University of Washington

University System of Maryland

Turun Yliopisto

Other

University of Glasgow

Institute for Systems Biology

The Institute of Systems Biology

Micromass UK Limited

David R Goodlett

Richard Dale Smith

James Ian Langridge

Robert K Ernst

Riitta Lahesmaa

Robert Moulder

Santosh Bhosale

Scott R Heron

Harri Lähdesmäki

Olli Simell

Jonathan Cooper

Beate Rist

James E Bruce

Ruedi Aebersold

Andrew Keller

Ying Sonia Ting

Yu Chieh “Philip” Kao

Jon Cooper

Chris Hughes

Rudolf H Aebersold

The present invention relates to methods for predicting a risk of a subject for Type 1 diabetes (T1D) on the basis of expression levels of protein markers in a sample obtained from the subject. The present invention also relates to in vitro kits for use in said methods.

Means and methods for determining risk of type-1 diabetes by serum protein biomarkers

Methods for identifying fungal species by analysis of fungal membrane lipids, such as glycerophospholipids, sphingolipids and sterols, using mass spectrometry ionization patterns are disclosed.

Methods for identifying fungi

The present invention provides methods for identifying bacteria by analysis of lipid A and/or lipoteichoic acid structure and/or mass spectrometry ionization patterns.

Methods for identifying bacteria

The invention provides methods for identifying polypeptides. The method can include the steps of simultaneously determining the mass of a subset of parent polypeptides from a population of polypeptides and the mass of fragments of the subset of parent polypeptides; comparing the determined masses to an annotated polypeptide index; and identifying one or more polypeptides of the annotated polypeptide index having the determined masses. The method can further include the steps of determining one or more additional characteristics associated with one or more of the parent polypeptides; comparing the determined characteristics to the annotated polypeptide index; and optionally repeating the steps one or more times, wherein a set of characteristics is determined that identifies a parent polypeptide as a single polypeptide in the annotated polypeptide index. The method can additionally include the step of quantitating the amount of the identified polypeptide in a sample containing the polypeptide.

Method of mass spectrometry for identifying polypeptides

The present invention relates generally to mass spectrometry. The present invention relates more particularly to methods and systems for use in mass spectrometric identification of a variety of analytes, including high molecular weight species such as proteins. One embodiment of the invention is a method for analyzing an analyte. The method includes nebulizing a suspension of the analyte in a solvent with a surface acoustic wave transducer; and performing mass spectrometry on the nebulized suspension. The surface acoustic wave transducer can be used, for example, to transfer non-volatile peptides and proteins (as well as other analyztes, such as oligonucleotides and polymers) to the gas phase at atmospheric pressure. Nebulization using surface acoustic waves can be conducted in a discontinuous or pulsed mode, similar to that used in MALDI, or in a continuous mode, as in ESI.

Methods and systems for mass spectrometry

The invention provides a method of determining an amino acid sequence of a parent polypeptide. The method consists of: (a) obtaining mass spectra of two or more differentially labeled polypeptide fragments of a parent polypeptide; (b) assigning a mass and a weighting characteristic to two or more paired signals having a difference in mass corresponding to an integer value of said differential label, the weighting characteristic combining properties of each signal within said paired signals; (c) selecting from the mass spectra a paired signal having the assigned mass and a weighting characteristic distinguishable from non-peptide signals, the assigned mass indicating the mass of a polypeptide fragment within the spectra; (d) determining the difference in mass of the polypeptide fragments; (e) assigning the mass differences a satisfying amino acid name, and (f) orienting the assigned amino acid names. Also provided is a method of determining the amino acid sequence of a polypeptide. The method consists of: (a) constructing a graph from mass spectra of two or more differentially labeled polypeptides, the graph comprising a node with mass m, number of labels n, intensity i, and mass differential of labels &dgr;; (b) creating a node corresponding to a paired signal having masses of about m and about m&plus;n&dgr;, and (c) adding a labeled weighted directed edge to the graph between any two nodes corresponding to a mass of an amino acid, the labeled weighted directed edge combining properties of the paired signals.

Methods for quantification and de novo polypeptide sequencing by mass spectrometry

The present invention provides methods and reagents for identifying specific masses of compounds in a complex mixture. In particular, the present invention describes an isotope distribution encoded tag (IDEnT) concept wherein the ability to distinguish an analyte encoded with a non-native isotope from those not encoded with the isotope or from those encoded with a different isotope is used for protein identification, enzyme active site identification, peptide sequencing, and the like. Reagents used in the IDEnT strategy consist of a chemical element with a unique isotope distribution not normally found in the analyte class being studied, chemically bonded to, or an integral part of a chemical reagent with a high selectivity of affinity for specific functional group in the analyte.

Isotope distribution encoded tags for protein identification

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Seattle, WA, United States of America

David R Goodlett