A method for determining the spatial location of a nucleic acid and a protein in a biological sample comprising: a) providing a spatial array comprising a first and second plurality of capture probes, wherein each of the first and second plurality of capture probes comprises a spatial barcode and a capture domain, b) contacting the spatial array with the biological sample, c) contacting the biological sample with (i) a plurality of analyte capture agents, wherein an analyte capture agent of the plurality of analyte capture agents comprises a protein binding moiety and an oligonucleotide comprising a protein binding moiety barcode and an analyte capture sequence, wherein the analyte capture sequence comprises a sequence complementary to the capture domain of the second plurality of capture probes, and (ii) a plurality of templated ligation probes, wherein one of the templated ligation probes comprises a sequence complementary to the capture domain of the first plurality of capture probes, d) binding the protein binding moiety of the analyte capture agent to a target protein, e) hybridizing the plurality of templated ligation probes to a target nucleic acid and ligating the hybridized templated ligation probes to produce a templated ligation product, f) hybridizing: (i) the templated ligation product to the capture domain of the first plurality of capture probes and (ii) the analyte capture sequence of the bound analyte capture agent to the capture domain of the second plurality of capture probes on the spatial array, and g) determining: (i) the sequence or a portion thereof of the captured templated ligation product, or a complement thereof, and the sequence of the spatial barcode of the first plurality of capture probes, or a complement thereof, that is associated with the templated ligation product, and (ii) the sequence of the protein binding moiety barcode, or a complement thereof, of the bound analyte capture agent, and the sequence of the spatial barcode of the second plurality of capture probes, or a complement thereof, that is associated with the analyte capture agent, thereby determining the spatial location of the nucleic acid and the protein in the biological sample. a) providing a spatial array comprising a first and second plurality of capture probes, wherein each of the first and second plurality of capture probes comprises a spatial barcode and a capture domain, b) contacting the spatial array with the biological sample, c) contacting the biological sample with (i) a plurality of analyte capture agents, wherein an analyte capture agent of the plurality of analyte capture agents comprises a protein binding moiety and an oligonucleotide comprising a protein binding moiety barcode and an analyte capture sequence, wherein the analyte capture sequence comprises a sequence complementary to the capture domain of the second plurality of capture probes, and (ii) a plurality of templated ligation probes, wherein one of the templated ligation probes comprises a sequence complementary to the capture domain of the first plurality of capture probes, (i) a plurality of analyte capture agents, wherein an analyte capture agent of the plurality of analyte capture agents comprises a protein binding moiety and an oligonucleotide comprising a protein binding moiety barcode and an analyte capture sequence, wherein the analyte capture sequence comprises a sequence complementary to the capture domain of the second plurality of capture probes, and (ii) a plurality of templated ligation probes, wherein one of the templated ligation probes comprises a sequence complementary to the capture domain of the first plurality of capture probes, d) binding the protein binding moiety of the analyte capture agent to a target protein, e) hybridizing the plurality of templated ligation probes to a target nucleic acid and ligating the hybridized templated ligation probes to produce a templated ligation product, f) hybridizing: (i) the templated ligation product to the capture domain of the first plurality of capture probes and (ii) the analyte capture sequence of the bound analyte capture agent to the capture domain of the second plurality of capture probes on the spatial array, and g) determining: (i) the sequence or a portion thereof of the captured templated ligation product, or a complement thereof, and the sequence of the spatial barcode of the first plurality of capture probes, or a complement thereof, that is associated with the templated ligation product, and (ii) the sequence of the protein binding moiety barcode, or a complement thereof, of the bound analyte capture agent, and the sequence of the spatial barcode of the second plurality of capture probes, or a complement thereof, that is associated with the analyte capture agent, thereby determining the spatial location of the nucleic acid and the protein in the biological sample.