System and method for determining differential protein expression, diagnostic biomarker discovery system and method of using the same, and protein biomarkers and therapeutic and diagnostic uses thereof

A diagnostic system, comprising:

• a database that stores protein patterns associated with subject characteristics;
• a protein data processing unit that separates a protein content of a tissue or specimen sample from a respective subject into protein subgroups;
• a mass spectrometer that independently performs mass spectroscopy on each of the protein subgroups from the respective subject's sample, and outputs respective mass spectra subgroup data;
• and
• a diagnostic unit that analyzes the mass spectra subgroup data to create a protein profile for the tissue or specimen sample, and that compares the protein profile with the stored protein patterns to predict the existence or non-existence of at least one subject characteristic in the respective subject.

A biomarker diagnostic method, comprising the steps of:

• collecting a tissue or specimen sample;
• fractioning protein content from the sample into protein subgroups;
• separately performing mass spectroscopy on each of said protein subgroups and storing resulting mass spectra subgroup data;
• analyzing said resulting mass spectra subgroup data to yield a protein profile for said sample.

A method for rapidly identifying protein biomarkets, comprising the steps of:

• collecting a diseased tissue or specimen sample from at least one patient;
• fractionating protein content from said diseased tissue or specimen sample into protein subgroups;
• separately performing mass spectroscopy on each of said protein subgroups and storing resulting mass subgroup data;
• analyzing said resulting mass spectra subgroup data to yield a protein profile for said diseased tissue or specimen sample;
• comparing said protein profile for said diseased tissue sample or specimen against at least one protein profile from at least one normal tissue sample or specimen from said patient or other individuals;
• and
• identifying the differences between said diseased tissue sample or specimen and said at least one protein profile for a normal tissue sample or specimen, thereby identifying protein biomarkers.

A diagnostic method, comprising:

• collecting a tissue or specimen sample from a patient;
• fractionating protein content from said sample into protein subgroups;
• separately performing mass spectroscopy on each of said protein subgroups and storing resulting mass subgroup data;
• analyzing said resulting mass spectra subgroup data to yield a protein profile for said sample;
• comparing said protein profile for said tissue sample or specimen against a protein profile library;
• and diagnosing presence or absence of a disease or other biological condition.