Systems and methods for discovery and analysis of markers

Abstract

A business method for use in classifying patient samples. The method includes steps of collecting case samples representing a clinical phenotypic state and control samples representing patients without said clinical phenotypic state. Preferably the system uses a mass spectrometry platform system to identify patterns of polypeptides in said case samples and in the control samples without regard to the specific identity of at least some of said polypeptides. Based on identified representative patterns of the state, the business method provides for the marketing of diagnostic products using representative patterns. The present invention relates to systems and methods for identifying new markers, diagnosing patients with a biological state of interest, and marketing/commercializing such diagnostics. The present invention relates to systems and methods of greater sensitivity, specificity, and/or cost effectiveness.

What is claimed is: 
     
         1 . A method comprising:
 a) collecting more than 10 case samples representing a clinical phenotypic state and more than 10 control samples representing individuals without said clinical phenotypic state;   b) using electrophoresis followed by a mass spectrometry platform system to obtain mass spectral components in said case samples and in said control samples without regard to a specific sequence of at least some of said mass spectral components;   c) identifying in a computer system representative patterns of markers that distinguish datasets from case samples and control samples wherein said patterns contain more than 15 markers that are represented on output of said mass spectrometer, but the specific sequence of said more than 15 markers is not known;   d) from blood samples of patients, in a computer system, identifying in patient samples said more than 15 markers wherein the specific sequence of said more than 15 markers is not known.   
     
     
         2 . The method as recited in  claim 1 , wherein diagnostic products are marketed using said markers in a clinical reference laboratory. 
     
     
         3 . The method as recited in  claim 1 , further comprising the step of collecting said samples in collaboration with a collaborator. 
     
     
         4 . The method as recited in  claim 3 , wherein said collaborator is an academic collaborator. 
     
     
         5 . The method as recited in  claim 3 , wherein said collaborator is a pharmaceutical company. 
     
     
         6 . The method as recited in  claim 5 , wherein said pharmaceutical company collects said samples in a clinical trial. 
     
     
         7 . The method as recited in  claim 1 , wherein data from one of said samples are being processed computationally while another of said samples are in said mass spectrometry platform. 
     
     
         8 . The method as recited in  claim 1 , wherein said markers are polypeptides. 
     
     
         9 . The method as recited in  claim 8 , wherein said patterns contain more than 30 polypeptides that are represented on output of said mass spectrometer, but the specific sequence of said more than 30 polypeptides is not known. 
     
     
         10 . The method as recited in  claim 8 , wherein said patterns contain more than 50 polypeptides that are represented on output of said mass spectrometer, but the specific sequence of said more than 50 polypeptides is not known. 
     
     
         11 . The method as recited in  claim 8 , wherein said patterns contain more than 100 polypeptides that are represented on output of said mass spectrometer, but the specific sequence of said more than 100 polypeptides is not known. 
     
     
         12 . The method as recited in  claim 8 , wherein said samples contain more than 1000 polypeptides that are represented on output of said mass spectrometer, but the specific sequence of said more than 1000 polypeptides is not known. 
     
     
         13 . The method as recited in  claim 1 , wherein more than 50 of said cases samples and 50 of said control samples are used. 
     
     
         14 . The method as recited in  claim 1 , wherein more than 100 of said case samples and 100 of said control samples are used. 
     
     
         15 . The method as recited in  claim 1 , wherein said diagnostic products use said mass spectrometry platform. 
     
     
         16 . The method as recited in  claim 1 , wherein said step of using a mass spectrometry platform is preceded by the step of preparing said samples on a microfluidics device. 
     
     
         17 . The method as recited in  claim 16 , wherein said diagnostic products are marketed with a disposable microfluidics device, said disposable microfluidics device processing diagnostic samples for use in said mass spectrometry platform. 
     
     
         18 . The method as recited in  claim 16 , wherein said microfluidics device comprises a separations device. 
     
     
         19 . The method as recited in  claim 1 , wherein said mass spectrometry platform is a time of flight mass spectrometer. 
     
     
         20 . The method as recited in  claim 1 , wherein said mass spectrometer is a Hadamard time of flight mass spectrometer. 
     
     
         21 . The method as recited in  claim 1 , wherein said diagnostic products are marketed by a diagnostic partner. 
     
     
         22 . The method as recited in  claim 1 , wherein said phenotype is a disease diagnostic phenotype. 
     
     
         23 . The method as recited in  claim 16 , wherein said microfluidics device comprises an electrospray source. 
     
     
         24 . The method as recited in  claim 1 , wherein said samples contain complex mixtures of polypeptides.