David R Goodlett

Author:

David Eugene Goodlett

ISBN #:

0773453989

US Patent:

6829539, Dec 7, 2004

Filed:

Apr 13, 2001

Appl. No.:

09/835072

Inventors:

David R. Goodlett - Seattle WA
Andrew Keller - Seattle WA

Assignee:

The Institute For Systems Biology - Seattle WA

International Classification:

G01N 3348

US Classification:

702 20, 435 6

Abstract:

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 ; (b) creating a node corresponding to a paired signal having masses of about m and about m+n , 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.

US Patent:

8415619, Apr 9, 2013

Filed:

Nov 15, 2011

Appl. No.:

13/296793

Inventors:

David R. Goodlett - Seattle WA, US
Scott R. Heron - East Kilbride, GB
Jonathan Cooper - Glasgow, GB

Assignee:

University of Glascgow - Glasgow

International Classification:

H01J 49/26
G01N 23/00

US Classification:

250288, 250281, 250282, 4351731, 4351736, 435461

Abstract:

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.

US Patent:

20020115056, Aug 22, 2002

Filed:

Dec 26, 2000

Appl. No.:

09/748783

Inventors:

David Goodlett - Seattle WA, US

International Classification:

C12Q001/00
G06F019/00
G01N033/48
G01N033/00

US Classification:

435/004000, 436/086000, 702/019000

Abstract:

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.

US Patent:

20020119490, Aug 29, 2002

Filed:

Dec 26, 2000

Appl. No.:

09/748793

Inventors:

Ruedi Aebersold - Mercer Island WA, US
David Goodlett - Seattle WA, US

International Classification:

G01N033/53
G06F019/00
G01N033/48
G01N033/50

US Classification:

435/007100, 702/019000, 436/086000

Abstract:

The invention provides methods for identifying a polypeptide. The method can include determining two or more characteristics associated with the polypeptide, or a fragment thereof, one of the characteristics being mass of a fragment of the polypeptide, the fragment mass being determined by mass spectrometry; comparing the characteristics associated with the polypeptide to an annotated polypeptide index; and identifying one or more polypeptides in the annotated polypeptide index having the characteristics. The method can further include the steps of determining one or more additional characteristics associated with the polypeptide; comparing the determined characteristics to the annotated polypeptide index; optionally repeating the steps one or more times, wherein a set of characteristics is determined that identifies a single polypeptide in the annotated polypeptide index, and optionally quantitating the amount of identified polypeptide in a sample containing the polypeptide. The invention also provides methods for generating a polypeptide identification index.

US Patent:

20060008851, Jan 12, 2006

Filed:

Sep 9, 2005

Appl. No.:

11/223269

Inventors:

Rudolf Aebersold - Mercer Island WA, US
David Goodlett - Seattle WA, US

Assignee:

Institute for Systems Biology - Seattle WA
University of Washington - Seattle WA

International Classification:

G01N 33/53

US Classification:

435007100

Abstract:

The invention provides methods for identifying a polypeptide. The method can include determining two or more characteristics associated with the polypeptide, or a fragment thereof, one of the characteristics being mass of a fragment of the polypeptide, the fragment mass being determined by mass spectrometry; comparing the characteristics associated with the polypeptide to an annotated polypeptide index; and identifying one or more polypeptides in the annotated polypeptide index having the characteristics. The method can further include the steps of determining one or more additional characteristics associated with the polypeptide; comparing the determined characteristics to the annotated polypeptide index; optionally repeating the steps one or more times, wherein a set of characteristics is determined that identifies a single polypeptide in the annotated polypeptide index, and optionally quantitating the amount of identified polypeptide in a sample containing the polypeptide. The invention also provides methods for generating a polypeptide identification index.

US Patent:

20060009915, Jan 12, 2006

Filed:

Sep 12, 2005

Appl. No.:

11/225265

Inventors:

David Goodlett - Seattle WA, US

Assignee:

Institute of Systems Biology - Seattle WA

International Classification:

G06F 19/00
G01N 33/00

US Classification:

702019000, 436086000

Abstract:

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.

US Patent:

20060020393, Jan 26, 2006

Filed:

Dec 2, 2004

Appl. No.:

11/004570

Inventors:

David Goodlett - Seattle WA, US
Andrew Keller - Seattle WA, US

Assignee:

The Institute for Systems Biology - Seattle WA

International Classification:

G01N 33/53

US Classification:

702019000, 436086000

Abstract:

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 δ; (b) creating a node corresponding to a paired signal having masses of about m and about m+nδ, 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.

US Patent:

20120197535, Aug 2, 2012

Filed:

Jan 3, 2012

Appl. No.:

13/342694

Inventors:

David R. Goodlett - Seattle WA, US
Robert K. Ernst - Silver Spring MD, US
Ying Sonia Ting - Seattle WA, US
Yu Chieh Philip Kao - Seattle WA, US

International Classification:

G06F 19/00
H01J 49/26

US Classification:

702 19

Abstract:

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