Methods of polypeptide identification and compositions therefor

Abstract

Methods are disclosed for identifying one or more proteins or polypeptides comprised by a sample. The methods comprise determining binding of each polypeptide with respect to each binding pool of a plurality of binding pools, wherein each binding pool comprises one or more probes which bind a structure comprised by a protein or polypeptide. In some aspects, polypeptides can be denatured and separated into individual polypeptide strands and immobilized on a solid support prior to determining binding of the binding pools. A protein, polypeptide or polypeptide strand can be identified by searching, in at least one database, for a protein or polypeptide sequence comprising binding pool targets either identical to or most similar to the binding pool targets comprised by the protein, polypeptide or polypeptide strand to be identified. Kits for identifying proteins, polypeptides and polypeptide strands are also disclosed.

What is claimed is: 
     
         1 . A method of characterizing properties of p polypeptide stran.ds, the method comprising:
 immobilizing, on a solid support, a plurality of p polypeptide strands, such that each polypeptide strand is spatially separated by an optically resolvable distance from o€:her polypeptide strands comprised by the sample,   applying one or more binding pools, wherein the one or more binding pools comprise n number of probes, wherein each binding pool can recognize and bind to one or more structures comprised by the polypeptide. strand(s), wherein one or more probes is degenerate, and wherein the one or more probes comprised by the binding pool is attached directly or indirectly to a label, wherein n and p are integers, and p is greater than n;   alter each application of the one or more binding pools to the solid support:
 detecting the presence or absence of the label attached to the one or more probes, thereby detecting binding of the probe(s) to the polypeptide strands; and 
 determining the presence or absence of a binding pool target in a polypeptide strand to be identified, wherein each binding pool target comprises one or more binding targets for one or more probes comprised by the binding pool. 
   
     
     
         2 . The method of claim  24 , which further comprises assigning a binding pool target signature to each polypeptide strand to be identified, thereby characterizing structural properties of the polypeptide strands. 
     
     
         3 . The method of claim  24 , which further comprises identifying, in at least one database, a protein or polypeptide comprising one or more binding pool targets most similar to the one or more binding pool targets comprised by the polypeptide strand to be identified. 
     
     
         4 . The method of claim  24 , wherein the one or more probes comprised by the binding pool specifically recognizes and binds to a structure comprised by a protein or polypeptide.. 
     
     
         5 . The method of claim  24 , wherein the one or more probes comprised by the binding pool can recognize and bind to a target peptide motif that comprises contiguous amino acids or non-contiguous amino acids in a protein or polypeptide chain. 
     
     
         6 . The method of claim  28 , wherein the peptide motif comprises a peptide motif selected from the group consisting of a peptide motif of at least two contiguous amino acids, a peptide motif of at least three contiguous amino acids, a peptide motif of at least four contiguous amino acids, a peptide motif of at least five contiguous amino acids, and a peptide motif of at least six contiguous amino acids. 
     
     
         7 . The method of claim  24 , which utilizes a set of at least about 10 binding pools. 
     
     
         8 . The method of claim  24 , wherein n is greater than log 2 (p), n being the number of probes and p being the number of the polypeptide strands to be characterized. 
     
     
         9 . The method of claim  24 , wherein the target of a probe comprised by a binding pool comprises a structure selected from the group consisting of a peptide motif comprising at least one amino acid, a peptide up to about six amino acids, a glycosyl moiety of a glycopeptide or a glycoprotein, a GPI anchor, a disulfide linkage, a pyroglutamic acid, and a nitrotyrosine. 
     
     
         10 . The method of claim  32 , wherein the amino acid recognized by a probe comprises a phosphorylated amino acid, a methylated amino acid, an acylated amino acid, a hydroxyproline or a sulfated amino acid. 
     
     
         11 . The method of claim  24 , wherein the solid support comprises a planar substrate. 
     
     
         12 . The method of claim  34 , wherein the planar substrate is a glass or plastic microscope slide. 
     
     
         13 . The method of claim  34 , wherein the solid support comprises a reactive moiety which covalently binds to the polypeptide strands or a chemical cross-linker. 
     
     
         14 . The method of claim  24 , wherein the label is selected from the group consisting of a radioisotope, a chromophore, a fluorophore, a quantum dot, an enzyme and a resonance light scattering (RLS) particle. 
     
     
         15 . The method of claim  25 , wherein a digital signature of each polypeptide strand to be identified is searched in the database or compared to digital signatures of the database of polypeptide sequences. 
     
     
         16 . The method of claim  26 , wherein the database is recorded in a digital medium. 
     
     
         17 . The method of claim  24 , wherein each binding pool comprises a collection of probes, which, in the aggregate, bind to more than one structure that can be comprised by a protein or polypeptide described in a database. 
     
     
         18 . The method of claim  24 , further comprising denaturing the polypeptide strands to be characterized prior to immobilizing on the solid support. 
     
     
         19 . The method of claim  24 , wherein the polypeptide strands to be characterized can form part of a mixture comprising other proteins or polypeptides. 
     
     
         20 . The method of claim  24 , which is used for identifying two or more proteins or polypeptides in a sample.