Droplet libraries

1. A method for detecting target molecules in a fluid sample, the method comprising:

providing, to a microfluidic device, a fluid sample comprising target molecules, a plurality of beads each comprising a bead-identifying label that identifies the bead and a reactive component for binding a target molecule thereto, and a detection component for binding to a target molecule that is bound to a bead;

partitioning, in the microfluidic device, the fluid sample into plurality of separate and isolated partitions of fluid, wherein at least one of the plurality of partitions comprises an immunocomplex comprising a target molecule bound between a single bead, via an associated reactive component, and an associated detection component; and

simultaneously detecting from within an intact partition of the plurality of partitions the bead-identifying label and an event associated with contents of the intact partition.

2. The method of claim 1 , wherein the plurality of partitions comprises a first subset and a second subset, wherein the first subset comprises partitions that each comprise no bead and the second subset comprises partitions that each comprise a single bead, wherein a majority of the plurality of partitions are provided within the second subset.

3. The method of claim 1 , wherein the reactive component and the detection component comprise a first and a second antibody, respectively.

4. The method of claim 1 , wherein the detection component comprises one or more detectable labels.

5. The method of claim 4 , wherein the event comprises release of a detectable label in at least one of the plurality of partitions.

6. The method of claim 5 , further comprising conducting a reaction in the at least one of the plurality of partitions, wherein the reaction results in release of the detectable label.

7. The method of claim 6 , wherein the reaction is an enzymatic reaction in one or more partitions containing an immunocomplex comprising a target molecule bound between a single bead, via an associated reactive component, and an associated detection component, wherein, in response to the enzymatic reaction, the detectable label from each detection component is released.

8. The method of claim 1 , wherein the target molecule is a protein.

9. The method of claim 1 , wherein each of the plurality of partitions of fluid are separated and isolated from one another by a fluid immiscible with the fluid sample, wherein the immiscible fluid is an oil.

10. The method of claim 1 , wherein the bead-identifying label comprises an optical label, the detection component comprises a readout enzyme, the partitions include a fluorogenic substrate, and wherein the detecting step comprises reading an optical signal indicating a bead type and immunoassay information while simultaneously reading fluorescent signal from a partition.

11. The method of claim 10 , wherein the partitions are aqueous droplets and the detecting step uses droplets containing exactly one bead.

12. The method of claim 11 , further comprising discarding droplets with more than one bead.

13. The method of claim 11 , wherein the reactive component comprises a first antibody linked to the bead, and the detection component comprises a second antibody linked to the readout enzyme.

14. The method of claim 13 , wherein the readout enzyme is linked to the second enzyme via a streptavidin linkage.

15. The method of claim 14 , wherein fluorogenic substrate is added to the droplets under co-flow conditions at the time of droplet generation.

16. The method of claim 13 , further comprising removing droplets containing excess beads.

17. The method of claim 13 , wherein the fluorescent signal is proportional to a concentration of the target molecules in the fluid sample.

18. The method of claim 17 , wherein the readout enzyme is selected from the group consisting of galactasidase, alkaline phosphatase, and horseradish peroxidase.