Multiplexed bead arrays for proteomics

Abstract

Bead arrays suitable for analysis by mass spectrometry are disclosed. In an embodiment, a bead array includes multiple reactive sites, each of the reactive sites being capable of binding multiple distinct target analytes.

What is claimed is: 
     
         1 . A method for supplying a bead array system that is intended for analyzing a sample, the method comprising:
 providing a bead array, the bead array comprising a first reactive site and a second reactive site, the first reactive site comprising a first bead and a first capture agent, wherein the first capture agent is configured to specifically bind a first target and a second target, a molecular weight of the first target being different from a molecular weight of the second target, the second reactive site comprising a second bead and a second capture agent, the second capture agent being distinct from the first capture agent, wherein the second capture agent is configured to specifically bind a third target   and   providing a decoding table, the decoding table containing information that is obtained prior to analyzing the sample, said information comprising values that are derived from the molecular weight of the first target, the molecular weight of the second target and the molecular weight of the third target.   
     
     
         2 . The method of  claim 1  wherein the first, the second and the third targets are distinct proteolytic fragments of a naturally occurring protein. 
     
     
         3 . The method of  claim 1  wherein the first, the second and the third targets are polypeptides that contain distinct amino acid modifications within an otherwise identical amino acid sequence. 
     
     
         4 . The method of  claim 1  wherein the first capture agent is one of a monoclonal antibody, a polyclonal antibody, an antibody fragment, a single domain antibody, an aptamer, a protein, a polypeptide, a receptor, a ligand, an enzyme, an enzyme substrate and an enzyme inhibitor. 
     
     
         5 . The method of  claim 1  wherein the decoding table further contains an entry that is associated with the first reactive site, the entry containing information about a target that does not specifically bind to the first reactive site. 
     
     
         6 . The method of  claim 1  wherein the decoding table is provided electronically. 
     
     
         7 . The method of  claim 1  wherein the decoding table information is generated by a computer algorithm. 
     
     
         8 . The method of  claim 1  wherein the decoding table further contains a sequence information that is obtained by mass spectrometry. 
     
     
         9 . The method of  claim 1  wherein the decoding table further contains estimated abundances of the first target and the second target in the sample. 
     
     
         10 . A method for using a bead array system, the method comprising:
 contacting a sample with a bead array, the bead array comprising a first reactive site and a second reactive site, the first reactive site comprising a first bead and a first capture agent, wherein the first capture agent is configured to specifically bind a first target and a second target, a molecular weight of the first target being different from a molecular weight of the second target, the second reactive site comprising a second bead and a second capture agent, the second capture agent being distinct from the first capture agent, wherein the second capture agent is configured to specifically bind a third target,   receiving a decoding table, the decoding table containing information that is obtained prior to analyzing the sample, said information comprising values that are derived from the molecular weight of the first target, the molecular weight of the second target and the molecular weight of the third target,   after the contacting step, analyzing the bead array using mass spectrometry, detecting a signal in a mass spectrum   and   identifying a target analyte that is associated with the signal by verifying that an m/z value of the signal or an equivalent thereof is present in the decoding table.   
     
     
         11 . The method of  claim 10  wherein the first, the second and the third targets are distinct proteolytic fragments of a naturally occurring protein. 
     
     
         12 . The method of  claim 10  wherein the first, the second and the third targets are polypeptides that contain distinct amino acid modifications within an otherwise identical amino acid sequence. 
     
     
         13 . The method of  claim 10  wherein the first capture agent is one of a monoclonal antibody, a polyclonal antibody, an antibody fragment, a single domain antibody, an aptamer, a protein, a polypeptide, a receptor, a ligand, an enzyme, an enzyme substrate and an enzyme inhibitor. 
     
     
         14 . The method of  claim 10  wherein the decoding table further contains an entry that is associated with the first reactive site, the entry containing information about a target that does not specifically bind to the first reactive site. 
     
     
         15 . The method of  claim 10  wherein the decoding table is received electronically. 
     
     
         16 . The method of  claim 10  wherein the decoding table information is generated by a computer algorithm. 
     
     
         17 . The method of  claim 10  wherein the decoding table further contains a sequence information that is obtained by mass spectrometry. 
     
     
         18 . The method of  claim 10  wherein the decoding table further contains estimated abundances of the first target and the second target in the sample.