Arrays of protein capture agents and methods of use thereof

Abstract

Arrays of protein-capture agents useful for the simultaneous detection of a plurality of proteins which are the expression products, or fragments thereof, of a cell or population of cells in an organism are provided. A variety of antibody arrays, in particular, are described. Methods of both making and using the arrays of protein-capture agents are also disclosed. The invention arrays are particularly useful for various proteomics applications including assessing patterns of protein expression and modification in cells.

1 - 45 . (canceled) 
     
     
         46 . A method for screening a plurality of proteins for their ability to interact with a component of a fluid sample, comprising delivering the fluid sample to a protein array comprising the plurality of proteins comprising at least 100 different proteins, and simultaneously detecting for the presence of an interaction of the component with each protein of the plurality of proteins, wherein the protein array comprises the plurality of proteins each immobilized site-specifically on different discrete, known regions of a substrate, wherein the discrete, known regions are present at a density of at least 100 per cm 2 , thereby detecting an interaction of a protein of the plurality of proteins and the component of the fluid sample,
 wherein each of the proteins in the plurality of proteins is a different purified recombinant fusion protein, and the proteins in the plurality of proteins are structurally related, functionally related, suspected of being functionally related, suspected of being structurally related, or are members of the same family.   
     
     
         47 . The method of  claim 46 , wherein detecting comprises detecting an enzyme/substrate interaction. 
     
     
         48 . The method of  claim 46 , wherein the plurality of proteins comprises at least 1000 different human proteins. 
     
     
         49 . The method of  claim 46 , wherein the proteins are members of an enzyme family. 
     
     
         50 . The method of  claim 46 , wherein the proteins are enzymes and the enzymes are kinases. 
     
     
         51 . The method of  claim 46 , wherein the component is a protein, and wherein the method detects a protein-protein interaction. 
     
     
         52 . The method of  claim 46 , wherein the component is a nucleic acid. 
     
     
         53 . The method of  claim 46 , wherein the plurality of proteins comprise at least 1000 different proteins. 
     
     
         54 . The method of  claim 46 , wherein the proteins are members of the same receptor family, ligand family, enzyme family, or transcription factor family. 
     
     
         55 . The method of  claim 46 , wherein the proteins are proteases, kinase, phosphatases, ras-like GTPases, or hydrolases. 
     
     
         56 . The method of  claim 46 , wherein the proteins are kinases. 
     
     
         57 . The method of  claim 56 , wherein the proteins are functional proteins. 
     
     
         58 . The method of  claim 56 , wherein the proteins are human proteins. 
     
     
         59 . The method of  claim 56 , wherein the kinases comprise different kinases. 
     
     
         60 . The method of  claim 56 , wherein the kinases comprise 100 different mammalian kinases. 
     
     
         61 . The method of  claim 56 , wherein the kinases comprise  100  different human kinases. 
     
     
         62 . The method of  claim 56 , wherein the kinases comprise 100 different recombinant kinases. 
     
     
         63 . The method of  claim 56 , wherein the kinases comprise 100 different functional kinases. 
     
     
         64 . The method of  claim 56 , wherein all of the proteins in the protein array are human proteins.