Serum proteomics system and associated methods

1. A method for comparing multiple mass spectra from different biological samples, locating mass ions that are quantitatively different after using approaches to compensate for non-biological variability, and isolating and sequencing at least one peptide of interest thus allowing for identification of the peptide from a biological sample, comprising:

fractionating each of a plurality of biological samples to form a plurality of elutions;

obtaining a plurality of mass spectra from each of the plurality of elutions at a plurality of elution times;

finding a molecular ion peak of interest that appears to be quantitatively different between biological samples;

identifying a mass spectrum reference peak corresponding to an endogenous reference molecule that is substantially consistent between biological samples, the endogenous reference molecule having an elution time and a mass to charge ratio that are substantially similar to the peak of interest;

compensating for non-biological variation for each biological sample across the plurality of elutions by normalizing the peak of interest to a mass spectrum peak of the endogenous reference molecule; and

fractionating at least one of the biological samples containing the peptide associated with the peak of interest to at least partially isolate the peptide;

obtaining mass spectra of the peptide;

accelerating the peptide into a collision chamber at a plurality of discrete collision energies for a discrete period of time to form a plurality of peptide fragments for each of the plurality of discrete collision energies;

obtaining a plurality of fragmentation mass spectra from the plurality of peptide fragments for each of the plurality of discrete collision energies;

summing the plurality of fragmentation mass spectra from each of the plurality of discrete collision energies to form a plurality of discrete collision energy mass spectra, one discrete collision energy mass spectra from each discrete collision energy;

summing the plurality of discrete collision energy mass spectra to form a final mass spectrum for the peptide fragments; and

identifying a sequence of amino acids corresponding to the peptide from the final mass spectrum.

2. The method of claim 1 , wherein the biological samples are blood serum samples.

3. The method of claim 1 , further comprising:

identifying a plurality of mass spectrum elution time alignment peaks in the plurality of mass spectra corresponding to a plurality of endogenous alignment molecules such that each of the plurality of elutions contains at least one mass spectrum elution time alignment peak; and

aligning at least a portion of the plurality of mass spectra by aligning at least a portion of the plurality of mass spectrum elution time alignment peaks.

4. The method of claim 3 , wherein aligning the pluralities of mass spectra further includes visually aligning the pluralities of mass spectra using the mass spectrum alignment peak as a reference.

5. The method of claim 1 , wherein the endogenous alignment molecules have a substantially uniform abundance in each of the plurality of biological samples.

6. The method of claim 1 , wherein fractionating each of the plurality of biological samples further includes fractionating each of the biological samples by capillary liquid chromatography.

7. The method of claim 1 , wherein the discrete period of time is approximately equal to the peptide's elution duration.

8. The method of claim 6 , wherein the discrete period of time is greater than or equal to the peptide's elution duration.

9. The method of claim 1 , wherein the discrete period of time is less than the peptide's elution duration.

10. The method of claim 1 , wherein the discrete period of time is from about 30 seconds to about 3 minutes.

11. The method of claim 10 , wherein the endogenous reference molecule has a substantially representative abundance in each of the plurality of biological samples.

12. A method of sequencing a peptide, comprising:

fractionating a biological sample containing a peptide of interest to at least partially isolate the peptide;

obtaining mass spectra of the peptide;

accelerating the peptide into a collision chamber at a plurality of discrete collision energies for a discrete period of time to form a plurality of peptide fragments for each of the plurality of discrete collision energies;

obtaining a plurality of fragmentation mass spectra from the plurality of peptide fragments for each of the plurality of discrete collision energies;

summing the plurality of fragmentation mass spectra from each of the plurality of discrete collision energies to form a plurality of discrete collision energy mass spectra, one discrete collision energy mass spectra from each discrete collision energy;

summing the plurality of discrete collision energy mass spectra to form a final mass spectrum for the peptide fragments; and

identifying a sequence of amino acids corresponding to the peptide of interest from the final mass spectrum.

13. The method of claim 12 , wherein the discrete period of time is approximately equal to the peptide's elution duration.

14. The method of claim 12 , wherein the discrete period of time is greater than or equal to the peptide's elution duration.

15. The method of claim 12 , wherein the discrete period of time is from about 30 seconds to about 3 minutes.

16. The method of claim 12 , wherein the plurality of discrete collision energies is at least 3 discrete collision energies.

17. The method of claim 12 , wherein the plurality of discrete collision energies is at least 5 discrete collision energies.

18. The method of claim 12 , wherein the plurality of discrete collision energies is at least 7 discrete collision energies.