A method of sequencing selected antibody secreting cells, comprising: segregating a sample, or a portion thereof, into individual compartments, wherein each individual compartment comprises a single cell, wherein the cell is a plasmablast or a plasma cell, the samples comprising a cell or a population of cells, wherein the individual compartment comprises one target polypeptide and one target nucleic acid encoding the target polypeptide, wherein the target polypeptides are antibodies expressed by the cell, the polypeptide capture molecule is an antigen, and the target nucleic acids comprise mRNAs encoding a light chain, mRNAs encoding a heavy chain, mRNAs encoding a CDR, or a combination thereof, wherein the individual compartments comprise origin specific barcodes and polypeptide capture molecules, wherein the origin specific barcodes comprise a unique nucleic acid sequence identifying the individual compartment and the polypeptide capture molecules comprises a capture molecule nucleic acid identifier identifying the polypeptide capture molecule, wherein the origin specific barcodes comprise two or more populations of origin-specific barcodes, a first population comprises a first origin specific barcode type comprising a target nucleic acid binding sequence, and a second population comprises a second origin specific barcode type that comprises a capture molecule nucleic acid identifier binding sequence, wherein for a given individual compartment both the first and second type of origin specific barcode comprise the same or matching unique nucleic acid sequence identifying the individual compartment, wherein the origin specific barcodes are reversibly attached to a solid substrate,; lysing the cell or the population of cells; binding target polypeptides expressed in each individual compartment with the polypeptide capture molecules to generate bound target polypeptide - polypeptide capture molecule complexes; releasing the oligonucleotide barcodes from the solid substrate; labeling expressed target nucleic acids and the capture molecule specific nucleic acid identifiers of the bound polypeptide capture molecules with the origin specific barcodes to generate barcoded expressed target nucleic acids and barcoded polypeptide capture molecules; pooling all of the samples; isolating the target polypeptides; amplifying the barcoded expressed target nucleic acids; detecting the sequence of the barcoded expressed target nucleic acids and barcoded capture molecule nucleic acid identifiers; grouping expressed target nucleic acids and expressed target polypeptides by common origin specific barcodes thereby identifying the types of polypeptide capture molecules bound by expressed target polypeptides in an individual compartment along with target nucleic acids expressed in the same individual compartment. segregating a sample, or a portion thereof, into individual compartments, wherein each individual compartment comprises a single cell, wherein the cell is a plasmablast or a plasma cell, the samples comprising a cell or a population of cells, wherein the individual compartment comprises one target polypeptide and one target nucleic acid encoding the target polypeptide, wherein the target polypeptides are antibodies expressed by the cell, the polypeptide capture molecule is an antigen, and the target nucleic acids comprise mRNAs encoding a light chain, mRNAs encoding a heavy chain, mRNAs encoding a CDR, or a combination thereof, wherein the individual compartments comprise origin specific barcodes and polypeptide capture molecules, wherein the origin specific barcodes comprise a unique nucleic acid sequence identifying the individual compartment and the polypeptide capture molecules comprises a capture molecule nucleic acid identifier identifying the polypeptide capture molecule, wherein the origin specific barcodes comprise two or more populations of origin-specific barcodes, a first population comprises a first origin specific barcode type comprising a target nucleic acid binding sequence, and a second population comprises a second origin specific barcode type that comprises a capture molecule nucleic acid identifier binding sequence, wherein for a given individual compartment both the first and second type of origin specific barcode comprise the same or matching unique nucleic acid sequence identifying the individual compartment, wherein the origin specific barcodes are reversibly attached to a solid substrate,; lysing the cell or the population of cells; binding target polypeptides expressed in each individual compartment with the polypeptide capture molecules to generate bound target polypeptide - polypeptide capture molecule complexes; releasing the oligonucleotide barcodes from the solid substrate; labeling expressed target nucleic acids and the capture molecule specific nucleic acid identifiers of the bound polypeptide capture molecules with the origin specific barcodes to generate barcoded expressed target nucleic acids and barcoded polypeptide capture molecules; pooling all of the samples; isolating the target polypeptides; amplifying the barcoded expressed target nucleic acids; detecting the sequence of the barcoded expressed target nucleic acids and barcoded capture molecule nucleic acid identifiers; grouping expressed target nucleic acids and expressed target polypeptides by common origin specific barcodes thereby identifying the types of polypeptide capture molecules bound by expressed target polypeptides in an individual compartment along with target nucleic acids expressed in the same individual compartment.