Methods and systems for analysis and correction of mass spectrometer data

1. A system for determining a background component of reporter ion signals, comprising:

a mass spectrometer that analyzes a plurality of samples that include a protein labeled with a plurality of isobaric reporter ions at a plurality of different times, producing a plurality of mass spectra for the plurality of isobaric reporter ions; and

a processor in communication with the mass spectrometer that

obtains the plurality of mass spectra from the mass spectrometer,

calculates a cumulative distribution for an inverse coefficient of differential expression of the plurality of mass spectra,

fits a Pearson Type IV distribution shifted by a constant value to the cumulative distribution and solves for the constant value, and

calculates a background component for each spectrum of the plurality of mass spectra from the constant value, a calculated coefficient of differential expression for the each spectrum, and an average reporter ion signal value for the each spectrum.

2. The system of claim 1 , wherein the plurality of mass spectra comprises at least four mass spectra.

3. The system of claim 1 , wherein the inverse coefficient of differential expression comprises an inverse of a standard deviation divided by a mean.

4. The system of claim 1 , wherein the Pearson Type IV distribution comprises an F-distribution.

5. The system of claim 1 , wherein the Pearson Type IV distribution comprises a Beta-prime distribution.

6. The system of claim 1 , wherein the processor fits a Pearson Type IV distribution shifted by a constant value using a nonlinearly fitting algorithm.

7. The system of claim 1 , wherein the processor further subtracts the background component from the each spectrum to determine a concentration ratio of the protein without background influence.

8. A method for determining a background component of reporter ion signals, comprising:

analyzing a plurality of samples that include a protein labeled with a plurality of isobaric reporter ions at a plurality of different times using a mass spectrometer, producing a plurality of mass spectra for the plurality of isobaric reporter ions;

obtaining the plurality of mass spectra from the mass spectrometer using a processor;

calculating a cumulative distribution for an inverse coefficient of differential expression of the plurality of mass spectra using the processor;

fitting a Pearson Type IV distribution shifted by a constant value to the cumulative distribution and solving for the constant value using the processor; and

calculating a background component for each spectrum of the plurality of mass spectra from the constant value, a calculated coefficient of differential expression for the each spectrum, and an average reporter ion signal value for the each spectrum using the processor.

9. The method of claim 8 , wherein the plurality of mass spectra comprises at least four mass spectra.

10. The method of claim 8 , wherein the inverse coefficient of differential expression comprises an inverse of a standard deviation divided by a mean.

11. The method of claim 8 , wherein the Pearson Type IV distribution comprises an F-distribution.

12. The method of claim 8 , wherein the Pearson Type IV distribution comprises a Beta-prime distribution.

13. The method of claim 8 , wherein fitting a Pearson Type IV distribution shifted by a constant value to the cumulative distribution comprises using a nonlinear fitting algorithm.

14. The method of claim 8 , further comprising subtracting the background component from the each spectrum to determine a concentration ratio of the protein without background influence.

15. A computer program product, comprising a tangible computer-readable storage medium whose contents include a program with instructions being executed on a processor so as to perform a method for determining a background component of reporter ion signals, the method comprising:

providing a system, wherein the system comprises distinct software modules, and wherein the distinct software modules comprise a measurement module, a distribution analysis module, and a background calculation module;

obtaining a plurality of mass spectra produced by analyzing a plurality of samples that include a protein labeled with a plurality of isobaric reporter ions at a plurality of different times using a mass spectrometer, wherein said obtaining is performed by the measurement module;

calculating a cumulative distribution for an inverse coefficient of differential expression of the plurality of mass spectra using the distribution analysis module;

fitting a Pearson Type IV distribution shifted by a constant value to the cumulative distribution and solving for the constant value using the distribution analysis module; and

calculating a background component for each spectrum of the plurality of mass spectra from the constant value, a calculated coefficient of differential expression for the each spectrum, and an average reporter ion signal value for the each spectrum using the background calculation module.

16. The method of claim 15 , wherein the plurality of mass spectra comprises at least four mass spectra.

17. The method of claim 15 , wherein the inverse coefficient of differential expression comprises an inverse of a standard deviation divided by a mean.

18. The method of claim 15 , wherein the Pearson Type IV distribution comprises an F-distribution.

19. The method of claim 15 , wherein the Pearson Type IV distribution comprises a Beta-prime distribution.

20. The method of claim 15 , wherein fitting a Pearson Type IV distribution shifted by a constant value to the cumulative distribution comprises using a nonlinear fitting algorithm.