Droplet libraries

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

partitioning, in a microfluidic device, a fluid sample comprising target molecules into partitions, wherein a plurality of the partitions each comprise:

a target molecule;

a bead comprising a first antibody capable of binding the target molecule and containing a unique label; and

a second antibody linked to a readout enzyme and capable of binding to the target molecule bound to the bead thereby to form an immunocomplex, wherein each of the plurality of partitions includes exactly one immunocomplex;

introducing a fluorogenic substrate to the immunocomplex in each partition; and

simultaneously detecting in each partition a fluorescent signal produced in said introducing step, and an optical signal from the unique label.

2. The method of claim 1 , wherein the fluorogenic substrate is exposed to horseradish peroxidase.

3. The method of claim 1 , wherein the target molecule is a single biological molecule.

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

5. The method of claim 1 , wherein each of the plurality of partitions of fluid are separated from one another by a fluid immiscible with the fluid sample.

6. The method of claim 5 , wherein the immiscible fluid is a fluorocarbon oil comprising a fluorosurfactant that includes perfluorinated polyether (PFPE).

7. The method of claim 1 , wherein the readout enzyme is horseradish peroxidase.

8. The method of claim 1 , wherein the plurality of partitions comprise a respective plurality of beads that each include a unique optical label in the bead that provides the optical signal, wherein the optical labels are dyes at concentrations that increase from one label to the next.

9. The method of claim 1 , wherein the immunocomplex is an ELISA sandwich.

10. A method for detecting a protein, the method comprising:

introducing a test fluid into partitions from an antibody library, wherein each partition comprises an optically-labeled, substrate-bound first antibody against a target antigen and an enzyme-linked second antibody against the target antigen;

forming at least one immunocomplex with the first and the second antibodies;

recovering beads from the partitions;

washing the beads;

isolating individual beads into ELISA assay droplets;

converting, by an enzyme of the enzyme-linked second antibody, fluorogenic substrate into a fluorescent signal in one droplet of the ELISA assay droplets; and

simultaneously reading from the one droplet the fluorescent signal and an optical signal from the optically-labeled, substrate-bound first antibody, wherein the optical signal uniquely identifies the first antibody.

11. The method of claim 10 , wherein the isolating step includes flowing the beads onto a microfluidic device at a low concentration of limiting dilution conditions result so that most of the ELISA assay droplets will contain zero beads and most bead-containing ELISA assay droplets will have only one bead.

12. The method of claim 10 , wherein the ELISA assay droplets comprise aqueous droplets in an immiscible fluorocarbon oil comprising a fluorosurfactant that includes perfluorinated polyether (PFPE).

13. The method of claim 10 , wherein the enzyme-linked second antibody comprises a readout enzymes and wherein the readout enzyme is horseradish peroxidase.

14. The method of claim 10 , wherein each bead includes an optical label in the bead that provides the optical signal.

15. The method of claim 14 , wherein the optical labels are dyes at concentrations that increase from one label to the next.

16. The method of claim 10 , wherein, during the reading step, each ELISA assay droplet comprises an ELISA sandwich.