Abstract: Embodiments in accordance with the present disclosure are directed to polymer beads and uses thereof, including forming libraries of compounds for screening and assay purposes. An example method includes using logic circuitry to: select a plurality of molecules that include a plurality of subgroups, each of the plurality of molecules exhibiting a mass spectrometry characteristic that is distinguishable from mass spectrometry characteristics of other molecules of the plurality, and assign the plurality of molecules with a position in a sequence of a plurality of synthetic compounds forming a library. The method further includes defining, as data in a memory circuit of the logic circuitry, the plurality of synthetic compounds that are sequenceable via mass spectrometry using the assigned positions of the plurality of molecules for communicating to other circuitry for formation thereof via coupling chemistry or screening of a particular function.

Abstract: An example binding assay includes a plurality of sub-regions, a plurality of synthetic compounds on beads, wherein each of the plurality of sub-regions includes one of the plurality of synthetic compounds, a biological target labeled with a first detectable label in each of the plurality sub-regions, and a biological counter target labeled with a second detectable label in each of the plurality of sub-regions. The biological counter target is configured to bind to the biological target when the biological target is in a first orientation. And, wherein a first subset of the plurality of synthetic compounds bind to the biological target and effect interactions between the biological target and the biological counter target.

Abstract: Embodiments in accordance with the present disclosure are directed to polymer beads and uses thereof, including forming libraries of compounds for screening and assay purposes. An example method includes using logic circuitry to: select a plurality of molecules that include a plurality of subgroups, each of the plurality of molecules exhibiting a mass spectrometry characteristic that is distinguishable from mass spectrometry characteristics of other molecules of the plurality, and assign the plurality of molecules with a position in a sequence of a plurality of synthetic compounds forming a library. The method further includes defining, as data in a memory circuit of the logic circuitry, the plurality of synthetic compounds that are sequenceable via mass spectrometry using the assigned positions of the plurality of molecules for communicating to other circuitry for formation thereof via coupling chemistry or screening of a particular function.

Abstract: This invention provides methods, compositions and kits for gene expression analysis and gene expression profiling. The methods of the invention are highly sensitive; have a wide dynamic range; are rapid and inexpensive; have a high throughput; and allow the simultaneous differential analysis of a defined set of genes. The methods, compositions and kits of the invention also provide tools for gene expression data collection and relational data analysis.

Abstract: This invention provides methods, compositions and kits for gene expression analysis and gene expression profiling. The methods of the invention are highly sensitive; have a wide dynamic range; are rapid and inexpensive; have a high throughput; and allow the simultaneous differential analysis of a defined set of genes. The methods, compositions and kits of the invention also provide tools for gene expression data collection and relational data analysis.

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

Abstract: Methods and reagents for obtaining simplified mixtures of peptides from a sample containing a number of peptides are disclosed. The methods entail the use of tagging moieties that include an amino-acid-specific reactive group (R). The tagging moieties “tag” peptides or proteins at specific amino acids (e.g., by reacting with an amino acid to form a covalent bond), ultimately allowing the isolation of peptides that contain those specific amino acids. Other methods entail the used of a reactive moiety (RP) that comprises a reagent that selectively interacts with selected proteins, either covalently or noncovalently. For example, RP can be a natural ligand for a receptor that is to be tagged or a protein that interacts with a second protein that is to be tagged. It can be an enzymatic substrate or other element of molecular recognition such as an antibody, ATP, GTP, NAD, NADP, NADH, NADPH, ubiquitin, or structural analogs thereof.

Abstract: Methods and apparatus, including computer program products, for quantifying peptides in a peptide mixture. A peptide mixture containing a plurality of peptides is received. One or more peptides are separated from the peptide mixture over a period of time. One or more of the peptides separated at a particular time are subjected to mass-to-charge analysis and an abundance of one or more of the mass analyzed peptides is calculated. A relative quantity for the one or more mass analyzed peptides is calculated by comparing the calculated abundance of the peptides with an abundance of one or more peptides in a reference sample that is external to the first peptide mixture. The techniques can be applied to arbitrary peptides, without requiring the use of differential mass labeling, and can be applied to other biological molecules, such as nucleic acids and small molecules.

Abstract: The present invention provides modified oligonucleotide primers designed to incorporate a cleavable moiety so that a 3? portion of the primer (linked to an extension product) can be released from an upstream 5? portion of the primer. Upon selective cleavage of the cleavable site, primer extension products that contain about five or fewer base pairs of the primer sequence are released, to provide more useful sizing and sequence information per fragment than extension products containing the entire primer.

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: This invention provides methods, compositions and kits for gene expression analysis and gene expression profiling. The methods of the invention are highly sensitive; have a wide dynamic range; are rapid and inexpensive; have a high throughput; and allow the simultaneous differential analysis of a defined set of genes. The methods, compositions and kits of the invention also provide tools for gene expression data collection and relational data analysis.

Abstract: This invention provides methods, compositions and kits for gene expression analysis and gene expression profiling. The methods of the invention are highly sensitive; have a wide dynamic range; are rapid and inexpensive; have a high throughput; and allow the simultaneous differential analysis of a defined set of genes. The methods, compositions and kits of the invention also provide tools for gene expression data collection and relational data analysis.

Abstract: This invention provides methods, compositions and kits for gene expression analysis and gene expression profiling. The methods of the invention are highly sensitive; have a wide dynamic range; are rapid and inexpensive; have a high throughput; and allow the simultaneous differential analysis of a defined set of genes. The methods, compositions and kits of the invention also provide tools for gene expression data collection and relational data analysis.