Feature list extraction from data sets such as spectra

• US 20030078739A1
• Filed: 10/04/2002
• Published: 04/24/2003
• Est. Priority Date: 10/05/2001
• Status: Abandoned Application

• Current Assignee: PPD Biomarker Discovery Sciences LLC (CellCarta Biosciences, Inc.)
• Original Assignee: Surromed Incorporated (Thermo Fisher Scientific Luxembourg I SARL)
• Inventors: Norton, Scott M., Heller, Jonathan, Hastings, Curtis A.
• Application Number:
  US10/265,302
• Publication Number:
  US 20030078739A1
• Time in Patent Office: Days
• US Class Current: 702/22
• CPC Class Codes: G06F 18/00 Pattern recognition
• CPC Class Codes: G06F 2218/08 Feature extraction

Abstract

A component list extraction method improves the quality of data extracted from a series of spectra, images, or other data sets, resulting in more accurate analysis and data mining. A series of spectra, such as mass spectra, are obtained and thresholded to distinguish peaks from noise. Conventionally, all data below the noise threshold are recorded as having zero intensity, which introduces an artificial discontinuity in the data. Instead, a composite peak list is constructed containing peaks occurring in at least a minimum number of spectra, and intensity values are recorded for corresponding peak locations in all spectra, even those having intensities below the noise threshold. The resulting intensities serve as inputs to a data mining or analysis method. The method can also be used as a peak detection method to determine components characterizing a sample type or patient population. The method is particularly useful for biological marker discovery and image processing.

Claims

1. A data processing method comprising:

obtaining a plurality of data sets;

applying a criterion to each data set to identify at least one feature in said data set;

retaining features present in at least an occurrence threshold number of said data sets; and

defining a location corresponding to each retained feature.

2. The method of claim 1, further comprising determining magnitudes of said retained features in at least one of said data sets.

3. The method of claim 1, wherein said criterion comprises an intensity threshold.

4. The method of claim 1, wherein said data sets comprise spectra and said features comprise peaks.

5. The method of claim 1, wherein said data sets comprises images.

6. The method of claim 5, wherein said images are images of electrophoresis gels and said features comprise spots.

7. A method for analyzing a set of spectra, comprising:

in each spectrum, identifying candidate peaks;

retaining candidate peaks present in at least an occurrence threshold number of said spectra; and

defining a spectral region corresponding to each retained peak.

8. The method of claim 7, wherein said spectra are mass spectra and said spectral region is defined by mass-to-charge ratios.

9. The method of claim 8, wherein said spectra are LC-MS spectra and said spectral region is further defined by chromatographic retention times.

10. The method of claim 7, wherein said set of spectra comprises replicate spectra associated with a particular chemical sample.

11. The method of claim 7, wherein said candidate peaks have intensity values exceeding a noise threshold.

12. The method of claim 11, wherein each of at least two different candidate peaks of a particular spectrum has an intensity value exceeding a different noise threshold.

13. The method of claim 7, further comprising determining intensity values in at least one spectrum corresponding to said spectral regions.

14. The method of claim 13, further comprising assembling said intensity values into a data matrix for input to a data mining algorithm.

15. The method of claim 14, further comprising determining the similarity among said spectra using said data mining algorithm.

16. The method of claim 13, further comprising determining additional intensity values corresponding to said identified peaks in an additional spectrum, wherein said additional spectrum is not in said set of spectra.

17. The method of claim 7, wherein said peaks are associated with a sample category.

18. The method of claim 17, wherein said sample category comprises a sample preparation method.

19. The method of claim 17, wherein said sample category comprises a sample type.

20. The method of claim 17, wherein said sample category comprises a subject population.

21. A program storage device accessible by a processor, tangibly embodying a program of instructions executable by said processor to perform method steps for a data processing method, said method steps comprising:

obtaining a plurality of data sets;

applying a criterion to each data set to identify at least one feature in said data set;

retaining features present in at least an occurrence threshold number of said data sets; and

defining a location corresponding to each retained feature.

22. The program storage device of claim 21, wherein said method steps further comprise determining magnitudes of said retained features in at least one of said data sets.

23. The program storage device of claim 21, wherein said criterion comprises an intensity threshold.

24. The program storage device of claim 21, wherein said data sets comprise spectra and said features comprise peaks.

25. The program storage device of claim 21, wherein said data sets comprises images.

26. The program storage device of claim 25, wherein said images are images of electrophoresis gels and said features comprise spots.