Methods for detection and quantification of nucleic acid or protein targets in a sample

1. An assay method for detection of a plurality of protein targets in a sample comprising

(a) combining target-specific probes with the sample under conditions in which at least 10 target-specific probes each bind a different specific target in the sample, if the specific target is present;

wherein each target-specific probe forms a target-specific probe product associated with the target if the target is present in the sample, thereby associating a nucleic acid tag sequence with the target by forming a target-specific probe product associated with the target;

wherein the target comprises a protein molecule;

(b) segregating aliquots of the sample; and

(c) querying each said aliquot for the presence or absence of a different target-specific probe product, wherein said querying comprises amplifying the nucleic acid tag sequence of the probe product using a first primer that binds a first primer binding site of the probe product and a second primer that binds a second primer binding site of the probe product; and detecting the presence or absence of a common nucleic acid tag sequence using a tag-detecting probe;

wherein at least two of said target-specific probe products do not have the same first primer binding sites and at least two of said target-specific probe products do not have the same second primer binding sites.

2. The method of claim 1 wherein target-specific probes sufficient to identify at least 25 different targets are combined with the sample.

3. The method of claim 2 wherein target-specific probes sufficient to identify at least 50 different targets are combined with the sample.

4. The method of claim 3 wherein target-specific probes sufficient to identify at least 100 different targets are combined with the sample.

5. The method of claim 4 wherein target-specific probes sufficient to identify at least 500 different targets are combined with the sample.

6. The method of claim 1 wherein said querying comprises quantifying the amount of the nucleic acid tag sequence in each aliquot and correlating the amount of the tag sequence with the amount of target in the sample.

7. The method of claim 6 in which the tag sequence is amplified using PCR.

8. The method of claim 7 wherein the amplified tag sequence is detected using a fluorogenic nuclease assay.

9. The method of claim 8 wherein the amplified tag sequence is quantified by the continuous measurement of PCR product accumulation using a dual-labeled fluorogenic oligonucleotide probe.

10. The method of claim 1 wherein the target-specific probe is a proximity probe.

11. The method of claim 1 wherein the assay has a dynamic range of at least 4 orders of magnitude.

12. The method of claim 1 wherein querying each aliquot of the sample for the presence of a different target-specific probe comprises combining each aliquot with a composition containing PCR primers and/or a tag detecting probe.

13. The method of claim 12 wherein querying each aliquot of the sample for the presence of a different target-specific probe comprises combining each aliquot with a composition containing PCR primers and a tag detecting probe.

14. The method of claim 13 wherein the tag-detecting probe is a dual-labeled fluorogenic oligonucleotide probe.

15. The method of claim 14 wherein each aliquot is queried using the same tag-detecting probe.

16. The method of claim 14 wherein each aliquot is queried using a different PCR primer pair.

17. The method of claim 1 , wherein each target-specific probe comprises a monoclonal antibody pair.

18. The method of claim 1 , wherein the target-specific probes comprise PCR primer sites that vary between each target specific probe.