Digital protein quantification

1. A method for generating a plurality of mixture partitions, the method comprising:

(i) providing a plurality of fixed and permeabilized single cells;

(ii) incubating the plurality of single cells with a library of at least 10 structurally distinct antibodies that have a specific binding affinity for target epitopes of cellular proteins, wherein each of the at least 10 antibodies is conjugated to a different epitope-specific oligonucleotide comprising a barcode sequence that identifies the target epitope, a unique molecular identifier (UMI), a first primer binding sequence, and a second primer binding sequence, wherein the incubating results in binding of the antibodies to their corresponding epitopes, if present, to form antibody-epitope complexes;

(iii) washing away unbound antibodies;

(iv) partitioning, after the incubating and washing steps, the plurality of fixed and permeabilized single cells into a plurality of mixture partitions; and

(v) providing a plurality of partition-specific oligonucleotides to each mixture partition, wherein each partition-specific oligonucleotide comprises a different barcode sequence and a primer binding sequence that is complementary to the first primer binding sequence of the epitope-specific oligonucleotides,

wherein each partition-specific oligonucleotide is covalently linked to a bead.

2. The method of claim 1 , wherein the method comprises incubating the plurality of single cells with the library of at least 10, and no more than about 10,000, structurally distinct antibodies conjugated to the epitope-specific oligonucleotides.

3. The method of claim 1 , wherein the method comprises performing (iv) before (v), and the partition-specific oligonucleotides are partitioned into a plurality of mixture partitions comprising the antibody-epitope complexes.

4. The method of claim 1 , wherein the method comprises performing (v) before (iv), and the antibody-epitope complexes are partitioned into a plurality of mixture partitions comprising the partition-specific oligonucleotides.

5. The method of claim 1 , wherein step (iv) comprises discarding mixture partitions that do not contain a single cell and/or contain multiple cells.

6. The method of claim 1 , wherein step (v) comprises discarding mixture partitions that do not contain a single partition-specific oligonucleotide and/or contain multiple partition-specific oligonucleotides.

7. The method of claim 1 , wherein the partition-specific oligonucleotides are covalently linked to a bead with a cleavable linker.

8. The method of claim 1 , wherein the cells are lysed.

9. The method of claim 1 , wherein the plurality of mixture partitions comprise a primer that binds to the second primer binding sequence.