Methods for diagnosing oncogenic human papillomavirus (HPV)

1. A method for diagnosing human papillomavirus (HPV) infection in a subject comprising:

a) generating a peptide fingerprinting pattern by peptide mass fingerprinting (PMF) for at least one target protein in a biological sample from the subject; and

b) determining the presence or absence of at least one biomarker associated with HPV infection in the biological sample by correlating the peptide fingerprinting pattern of the target protein with a known peptide fingerprinting pattern of at least one biomarker associated with HPV infection;

wherein the at least one biomarker is a protein encoded by the E2, E5, E6, E7, or E8 regions of oncogenic forms of HPV;

whereby a match of the peptide fingerprinting pattern of the target protein with the known peptide fingerprinting pattern indicates the presence of at least one biomarker in the sample;

whereby the presence of the at least one biomarker associated with HPV infection in the biological sample indicates HPV infection in the subject.

2. The method of claim 1 , wherein the presence or absence of at least two biomarkers associated with HPV infection is determined from the peptide fingerprinting pattern.

3. The method of claim 1 , wherein the quantity or presence of the at least one biomarker associated with HPV infection indicates the stage of HPV infection in the subject.

4. The method of claim 1 , wherein the HPV is HPV type 16 18, 31, 33, 35, 45, 51, 52, 56, 59, 68, 73, 39, 66, 82, 26, 30, 53, 69, or 58.

5. The method of claim 1 , wherein the biological sample is blood, serum, urine, prostatic fluid, seminal fluid, semen, tissue extract sample, or biopsy.

6. The method of claim 1 , wherein the subject is a woman.

7. A method for detecting at least one biomarker associated with HPV infection in a biological sample comprising:

a. digesting at least one biomarker into at least two peptide fragments using a first proteolytic enzyme, said biomarker being E2, E5, E6, E7, and/or E8 protein;

b. generating a mass spectrum for the at least two biomarker peptide fragments using mass spectrometry to obtain a reference mass spectrum;

c. recording the mass spectrum for the at least two biomarker peptide fragments

d. isolating at least one target protein in the biological sample;

e. digesting the at least one target protein in the biological sample into at least two peptide fragments using a second proteolytic enzyme, the second proteolytic enzyme being the same kind of proteolytic enzyme as the first proteolytic enzyme;

f. generating a mass spectrum for the at least two peptide fragments of the biological sample using mass spectrometry;

g. correlating the mass spectrum for the at least two peptide fragments of the biological sample with the reference mass spectrum of the biomarker;

whereby a match of the mass spectrum for the at least two peptide fragments of the biological sample and the reference mass spectrum indicates the presence of the biomarker in the biological sample.

8. The method of claim 7 , wherein the mass spectrometry is matrix-assisted laser desorption ionization/time of flight (MALDI-TOF), surface enhanced laser desorption ionization time of flight (SELDI-TOF), liquid chromatography coupled with mass spectrometry, tandem mass spectrometry (MS-MS), electrospray ionization (ESI-MS), or chemical ionization.

9. The method of claim 7 , wherein the step of correlating the mass spectrum for the at least two peptide fragments of the sample with the reference mass spectrum comprises:

a) transforming the mass spectrum obtained in step (f) into a computer readable form; and

b) comparing the computer readable form of the mass spectrum obtained in step (f) with a database containing the reference mass spectrum.

10. The method of claim 7 , wherein the step of correlating the mass profile data for the sample with a reference mass profile further indicates the strain of HPV infection in the subject.