Sequenom, Inc.

Sri International

Genetrace Systems, Inc.

Thermo Finnigan LLC

Ppd Biomarker Discovery Sciences, LLC

Althea Technologies, Inc.

Thomas Andrew Shaler

Christopher Hank Becker

Joseph Albert Monforte

Daniel J Pollart

Yuping Tan

Hua Lin

Pablo E Garcia

Mark David Steele

David E Cooper

Scott M Norton

Curtis A Hastings

Estevan Mendoza

Roger H Schmidt

James R Ladine

Sushmita Mimi Roy

Weixun Wang

Annalisa D'Andrea

Haihong Zhou

Praveen Kumar

Markus Anderle

Polly Chang

Travis Harrison

Dan Pollart

Christine Loehrlein

Kathy Stephens

Linda Wong

Robert Balog

Christina Swanson

Chia-Hui Paul Shieh

Various examples are directed to kits, apparatuses, and methods for determining a presence of(BP) in a biological sample. An example method includes causing a physical interaction between a biological sample from a subject and a set of first agents by exposing the biological sample to the set of first agents, the set of first agents being specific to one or more of a set of BP biomarkers associated with one or more proteins released from BP or associated with other molecules released from BP. The method further includes determining a presence of BP in the biological sample based on detected binding between one or more of the set of first agents and the one or more of the set of BP biomarkers.

Biomarkers for detection of burkholderia pseudomallei

Materials, systems and methods are provided for qualitative assessment of exposure of a person to ionizing radiation by measuring amounts of the biomarkers, wherein a change compared with corresponding un-irradiated control reference ranges of the biomarkers, provides the assessment, wherein the biomarkers include (i) alpha-1-Antichymotrypsin (ACT), (ii) Fms-related tyrosine kinase 3 ligand (Flt3L), and (iii) one or more additional proteins.

Biomarker panel for dose assessment of radiation injury and micro plasma filter

Releasable tag reagents for use in the detection and analysis of target molecules, particular in mass spectrometric analyzes are provided. Also provided are methods of detection that employ releasable tag reagents.

Releasable nonvolatile mass-label molecules

Releasable tag reagents for use in the detection and analysis of target molecules, particular in mass spectrometric analyses are provided. Also provided are methods of detection that employ releasable tag reagents.

Methods and reagents for obtaining simplified mixtures of peptides from a sample containing a number of peptides are disclosed. The simplified sample can be easier to analyze than the original peptide sample yet it is representative of all or nearly all of the proteins present in the mixed protein sample from which the original and more complex peptide sample was derived. 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 (R) that comprises a reagent that selectively interacts with selected proteins, either covalently or noncovalently. For example, Rcan 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.

Methods and kits useful for the simplification of complex peptide mixtures

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.

Mass spectrometric quantification of chemical mixture components

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&#x2032; 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.

Primers useful for sizing nucleic acids

Using nonvolatile, releasable, mass-labels, the present invention provides for the synthesis and use of mass-labeled compounds to specifically interact with biomolecular targets. Following binding of the mass-labeled compounds to the target molecule, the unique mass-label can be analyzed using mass spectrometry to identify and characterize the target molecule. In one embodiment of the invention, a mass-labeled oligonucleotide probe is used to identify a specific gene sequence. A myriad of mass-labeled compounds may be produced for use in a wide variety of interactions such as oligonucleotide-oligonucleotide hybridization, polynucleotide-polynucleotide interactions, enzyme-substrate or substrate analog/intermediate interactions, polypeptide-nucleic acid interactions, protein-ligand interactions, receptor-ligand interactions, polypeptide-metal interactions, nucleic acid-metal interactions or antigen-antibody interactions. Also contemplated are combinatorial processes for creating large libraries of compounds permitting rapid screening for a wide variety of targets.

Releasable nonvolatile mass label molecules

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.

Methods for analysis of gene expression

This invention relates to methods for screening nucleic acids for polymorphisms by analyzing amplified target nucleic acids using mass spectrometric techniques and to procedures for improving mass resolution and mass accuracy of these methods of detecting polymorphisms.

Methods of preparing nucleic acids for mass spectrometric analysis

This invention relates to methods for screening nucleic acids for mutations by analyzing nonrandomly fragmented nucleic acids using mass spectrometric techniques and to procedures for improving mass resolution and mass accuracy of these methods of detecting mutations.

Methods of screening nucleic acids using volatile salts in mass spectrometry

This invention relates to methods for screening nucleic acids for mutations by analyzing nonrandomly fragmented nucleic acids using mass spectrometric techniques and to procedures for improving mass resolution and mass accuracy of these methods of detecting

Methods of screening nucleic acids using mass spectrometry

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.

Oligonucleotide sizing using cleavable primers

The present invention provides modified oligonucleotide primers that (i) are designed for attachment to a solid support in a manner that does not block the ability to extend the primer from its 3' end, and (ii) incorporate a clearable moiety so that a 3' portion of the primer (linked to an extension product) can be released from an immobilized 5' portion. Upon selective cleavage of the cleavable site, a large portion of the primer fragment remains affixed to the solid support. This enables the release of primer extension products that contain about five or fewer base pairs of the primer sequence, to provide more useful sizing and sequence information per fragment than extension products containing the entire primer.

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Menlo Park, CA, United States of America

Thomas Andrew Shaler