using, for example, mass spectrometry systems, antibody based techniques, or nucleic acid based techniques. The present invention also includes therapeutic and prophylactic agents that target the biomarkers described herein. Also, the present invention provides methods for the treatment of prostate cancer using the markers described herein or agents that mimic the properties of these markers.

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: Methods and apparatus for analyzing ions by pipelining data acquisitions with an orthogonal time-of-flight (OTOF) mass spectrometer. A predetermined push sequence is established for launching packets of ions from a source region into a flight tube towards a detection region within the OTOF mass spectrometer such that ions which are launched in adjacent packets do not overlap prior to reaching the detection region. These discrete packets of ions do not intermingle and are launched in accordance with the predetermined push sequence along a propagation path from the source region toward the detection region such that portions of the packets of ions are simultaneously in-flight within the flight tube of the OTOF mass spectrometer. The times of arrival of ions are detected at the detection region to produce time-of-flight scans with signals corresponding to times of arrival for the ions in the launched packets of ions to provide a mass spectrum derived from pipelined data acquisitions.

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 psuedo-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 tapered electrospray ionization tip for mass spectrometric analysis. The fluid channels may be formed onto a channel plate that are in fluid communication with corresponding reservoirs. The electrospray tip can be formed along a defined distal portion of the channel plate that can include a single or multiple tapered surfaces. The fluid channels may terminate at an open-tip region of the electrospray tip. A covering plate may substantially enclose most portions of the fluid channels formed on the channel 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 tapered electrospray tip having an open-tip region.

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 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.