Abstract: Pre-coated analysis substrates, and methods of making the substrates and using them to analyze animal tissue, are described. The pre-coated analysis substrates can be made by forming a matrix surface on an analysis substrate; adding a protease to the matrix surface to form a pre-coated analysis substrate; and placing an animal tissue specimen on the matrix surface. The animal tissue can then be analyzed by allowing the protease to partially digest the animal tissue specimen; and analyzing the partially digested animal tissue specimen by mass spectrometry.

Abstract: This disclosure relates to apparatus and methods for sublimation and deposition of chemicals. In particular aspects, this disclosure relates to apparatus and methods for patterned sublimation and deposition of chemicals for use in matrix assisted laser desorption ionization imaging mass spectrometry (MALDI IMS). In specific aspects, the apparatus comprises a vacuum chamber and a template comprising a planar surface containing the chemical to be sublimed, where the template is located within the vacuum chamber.

Abstract: The present disclosure provides for rapid identification of mechanism of action (MOA) for drugs and toxins, and does so in a rapid (30 days or less) fashion. The methods use a combination of high throughput bioinformatics and pathway analysis that examine a wide variety of biological parametics.

Abstract: The present disclosure provides for rapid identification of mechanism of action (MOA) for drugs and toxins, and does so in a rapid (30 days or less) fashion. The methods use a combination of high throughput bioinformatics and pathway analysis that examine a wide variety of biological parametics.

Abstract: Pre-coated analysis substrates, and methods of making the substrates and using them to analyze animal tissue, are described. The pre-coated analysis substrates can be made by forming a matrix surface on an analysis substrate; adding a protease to the matrix surface to form a pre-coated analysis substrate; and placing an animal tissue specimen on the matrix surface. The animal tissue can then be analyzed by allowing the protease to partially digest the animal tissue specimen; and analyzing the partially digested animal tissue specimen by mass spectrometry.

Abstract: Systems and methods are provided for generating a model relating parameters generated via a first molecular imaging modality to parameters generated via a second molecular imaging modality. First and second feature extractors extract, from images of a region of interest obtained via respective first and second molecular imaging modalities, respective sets of parameters for respective first and second sets of locations. A mapping component associates respective locations of the first and second sets of locations according to their spatial relationship within the region of interest to produce a training set. Each example in the training set comprises a set of parameters associated with a location in the first set of locations and a set of parameters associated with a location in the second set. A modeling component generates a predictive model relating the parameters associated with the first modality with at least one parameter associated with the second modality.

Abstract: Systems and methods are provided for generating a model relating parameters generated via a first molecular imaging modality to parameters generated via a second molecular imaging modality. First and second feature extractors extract, from images of a region of interest obtained via respective first and second molecular imaging modalities, respective sets of parameters for respective first and second sets of locations. A mapping component associates respective locations of the first and second sets of locations according to their spatial relationship within the region of interest to produce a training set. Each example in the training set comprises a set of parameters associated with a location in the first set of locations and a set of parameters associated with a location in the second set. A modeling component generates a predictive model relating the parameters associated with the first modality with at least one parameter associated with the second modality.

Abstract: A method for analyzing the polypeptide content of animal tissue is described. The method includes the steps of (a) providing an animal tissue specimen; (b) depositing one or more portions of a hydrogel mixture including a protease on spatially discrete portions of the animal tissue specimen; (c) allowing sufficient time to pass for animal tissue under the hydrogel mixture to be form a digested mixture of animal tissue and hydrogel mixture; (d) removing the digested mixture from the animal tissue and extracting the polypeptides from the digested mixture to provide an extract; and (e) analyzing the polypeptide content of the extract by mass spectrometry.

Abstract: The present invention provides for a mass spectrometry proteomic approach to distinguishing Spitz nevi from Spitzoid malignant melanoma. Histology directed mass spectral profiling allows for targeted analysis of sites of melanocytic lesion within formalin-fixed, paraffin embedded excisional biopsies. The classification system identified 5 peptide peaks, of which two have been identified as originating from vimentin and actin. A sensitivity and specificity for Spitz nevi of 97% and 90%, respectively, were achieved.

Abstract: Methods and apparatuses for analyzing proteins and other biological materials and xenobiotics within a sample. A specimen is generated, which may include an energy absorbent matrix. The specimen is struck with laser beams such that the specimen releases proteins. The atomic mass of the released proteins over a range of atomic masses is measured. An atomic mass window of interest within the range of atomic masses is analyzed to determine the spatial arrangement of specific proteins within the sample, and those specific proteins are identified as a function of the spatial arrangement. By analyzing the proteins, one may monitor and classify disease within a sample.

Abstract: The present invention provides for the simultaneous assessment of a plurality of tissue regions or microregions, the benefit being homogeneity of the sampling, both in terms of tissue content and timing. Discrete regions of a tissue sample, such as those demarcated by microwells formed within the tissue itself or tissue plugs removed from the tissue in a spatially referenced fashion, can be treated with one or more physical or chemical treatments to liberate target molecules of interest. Subsequent analysis of said target molecules by, e.g., mass spectroscopy, permits identification of a variety of biological parameters, including those associated with disease or therapy.

Abstract: Sample preparation can be a tedious and time consuming task. For example, MALDI imaging of tissue samples can require the tedious process of hand or robotically spotting solutions containing chemical species referred to as “matrix” onto a tissue sample prior its mass spectral analysis. Provided is a process for preparing a sample comprising immersing a solid support that has a surface comprising a first part that is more hydrophilic than a second part into a target compound solution, wherein the target compound is deposited primarily onto the more hydrophilic part; and/or applying and evaporating the target compound solution onto the substrate to produce the pre-coated substrate. A tissue or other sample may then be placed on the substrate for analysis.

Abstract: The present invention provides for the simultaneous assessment of a plurality of tissue regions or microregions, the benefit being homogeneity of the sampling, both in terms of tissue content and timing. Discrete regions of a tissue sample, such as those demarcated by microwells formed within the tissue itself or tissue plugs removed from the tissue in a spatially referenced fashion, can be treated with one or more physical or chemical treatments to liberate target molecules of interest. Subsequent analysis of said target molecules by, e.g., mass spectroscopy, permits identification of a variety of biological parameters, including those associated with disease or therapy.

Abstract: The present invention provides for a proteomic approach to grading gliomas, and for predicting patient survival. In addition to employing global protein expression patterns, such as by mass spectrometry, particular target proteins whose expression is altered in various gliomas can be used to predict the stage/classification of a glioma, as well as to indicate whether a given patient will be a short- or long-term survivor.

Abstract: The present invention provides for the simultaneous assessment of a plurality of tissue regions or microregions, the benefit being homogeneity of the sampling, both in terms of tissue content and timing. Discrete regions of a tissue sample, such as those demarcated by microwells formed within the tissue itself or tissue plugs removed from the tissue in a spatially referenced fashion, can be treated with one or more physical or chemical treatments to liberate target molecules of interest. Subsequent analysis of said target molecules by, e.g., mass spectroscopy, permits identification of a variety of biological parameters, including those associated with disease or therapy.

Abstract: The present invention provides for a proteomic approach to grading gliomas, and for predicting patient survival. In addition to employing global protein expression patterns, such as by mass spectrometry, particular target proteins whose expression is altered in various gliomas can be used to predict the stage/classification of a glioma, as well as to indicate whether a given patient will be a short- or long-term survivor.

Abstract: The present invention provides for devices and methods of sampling and analyzing body fluid analytes, including proteins, nucleic acids, drugs, carbohydrates and lipids. Body fluids include blood, serum, sputum, saliva, urine, cerebrospinal fluid, and ascites.

Abstract: A method of modifying protein samples that comprises combining the sample with a peroxycarbonate solution and inserting the sample into a mass spectrometer. The present invention also includes methods of N-terminus characterization.

Abstract: The present invention provides for a proteomic approach to grading gliomas, and for predicting patient survival. In addition to employing global protein expression patterns, such as by mass spectrometry, particular target proteins whose expression is altered in various gliomas can be used to predict the stage/classificiation of a glioma, as well as to indicate whether a given patient will be a short- or long-term survivor.

Abstract: The present invention provides a method for analyzing tissue from the surgical margin of resected tumor, and the use of such information to predict recurrence, survival, and treatment efficacy in cancer patients. Methods of treatment based thereon are provided.