Aspects of mass spectral calibration

1. A method for calibrating and analyzing data from a mass spectrometer, comprising the steps of:

a. acquiring raw profile mode data containing mass spectral responses of ions with or without isotopes;

b. calculating theoretical isotope distributions for each of at least one calibration ion based on elemental composition;

c. convoluting the theoretical isotope distributions with an initial peak shape function to obtain theoretical isotope profiles for each ion;

d. constructing a peak component matrix including the theoretical isotope profiles for calibration ions as peak components;

e. performing a regression analysis between the raw profile mode mass spectral data and the peak component matrix; and

f. reporting the regression coefficients as the relative concentrations for each of the components.

2. The method of claim 1 , further comprising:

g. using the relative concentrations as combination coefficients, to provide a linear combination of all calculated isotope distributions of step b.

3. The method of claim 2 , further comprising:

h. calculating at least one of a peak shape function and a calibration filter through convolution and deconvolution between the results of step a. and step g.

4. The method of claim 3 , further comprising:

i. when a calibration filter is calculated, applying the calibration filter to raw data from step a.; and

j. performing the convolution of step c. using a target peak shape function specified for calculation of the calibration filter in place of initial peak shape function.

5. The method of claim 4 , further comprising:

iteratively repeating steps d. through j. until the relative concentrations or calibration filter or both converge.

6. The method of claim 5 , where the process is iterative and includes calculating theoretical isotope profiles based on one of initial estimated peak shape functions and refined peak shape functions.

7. The method of claim 3 , wherein:

k. the convolution of step c. is performed using the peak shape function.

8. The method of claim 7 , further comprising:

iteratively repeating steps d. through h. and k. until the relative concentrations or calibration filter or both converge.

9. The method of claim 1 , wherein baseline components are included in the regression analysis.

10. The method of claim 9 , wherein baseline components are represented as linear or nonlinear functions.

11. The method of claim 1 , where the regression is a multiple linear regression.

12. The method of claim 11 , where the multiple linear regression is performed with weights for each mass spectral point.

13. The method of claim 11 , where the multiple linear regression is performed with mass spectral centroids after peak analysis on both the profile mode mass spectral data and theoretical isotope profiles.

14. The method of claim 1 , where the process is iterative and starts with initial estimated peak shape functions.

15. The method of claim 1 , where the process becomes a single pass process when the relative contributions of overlapped ions are known or given.

16. The method of claim 1 , where one of actual peak shape function and calibration filter is obtained by using a deconvolution operation involving actual measured mass spectral profile mode data and a linear combination of theoretically calculated isotope distributions.

17. A method for calibrating a mass spectrometer, comprising:

generating fragment ions of known elemental compositions within the mass spectrometer;

acquiring profile mode mass spectral data of the fragment ions;

calculating theoretical isotope distribution for each of the fragment ions; and

calculating mass spectral calibration filters through at least one of convolution and deconvolution involving the acquired profile mode mass spectral data and theoretical isotope distributions for said ions.

18. A method to avoid mass spectral nonlinearity in one of mass spectral calibration and mass spectral data analysis, comprising:

acquiring mass spectral data in profile mode in a mass spectral range;

measuring one of ion counts or relative abundances for isotope clusters within said mass spectral range and comparing to a nonlinearity threshold;

excluding all the mass spectral sub-regions with nonlinearity from later mass spectral calibration and mass spectral data analysis;

excluding corresponding isotopes from the theoretically calculated isotope distributions; and

performing a mass spectral calibration or mass spectral data analysis involving theoretical isotope distributions and acquired profile mode data through one of convolution, deconvolution, and regression operation.

19. A method for calibrating a mass spectrometer for higher mass accuracy than otherwise available, comprising:

operating the mass spectrometer at a slower scanning and higher resolution mode;

acquiring profile mode mass spectral data containing at least one standard ions of known elemental compositions in one or more mass spectral segments;

calculating theoretical isotope distribution for each of the standard ions; and

calculating mass spectral calibration filters through at least one of convolution and deconvolution involving the acquired profile mode mass spectral data and theoretical isotope distributions for said ions.

20. A mass spectrometer system operated in accordance with any one of claims 1 to 19 .

21. A computer readable medium having computer readable program instructions readable by the computer for causing a mass spectrometer system to perform in accordance with the methods of any one of claims 1 to 19 .