Wilfred H Tang

US Patent:

7982180, Jul 19, 2011

Filed:

Jun 1, 2009

Appl. No.:

12/476141

Inventors:

Ignat V. Shilov - Palo Alto CA, US
Wilfred H. Tang - Albany CA, US

Assignee:

DH Technologies Development Pte. Ltd. - Singapore

International Classification:

B01D 59/44
H01J 49/00

US Classification:

250281, 250282, 2502521, 436173, 435 71

Abstract:

A background component of reporter ion signals is determined by fitting a distribution function. A plurality of samples that include a protein labeled with a plurality of isobaric reporter ions is analyzed at a plurality of different times using a mass spectrometer, producing a plurality of mass spectra for the plurality of isobaric reporter ions. A cumulative distribution is calculated for an inverse coefficient of differential expression of the plurality of mass spectra using a processor. A Pearson Type IV distribution shifted by a constant value is fitted to the cumulative distribution and the constant value is solved for using the processor. A background component for each spectrum of the plurality of mass spectra is calculated from the constant value, a calculated coefficient of differential expression for each spectrum, and an average reporter ion signal value for each spectrum using the processor.

US Patent:

20060030053, Feb 9, 2006

Filed:

Dec 20, 2004

Appl. No.:

11/019661

Inventors:

Sean Seymour - Berkeley CA, US
Alex Loboda - Belmont CA, US
Wilfred Tang - San Mateo CA, US

Assignee:

Applera Corporation - Foster City CA

International Classification:

G06F 19/00
G01N 33/00
G01N 33/48
G01N 33/50

US Classification:

436086000, 702019000

Abstract:

The present teachings provide methods and systems for the identification of proteins via peptide analysis. Some embodiments analyze proteins identified by analysis techniques such as mass spectrometry and build protein groups out of results. Groups can be formed by collecting like proteins and examining the group so as to identify if it is likely that only one form of a protein is present or, if there is enough evidence to support the presence of alternate forms. Various embodiments provide visual reports that can be interactive. These reports can allow a user to visualize relationships between proteins both intra- and inter-group. Methods are also introduced that can reduce the identification of false positives by taking into account a priori information.

US Patent:

20090053819, Feb 26, 2009

Filed:

Dec 26, 2007

Appl. No.:

11/964622

Inventors:

Sean L. Seymour - Berkeley CA, US
Alex Loboda - Belmont CA, US
Wilfred Tang - San Mateo CA, US

Assignee:

Applera Corporation - Foster City CA

International Classification:

G01N 33/68

US Classification:

436 86

Abstract:

The present teachings provide methods and systems for the identification of proteins via peptide analysis. Some embodiments analyze proteins identified by analysis techniques such as mass spectrometry and build protein groups out of results. Groups can be formed by collecting like proteins and examining the group so as to identify if it is likely that only one form of a protein is present or, if there is enough evidence to support the presence of alternate forms. Various embodiments provide visual reports that can be interactive. These reports can allow a user to visualize relationships between proteins both intra- and inter-group. Methods are also introduced that can reduce the identification of false positives by taking into account a priori information.

US Patent:

20090065686, Mar 12, 2009

Filed:

Sep 10, 2008

Appl. No.:

12/208277

Inventors:

Ignat V. Shilov - Palo Alto CA, US
Wilfred H. Tang - Albany CA, US

International Classification:

G01D 18/00
B01D 59/44

US Classification:

2502521, 250282

Abstract:

A corrected reporter ion intensity is calculated in tandem mass spectrometry based quantitation using isobaric labels. An analyte in each of two or more samples of a mixture of samples is labeled with a different isobaric label. The analyte is eluted from the mixture of samples and intensities of the eluting analyte are measured. An analyte intensity is selected at each of at least two times from the measured intensities. Tandem mass spectrometry is performed on the eluting analyte at each of the at least two times. A plurality of reporter ion intensities is produced. A system of linear equations is created expressing each reporter ion intensity of the plurality of reporter ion intensities as a sum of a background noise intensity and the product of a fragmentation efficiency and an analyte intensity. A corrected reporter ion intensity is calculated from a solution of the system of linear equations.