Spatially Encoded Biological Assays

Abstract

The present invention provides assays and assay systems for use in spatially encoded biological assays. The invention provides an assay system comprising an assay capable of high levels of multiplexing where reagents are provided to a biological sample in defined spatial patterns; instrumentation capable of controlled delivery of reagents according to the spatial patterns; and a decoding scheme providing a readout that is digital in nature.

1 . (canceled) 
     
     
         2 . A system for analyzing a target biological molecule of a tissue sample, the system comprising:
 a laser configured to deliver radiation to a tissue sample comprising a plurality of probes, wherein a probe of the plurality of probes comprises a peptide that specifically binds a target biological molecule of the tissue sample and a mass tag conjugated to the peptide;   a matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) detection apparatus comprising a mass analyzer configured to:
 receive a chemical moiety comprising at least a portion of the mass tag after liberation of the chemical moiety from a location of interest in the sample; and 
 detect and mass analyze the at least a portion of the mass tag. 
   
     
     
         3 . The system of  claim 2 , wherein the detection apparatus is configured to determine a relative abundance of the at least a portion of the mass tag from the location of interest in the tissue sample. 
     
     
         4 . The system of  claim 2 , wherein the laser is configured to liberate the chemical moiety from the location of interest in the tissue sample. 
     
     
         5 . The system of  claim 2 , wherein the chemical moiety is the mass tag. 
     
     
         6 . The system of  claim 2 , wherein the peptide specifically binds a complementary region of the target biological molecule. 
     
     
         7 . The system of  claim 2 , wherein the probe is a first probe comprising a first peptide that specifically binds a first target biological molecule of the tissue sample and a first mass tag conjugated to the first peptide, and wherein a second probe of the plurality of probes comprises a second peptide that specifically binds a second target biological molecule of the tissue sample and a second mass tag conjugated to the second peptide. 
     
     
         8 . The system of  claim 7 , wherein the first and second mass tags are different. 
     
     
         9 . The system of  claim 7 , wherein the first and second target biological molecules are the same. 
     
     
         10 . The system of  claim 7 , wherein the first and second target biological molecules are different. 
     
     
         11 . The system of  claim 2 , further comprising a processing circuit comprising instructions that, when executed, cause the processing circuit to obtain information about the location of interest in the tissue sample. 
     
     
         12 . The system of  claim 11 , wherein the processing circuit is configured to obtain information about multiple locations of interest in the tissue sample, and the detection apparatus is configured to determine information corresponding to a relative abundance of the at least a portion of the mass tag at different locations in the tissue sample corresponding to the multiple locations of interest. 
     
     
         13 . The system of  claim 11 , wherein the processing circuit comprises instructions that, when executed, cause the processing circuit to receive the information about the location of interest in the tissue sample from a user of the system. 
     
     
         14 . The system of  claim 2 , wherein the target biological molecule comprises a protein. 
     
     
         15 . The system of  claim 2 , wherein the tissue sample comprises a fresh-frozen or formalin-fixed paraffin embedded (FFPE) tissue sample. 
     
     
         16 . The system of  claim 2 , wherein the peptide forms a portion of an antibody that specifically binds the target biological molecule. 
     
     
         17 . The system of  claim 12 , wherein each of the multiple locations of interest corresponds to a different group of one or more cells in the tissue sample. 
     
     
         18 . The system of  claim 12 , wherein each of the multiple locations of interest corresponds to a different cell type in the tissue sample. 
     
     
         19 . The system of  claim 12 , wherein each of the multiple locations of interest corresponds to a different cell in the tissue sample. 
     
     
         20 . A method for analyzing a target biological molecule of a tissue sample, the method comprising:
 obtaining a tissue sample comprising a plurality of probes, wherein a probe of the plurality of probes comprises a peptide that specifically binds a target biological molecule of the tissue sample and a mass tag conjugated to the peptide;   directing radiation to the tissue sample to liberate a chemical moiety comprising at least a portion of the mass tag from a location of interest in the sample; and   mass analyzing the at least a portion of the mass tag.   
     
     
         21 . The method of  claim 20 , further comprising determining a relative abundance of the at least a portion of the mass tag at the location of interest in the tissue sample. 
     
     
         22 . The method of  claim 20 , comprising liberating the chemical moiety from the location of interest in the tissue by ionizing the chemical moiety. 
     
     
         23 . The method of  claim 22 , wherein the chemical moiety is the mass tag. 
     
     
         24 . The method of  claim 20 , wherein the peptide of the probe specifically binds a complementary region of the target biological molecule. 
     
     
         25 . The method of  claim 20 , wherein the probe is a first probe comprising a first peptide that specifically binds a first target biological molecule of the tissue sample and a first mass tag conjugated to the first peptide, and wherein a second probe of the plurality of probes comprises a second peptide that specifically binds a second target biological molecule of the tissue sample and a second mass tag conjugated to the second peptide. 
     
     
         26 . The method of  claim 25 , wherein the first and second mass tags are different. 
     
     
         27 . The method of  claim 20 , further comprising determining information corresponding to a relative abundance of the at least a portion of the mass tag at different locations in the tissue sample corresponding to multiple locations of interest in the tissue sample. 
     
     
         28 . The method of  claim 20 , wherein the target biological molecule comprises a protein. 
     
     
         29 . The method of  claim 20 , wherein the peptide forms a portion of an antibody that specifically binds the target biological molecule. 
     
     
         30 . The method of  claim 27 , wherein each of the multiple locations of interest corresponds to one of: a different group of one or more cells in the tissue sample, and a different cell type in the tissue sample.