Peptide identification

1. A method for correlating a query peptide to a protein comprising the steps of:

providing one or more mass spectra for a query peptide, the query peptide being a protein cleavage product by one or more cleaving agents having defined cleavage specificity, wherein each spectrum comprises masses of members selected from immonium ions, modified immonium ions, fragmented immonium ions, dipeptide ions, fragmented dipeptide ions, tripeptide ions, and fragmented tripeptide ions;

obtaining a qualitative amino acid composition of the query peptide from said one or more mass spectra, wherein the qualitative amino acid composition indicates the presence or absence of specific amino acids in the peptide, irrespective of the total number of each type of amino acid present;

comparing the qualitative amino acid composition of the query peptide to a list of qualitative amino acid compositions of a plurality of predicted peptides in a predicted peptide database, the predicted peptides being predicted cleavage products of parent proteins assuming the parent proteins, whose amino acid sequences are known, are subjected to cleavage by said one or more cleaving agents, wherein the comparing step is performed by a computer;

correlating the query peptide to the parent protein of a predicted peptide whose qualitative amino acid composition is matched to the amino acid composition of the query peptide; and

outputting to a user the identity of the parent protein to which the query peptide has been correlated.

2. The method of claim 1 , wherein the query peptide contains about 9 to about 31 amino acids.

3. The method of claim 1 , wherein the cleaving agent is selected from an enzyme and a chemical cleaving agent.

4. The method of claim 1 , wherein the cleaving agent is trypsin.

5. The method of claim 1 , wherein each predicted peptide is assigned an amino acid composition score which correlates to a unique qualitative amino acid composition.

6. The method of claim 1 , wherein the predicted peptide database further comprises a list of qualitative amino acid compositions of predicted peptides that are predicted to be generated when incomplete cleavage of the parent proteins by said one or more cleaving agents occurs.

7. The method of claim 1 , wherein the predicted peptide database further comprises a list of molecular masses of the predicted peptides.

8. The method of claim 1 , wherein the predicted peptide database is generated by a computer.

9. The method of claim 1 , further comprising the step of providing a molecular mass of the query peptide.

10. The method of claim 9 , wherein the query peptide is matched to a predicted peptide in the predicted peptide database based on both the qualitative amino acid composition and the molecular mass.

11. The method of claim 10 , wherein the molecular mass of the query peptide is adjusted for one or more post-translational modifications.

12. The method of claim 1 , wherein the one or more mass spectra are selected from collision induced disassociation spectra and post source decay spectra.

13. The method of claim 1 , wherein the one or more mass spectra are generated by matrix assisted laser desorptionlionization (MALDI) or matrix-free surface assisted laser desorptionlionization (SALDI).

14. The method of claim 1 , wherein the one or more mass spectra are generated by matrix-free surface assisted laser desorption/ionization (SALDI) using far UV excitation.

15. The method of claim 14 , wherein the UV employed is of a wavelength from about 157 nm to about 225 nm.

16. The method of claim 1 further comprising the step of assigning to the query peptide an amino acid composition score that correlates to a unique qualitative amino acid composition.

17. The method of claim 16 , wherein the amino acid composition score is a binary score wherein the presence of one particular amino acid residue in the query peptide is represented at a given digit of the binary score by one possible value and the absence of the particular amino acid residue is represented at the given digit of the binary score by the other possible value.

18. The method of claim 16 , wherein the query peptide is matched to a predicted peptide having the same or a closely matched amino acid composition score.

19. The method of claim 1 , wherein the query peptide is matched to a predicted peptide that differs from the query peptide by one amino acid measured by qualitative amino acid composition.

20. A method for identifying one or more proteins in a sample containing at least one protein, the method comprising the steps of:

cleaving the protein or proteins in the sample with one or more cleaving agents having defined cleaving specificity to generate query peptides; and

correlating one or more query peptides to one or more parent proteins according to the method of claim 1 wherein the parent proteins to which the query peptides correlate indicate the identity of the proteins present in the sample.