Method for analyzing mass spectra

• US 20040059530A1
• Filed: 09/23/2003
• Published: 03/25/2004
• Est. Priority Date: 11/16/2000
• Status: Active Grant

• Current Assignee: Bio-Rad Laboratories Incorporated
• Original Assignee: Ciphergen Biosystems Incorporated
• Inventors: Fung, Eric T., Rich, William E., Gavin, Edward J., Braginsky, Leonid, Paulse, Chris D.
• Granted Patent: US 7,027,933 B2
• Time in Patent Office: Days
• US Class Current: 702/76
• CPC Class Codes: G16B 20/00 ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
• CPC Class Codes: G16B 40/00 ICT specially adapted for biostatistics; ICT specially adapted for bioinformatics-related machine learning or data mining, e.g. knowledge discovery or pattern finding
• CPC Class Codes: G16B 40/10 Signal processing, e.g. from mass spectrometry [MS] or from PCR
• CPC Class Codes: G16B 40/20 Supervised data analysis
• CPC Class Codes: H01J 49/0036 Step by step routines describing the handling of the data generated during a measurement

Abstract

A method that analyzes mass spectra using a digital computer is disclosed. The method includes entering into a digital computer a data set obtained from mass spectra from a plurality of samples. Each sample is, or is to be assigned to a class within a class set having two or more classes and each class is characterized by a different biological status. A classification model is then formed. The classification model discriminates between the classes in the class set.

Claims

23-1. The method of claim 23 wherein the class is characterized by a disease status.

35. A computer readable medium comprising:

a) code for entering data derived from mass spectra from a plurality of samples, wherein each sample is, or is to be assigned to a class within a class set of two or more classes, each class characterized by a different biological status, and wherein each mass spectrum comprises data representing signal strength as a function of time-of-flight, mass-to-charge ratio or a value derived from mass-to-charge ratio or time-of-flight; and

b) code for forming a classification model using a classification process, the classification process comprising a recursive partitioning process, wherein the classification model discriminates between the classes in the class set.

36. The computer readable medium of claim 35 wherein the classification process is a classification and regression tree process.

37. A system comprising:

a gas phase ion spectrometer;

a digital computer adapted to process data from the gas phase ion spectrometer; and

the computer readable medium of claim 35 in operative association with the digital computer.

38. The system of claim 37 wherein the gas phase ion spectrometer is adapted to perform a laser desorption ionization process.