Target Discovery, Inc.

Sri International

Orasure Technologies, Inc.

Stc Technologies Inc.

Luke V Schneider

Michael P Hall

James G Kane

Norman A Peppers

Mark J Dyer

David A Zarling

Steve Y Ng

Gregory W Faris

Michel J Rossi

Robert Petesch

Jeffrey N Peterson

Keith W Kardos

R Sam Niedbala

David E Cooper

Jarrett Lee Burton

Angel Sanjurjo

Kai-Hung Lau

Naixiong Jiang

David M Lowe

Marie Johansson

Liqiang Jiang

Robert T Rewick

Naheed Mufti

Victor Wong

Anastasia Canizales

Methods and apparatuses for deriving the sequence of an oligomer. In one exemplary method for deriving the sequence of a polypeptide, a predetermined set of mass/charge values for amino acid sequences is stored. An abundance value from mass spectrum data for each mass/charge value in the predetermined set is determined to produce a plurality of abundance values. A first ranking, based on the plurality of abundance values, is calculated for each sequence of a set of amino acid sequences having a first number of amino acids. A second ranking, based on the plurality of abundance values, for each sequence of a set of amino acid sequences having a second number of amino acids is calculated. A cumulative ranking, based on the first ranking and the second ranking, is calculated for each sequence of a set of amino acid sequences having at least the second number of amino acids.

Methods for deriving a cumulative ranking

The present invention provides methods and apparatus for purifying metabolites of interest and conducting metabolic analyses. The methods generally involve determining metabolic flux values for a plurality of target analytes by monitoring the relative isotope abundance of a stable isotope in a substrate labeled with the stable isotope and/or one or more target metabolites formed through metabolism of the labeled substrate. Certain methods utilize multiple electrophoretic methods to separate the target analytes from other components within the sample being analyzed. The methods can be used in a variety of applications including screens to identify metabolites that are correlated with certain diseases and diagnostic screens for identifying individuals having, or susceptible to, a disease.

Methods for conducting metabolic analyses

A mass spectrometry ionization method in which electrospray droplets or solid sample matrices are exposed to an ion beam thereby increasing the unbalanced charge of the analyte is provided. In another embodiment, a mass spectrometry ionization method in which ionization of the sample is achieved by directing an ion beam at a liquid or solid sample matrix containing analyte thereby ionizing and adding unbalanced charge to the analyte is provided.

Increasing ionization efficiency in mass spectroscopy

Method for increasing ionization efficiency in mass spectroscopy

Mass tagging methods are provided that lead to mass spectrometer detection sensitivities and molecular discriminations that are improved over other methods. In particular the methods are useful for discriminating tagged molecules and fragments of molecules from chemical noise in the mass spectrum. These mass tagging methods are useful for oligomer sequencing, determining the relative abundances of molecules from different samples, and identifying individual molecules or chemical processing steps in combinatorial chemical libraries. The methods provided are useful for the simultaneous analysis of multiple molecules and reaction mixtures by mass spectrometric methods.

Mass defect labeling for the determination of oligomer sequences

The invention provides methods, compositions, apparatus, and a computer data retrieval system for conducting proteomics.

Polypeptide fingerprinting methods

The present method provides methods and apparatus for separating proteins using a series of electrophoretic methods that utilize controlled fractionation and labeling techniques to resolve mixtures of proteins. The samples for each electrophoretic method other than the initial method, contain only a subset of proteins resolved in the preceding method. The methods can be used in a variety of different applications including, creating proteomic databases, comparative expression studies, diagnostics, structure activity relationships and metabolic engineering investigations.

Protein separation via multidimensional electrophoresis

The present invention provides a method for protein sequencing using mass spectrometry. Also provided are protein labeling agents and labeled proteins for use in conjunction with the present method.

Methods for sequencing proteins

Polypeptide fingerprinting methods and bioinformatics database system

Growing community of inventors

Half Moon Bay, CA, United States of America

Luke V Schneider