Abstract: Nonlinear retention time variations in chromatography-mass spectrometry data sets are adjusted by time-alignment methods, enabling automated comparison of spectra for differential phenotyping and other applications.

Abstract: The amount of platelet surface proteins in a sample may be measured by collecting a sample containing platelets into a collection tube containing a platelet stabilizing composition, labeling the platelet surface protein and detecting by cytometry.

Abstract: The present invention provides an improved integrated system for biological marker identification. The system uses Microvolume Laser Scanning Microscopy (MLSC) in order to measure patterns of expression of biological markers in biological fluids. The system includes improved instrumentation for performing MLSC, and also includes improved particle detection and analysis methods. The system further comprises an informatics architecture for the analysis of data obtained from the MLSC in tandem with other medical information.

Abstract: Compositions, methods and kits useful for the diagnosis, prognosis, and treatment of renal cell cancer are provided.

Abstract: High-intensity, spiked noise is reduced in chromatography-mass spectrometry data by applying a nonlinear filter such as a moving median filter to the data. The filter is applied to individual mass chromatograms, plots of ion abundance versus retention time for each detected mass-to-charge ratio, and the filtered chromatograms are combined to form a filtered total ion current chromatogram. Standard linear filters are not effective for reducing noise in liquid chromatography-mass spectrometry (LC-MS) data because they assume a normal distribution of noise. LC-MS noise, however, is not normally distributed.

Abstract: A system for laser scanning provides spectral flexibility needed for the spectroscopic monitoring of highly multiplexed samples, such as cellular and particle assays in whole blood or other suspensions. In accordance with embodiments of the present invention, the system comprises a scanner to direct an excitation laser through a sample, an objective to collect light emitted by the sample in response to the excitation laser, a spectrograph to disperse the emitted light over a plurality of wavelengths as a spectrum, and a charge coupled device for detecting the spectrum. The system can be used with samples having a variety of reporter tags, including one or more SERS tags, fluorescent organic and protein tags, and quantum dot tags. A laser scanning apparatus and method of using the same is also provided.

Abstract: An automatic peak selection method for multidimensional data that selects peaks from very noisy data such as two-dimensional liquid chromatography-mass spectrometry (LC-MS) data is described. Such data are characterized by non-normally distributed noise that varies in different dimensions. The method computes local noise thresholds for each one-dimensional component of the data. Each point has a local noise threshold applied to it for each dimension of the data set, and a point is selected as a candidate peak only if its value exceeds all of the applied local noise thresholds. Contiguous candidate peaks are clustered into actual peaks. The method is preferably implemented as part of a high-throughput platform for analyzing complex biological mixtures.

Abstract: A biological marker identification method identifies biological markers within broad sets of biological data containing many more measurements than observations. For example, the data can contain thousands of measurements on each blood sample obtained from fewer than 100 subjects, each of which falls into one of a set of clinical classes or is associated with a value of a continuous clinical response variable. At least one biomarker, containing a small subset of measurements, is found that is capable of predicting a clinical endpoint. The biomarker can be used for, e.g., diagnosing disease or assessing response to a drug. First, the set of measurements is reduced to a smaller set of candidate measurements by eliminating measurements that either cannot distinguish among classes or are redundant. Biomarker subsets are then selected from the remaining set of measurements, either by an exhaustive search or a heuristic method that finds good but not necessary globally optimal biomarkers.

Abstract: Relative quantitative information about components of chemical or biological samples can be obtained from mass spectra by normalizing the spectra to yield peak intensity values that accurately reflect concentrations of the responsible species. A normalization factor is computed from peak intensities of those inherent components whose concentration remains constant across a series of samples. Relative concentrations of a component occurring in different samples can be estimated from the normalized peak intensities. Unlike conventional methods, internal standards or additional reagents are not required. The methods are particularly useful for differential phenotyping in proteomics and metabolomics research, in which molecules varying in concentration across samples are identified. These identified species may serve as biological markers for disease or response to therapy.

Abstract: Nonlinear retention time variations in chromatography-mass spectrometry data sets are adjusted by time-alignment methods, enabling automated comparison of spectra for differential phenotyping and other applications.

Abstract: Nonlinear retention time variations in chromatography-mass spectrometry data sets are adjusted by time-alignment methods, enabling automated comparison of spectra for differential phenotyping and other applications.

Abstract: Methods and instrumentation for performing charge coupled device (CCD)-based confocal spectroscopy with a laser spot array are provided. The methods and instruments of the invention are useful in any spectroscopic application, including, but not limited to, microscopy and microvolume laser scanning cytometry (MLSC).

Abstract: The invention provides methods of isolating and identifying biological markers of diabetes and metabolic syndrome and complications of these disease states. The biomarkers are useful in the evaluation, diagnosis and monitoring of these diseases.

Abstract: Disclosed are biomarkers, the expression of which is differentially regulated in subjects with multiple sclerosis (MS) as compared to subjects that do not have MS. Also described are methods of identification of such biomarkers, and methods of using such biomarkers as targets for the development and identification of therapeutic compounds and strategies for the treatment of MS, as well as methods and kits for the diagnosis of MS.

Abstract: A disposable cuvette cartridge for optical measurements is formed from three flexible thin layers. The middle layer is an adhesive sheet with cut out regions, typically between 30 and 50, serving as optical chambers bounded by the two outer layers. Inlet and vent holes in one of the outer sheets provide access to the optical chambers. At least one of the outer sheets is made of a material having low fluorescence, such as a cyclo-olefin copolymer. With its low background fluorescence, the cuvette cartridge is useful for high-throughput fluorescence measurements of biological samples.