Abstract: Zwitterionic polymers bearing positive and negative charges are readily prepared from easily accessible precursors. The polymers show enhanced binding affinities for analytes under high salt conditions, compared to similar polymers bearing a charge of a single polarity. The polymers can also include an energy absorbing moiety for use in matrix assisted laser desorption/ionization mass spectrometry. The polymer can also include a photo-curable group, which can be used to form cross-links within the bulk polymer or between the polymer and a surface functionalized with a polymerizable moiety. The polymers are incorporated into devices of use for the analysis, capture, separation, or purification of an analyte. In an exemplary embodiment, the invention provides a substrate coated with a polymer of the invention, the substrate being adapted for use as a probe for a mass spectrometer.

Abstract: Polymers bearing metal chelating groups are readily prepared from easily accessible precursors. The polymers are readily converted to the corresponding metal chelates. The polymers can also include an energy absorbing moiety for use in matrix assisted laser desorption/ionization mass spectrometry. The polymer can also include a photo-curable group, which can be used to form cross-links within the bulk polymer or between the polymer and a surface functionalized with a polymerizable moiety. The polymers are incorporated into devices of use for the analysis, capture, separation, or purification of an analyte. In an exemplary embodiment, the invention provides a substrate coated with a polymer of the invention, the substrate being adapted for use as a probe for a mass spectrometer.

Abstract: Methods for discriminating between related proteins and other analytes in a sample and for correlating protein expression with disease states.

Abstract: A method and a device for detecting an analyte, including a substrate having a chemically selective surface; and a fluidic system disposed on the substrate, the manifold having at least one fluid path in communication with at least a discrete region of the surface, wherein the one fluid path and the discrete region together define a contained sample region on the surface. The fluidic system has a removable portion, wherein the removal of the removable portion of the fluidic system renders the discrete region directly interrogatable by a surface-based analytical tool.

Abstract: Hydrogel polymer blends including precursors and crosslinked forms of the compositions. The blends provide an improved approach to achieve high quality, uniform coatings with better commercial viability than other approaches including copolymerization. Applications include mass spectral analysis of biomolecular analytes such as proteins. Dextran and acrylamide systems are preferred. Benzophenone groups can be used as photocrosslinking groups. Photoinitiators are not needed. Functionalities which can selectively bind to biomolecular analytes are included.

Abstract: A method that analyzes mass spectra using a digital computer is disclosed. The method includes entering into a digital computer a data set obtained from mass spectra from a plurality of samples. Each sample is, or is to be assigned to a class within a class set having two or more classes and each class is characterized by a different biological status. A classification model is then formed. The classification model discriminates between the classes in the class set.

Abstract: The present invention relates to the fields of protein expression and molecular biology. In particular, the present invention includes methods for monitoring the levels of polypeptide inhibition caused by inhibitory nucleic acids.

Abstract: The invention provides apparatus and methods for performing time-of-flight (TOF) mass spectrometry. A TOF mass spectrometer of the present invention comprises one or more ion focusing electric sectors. At least one of the electric sectors is associated with an ion optical element. The ion optical elements comprise at least one adjustable electrode, such that the adjustable electrode is able to modify the potential experienced by an ion entering or exiting the electric sector with which it is associated.

Abstract: A device for dynamically biasing an ion optic element, for example, in a mass spectrometer. The device includes a voltage source, a first ion optical element coupled with the voltage source, a second ion optical element resistively coupled with the first ion optical element; and a pulse generator capacitively coupled with the second ion optical element. The pulse generator is configured to apply a series of pulses to the second ion optical element. In steady state operation, a dynamic voltage bias is generated between the first ion optical element and the second ion optical element. The dynamic voltage bias is controllable by controlling the characteristics of the applied pulses, such as the pulse width, pulse amplitude, and pulse repetition rate of the applied pulses.

Abstract: Signal amplifiers having a non-linear transfer function. A high speed (high bandwidth) circuit with a non-linear transfer function over a limited range of input signal is provided. By appropriate choice of components, the non-linear transfer function can be used to accurately approximate any monotonic function such as a square root transfer function. In another aspect, a piecewise non-linear circuit arrangement using a set of non-linear sub-circuits is provided to accurately generate a desired non-linear transfer function over an extended dynamic range of input signal. In one implementation of such a circuit, each of the sub-circuits approximates the desired non-linear function over a portion of the input range.

Abstract: Laser desorption/ionization time-of-flight mass spectrometer (“LDI-TOF-MS”) devices, and methods, that accurately measure the mass of analytes contained in a sample and which also measure the quantities of analytes present in a sample in a consistent manner from instrument-to-instrument and over time on a single instrument. In particular, the invention provides LDI-TOF-MS devices and methods in which: 1) the energy of the laser pulse and the area of the sample illuminated (fluence) is consistent and controlled so as to produce consistent conditions for analyte desorption and ionization; 2) the mass analyzer behaves in a reproducible manner; and 3) the detection system produces a signal that consistently represents the arrival of ions of different masses.

Abstract: Methods for producing a preponderance of gas phase ions having higher order charge states during laser desorption ionization of an analyte are presented, the methods comprising irradiating the analyte in the presence of energy absorbing molecules at a mid-IR wavelength that is offset from an IR absorption maximum of the energy absorbing molecules.

Abstract: The present invention provides protein-based biomarkers and biomarker combinations that are useful in qualifying Chagas disease status in a patient. In particular, the biomarkers of this invention are useful to classify a subject sample as infected with Chagas disease or non-infected. The biomarkers can be detected by SELDI mass spectrometry.

Abstract: The present invention relates to the fields of molecular biology, combinatorial chemistry and biochemistry. Particularly, the present invention describes methods and kits for dynamically reducing the variance between analyte taken from complex mixtures.

Abstract: Systems and methods for rastering a series of illumination pulses across the surface of a sample under investigation in a mass spectrometer system so as to create a two dimensional illumination pattern (raster pattern) on the sample. A probe interface that engages a probe is configured to translate the probe along a first direction, and a pulse deflection mechanism is configured to vary the pulse-probe intersect position along a second direction. A control system, implementing a rastering algorithm, provides control signals to the pulse deflection mechanism to adjust the pulse path and the probe translation mechanism to adjust the probe position so that each illumination pulse impinges on one of a plurality of addressable locations on the sample. The resulting raster pattern may cover the entire sample or one or more portions of the sample, depending on the spot size and the displacement distances for each pulse along the first and second directions.

Abstract: This invention provides methods of retentate chromatography for resolving analytes in a sample. The methods involve adsorbing the analytes to a substrate under a plurality of different selectivity conditions, and detecting the analytes retained on the substrate by desorption spectrometry The methods are useful in biology and medicine, including clinical diagnostics and drug discovery.

Abstract: The invention provides apparatus and methods for performing time-of-flight (TOF) mass spectrometry. A TOF mass spectrometer of the present invention comprises one or more ion focusing electric sectors. At least one of the S electric sectors is associated with an ion optical element. The ion optical elements comprise at least one adjustable electrode, such that the adjustable electrode is able to modify the potential experienced by an ion entering or exiting the electric sector with which it is associated.

Abstract: Methods for processing spectra are disclosed. The method includes obtaining a plurality of spectra, each spectrum in the plurality of spectra comprising a signal including a signal strength as a function of time-of-flight, mass-to-charge ratio, or a value derived from time-of-flight or mass-to-charge ratio. Then, a signal cluster is formed by clustering signals from the plurality of spectra with time-of-flights, mass-to-charge ratios, or values derived from time-of-flights or mass-to-charge ratios that are within a window that is defined using an expected signal width value.

Abstract: Each embodiment includes a central sample reservoir and a plurality of satellite reservoirs. In a first embodiment, a first electrode in electrical contact with the central reservoir is charged and second electrodes in electrical contact with the satellite reservoirs are sequentially charged, thereby pI filtering molecules in the central reservoir into the satellite reservoirs. In a second embodiment, the central reservoir is configured to rotate so that molecules in a sample in the central reservoir are centrifugally pI-filtered into the satellite reservoirs. In a third embodiment, first and second electrodes proximate opposite first and second satellite reservoirs, respectively, are charged. Some molecules in a sample are pI filtered into the first and second satellite reservoirs. Third and fourth electrodes proximate opposite third and fourth satellite reservoirs, respectively, are then charged. Some molecules in a sample are pI filtered into the third and fourth satellite reservoirs.

Abstract: Laser desorption/ionization tandem mass spectrometer instruments that include immediate post source collisional cooling are presented, as are analytical methods that employ such instruments to achieve increased sensitivity and ion yield. Also presented are laser desorption/ionization mass spectrometry methods that improve sensitivity and relative ion yield by combining affinity capture probes with matrices having low melting point energy absorbing molecules combined with alkali metal scavengers.