Peptide or protein-capturing surfaces for high throughput MALDI mass spectrometry

Abstract

Methods and compositions useful for capturing proteins or peptides from a sample mixture and analyzing the captured proteins or peptides via high throughput electrospray ionization (ESI) or matrix-assisted laser desorption/ionization mass spectrometry (HT MALDI MS) are provided. The methods and compositions are useful in large scale, simultaneous analyses of proteins and peptides present in a cell(s), tissue(s), or biological fluid(s).

1 . (canceled)  
     
     
         2 . (canceled)  
     
     
         3 . (canceled)  
     
     
         4 . (canceled)  
     
     
         5 . (canceled)  
     
     
         6 . (canceled)  
     
     
         7 . (canceled)  
     
     
         8 . (canceled)  
     
     
         9 . (canceled)  
     
     
         10 . (canceled)  
     
     
         11 . (canceled)  
     
     
         12 . (canceled)  
     
     
         13 . A method of performing high throughput analysis of multiple samples, each of said samples comprising a mixture of peptides or proteins, said method comprising the steps of: 
 (a) providing a solid support comprising a plurality of separate compartments, wherein one or more of the compartments has a specific affinity layer attached thereto for capture of the peptides or proteins present in the samples;    (b) applying each of said samples or an aliquot thereof, to a separate compartment having the specific affinity layer attached thereto;    (c) washing the peptides or proteins which have been captured by the specific affinity layer, and    (d) performing high throughput electrospray ionization (ESI) or matrix-assisted laser desorption/ionization (MALDI) mass spectrometry analysis on the captured peptides or proteins.    
     
     
         14 . The method of  claim 13  wherein the specific affinity layer is attached to a first portion of the one or more compartments and a non-binding surface is located in a second portion of the one or more compartments.  
     
     
         15 . The method of  claim 13  wherein the one or more compartments having a specific affinity layer attached thereto further has a hydrophilic area devoid of and surrounded by the specific affinity layer.  
     
     
         16 . The method of  claim 13  wherein the specific affinity layer is attached to a first portion of the one or more compartments, wherein the first portion of the one or more compartments comprises a hydrophilic area devoid of and surrounded by the specific affinity layer attached thereto and wherein the one or more compartments further comprises a non-binding surface located in a second portion thereof.  
     
     
         17 . The method of any one of claims  13 - 16  wherein the specific affinity layer is at least one of a hydrophobic surface layer, an ionic surface layer, or a metal chelating surface layer.  
     
     
         18 . The method of any one of claims  13 - 16  wherein the solid support is a dish, slide, strip or plate.  
     
     
         19 . The method of  claim 18  wherein the solid support is a is a microwell plate or a microtiter dish.  
     
     
         20 . The method of any one of claims  13 - 16  wherein the specific affinity layer is at least one of a hydrophobic surface layer, an ionic surface layer, or a metal chelating surface layer.  
     
     
         21 . The method of  claim 20  wherein the hydrophobic layer comprises a long chain aliphatic.  
     
     
         22 . The method of  claim 21  wherein the long chain aliphatic is at least one of octadecyl vinyl ether (ODVE), octadecyl amine (ODAM), tri(ethylene glycol)-methyl-vinyl-ether (TMVE), stearyl alcohol (SA), nonylphenoxypoly(ethyleneoxy)ethyl-methacrylate (C9 poly), or stearyloxypolyethyleneoxy-ethyl-methacrylate (SPMA).  
     
     
         23 . The method of  claim 20  wherein the metal chelating surface layer is nickel.  
     
     
         24 . The method of any one of claims  13 - 16  wherein the solid substrate comprises a polymer injection molded plate, a glass bottom plastic plate or a gold deposited plastic plate  
     
     
         25 . The method of  claim 15  or  16  wherein a photo-excitable matrix is added to the captured peptides or proteins in the one or more compartments.  
     
     
         26 . The method of  claim 25  wherein the matrix is at least one of sinapinic acid, 3-hydroxypicolinic acid, alpha-cyano-4-hydroxycinnamic acid, alpha-cyano-4-hydroxycinnamic acid methyl ester, 2,5-dihydroxybenzoic acid, 2,3,4-trihydroxyacetophenone, 2,4,6-trihydroxyacetophenone, alpha-cyano-4-hydroxycinnamic acid methyl ester (a-CNME), 2,3,4-trihydroxyacetophenone (2,3,4-THAP), 2,4,6-trihydroxyacetophenone (2,4,6-THAP), nicotinic acid, succinic acid, or glycerol.