A method for detecting a plurality of analytes in a sample, comprising: a. contacting the sample with a composition comprising a plurality of detection reagents, wherein each subpopulation of the detection reagents targets at least one different analyte, wherein the analyte is fixed on a solid substrate or support and wherein the solid substrate or support is a chip, a microarray, a blotting membrane or a microscopic slide, and wherein each detection reagent comprises: at least one probe reagent targeting an analyte and at least one nucleic acid label comprising a plurality of pre-determined subsequences, wherein said at least one probe reagent and said at least one nucleic acid label are conjugated together; and wherein at least a portion of said plurality of pre-determined subsequences form an identifier of said at least one probe reagent; b. removing any unbound detection reagents; c. detecting in a temporally-sequential manner said plurality of pre-determined subsequences of said detection reagent, wherein said detection of the subsequences comprises: i) hybridizing a set of decoder probes with a subsequence of the detection reagents, wherein each subpopulation of said decoder probes comprises an optical detectable label, each optical detectable label generating an optical signal signature corresponding to each subsequence; ii) detecting said optical signal signature produced upon the hybridization of said set of decoder probes and obtaining an image; iii) removing said optical signal signature produced by the hybridization of said set of decoder probes; iv) repeating steps (i) through (iii) for other subsequences of said detection reagents, thereby producing a temporal order of optical signal signatures corresponding to the plurality of pre-determined subsequences, wherein the temporal order of the optical signal signatures corresponding to said plurality of pre-determined subsequences of said detection reagent identifies a subpopulation of the detection reagents and is unique for each subpopulation of the detection reagents; and d. comparing said temporal order of the optical signal signatures with different identifiers of said at least one probe reagent, wherein an agreement between the temporal order of the optical signal signatures and a particular identifier of said at least one probe reagent identifies the analyte in the sample. a. contacting the sample with a composition comprising a plurality of detection reagents, wherein each subpopulation of the detection reagents targets at least one different analyte, wherein the analyte is fixed on a solid substrate or support and wherein the solid substrate or support is a chip, a microarray, a blotting membrane or a microscopic slide, and wherein each detection reagent comprises: at least one probe reagent targeting an analyte and at least one nucleic acid label comprising a plurality of pre-determined subsequences, wherein said at least one probe reagent and said at least one nucleic acid label are conjugated together; and wherein at least a portion of said plurality of pre-determined subsequences form an identifier of said at least one probe reagent; b. removing any unbound detection reagents; c. detecting in a temporally-sequential manner said plurality of pre-determined subsequences of said detection reagent, wherein said detection of the subsequences comprises: i) hybridizing a set of decoder probes with a subsequence of the detection reagents, wherein each subpopulation of said decoder probes comprises an optical detectable label, each optical detectable label generating an optical signal signature corresponding to each subsequence; ii) detecting said optical signal signature produced upon the hybridization of said set of decoder probes and obtaining an image; iii) removing said optical signal signature produced by the hybridization of said set of decoder probes; iv) repeating steps (i) through (iii) for other subsequences of said detection reagents, thereby producing a temporal order of optical signal signatures corresponding to the plurality of pre-determined subsequences, wherein the temporal order of the optical signal signatures corresponding to said plurality of pre-determined subsequences of said detection reagent identifies a subpopulation of the detection reagents and is unique for each subpopulation of the detection reagents; and i) hybridizing a set of decoder probes with a subsequence of the detection reagents, wherein each subpopulation of said decoder probes comprises an optical detectable label, each optical detectable label generating an optical signal signature corresponding to each subsequence; ii) detecting said optical signal signature produced upon the hybridization of said set of decoder probes and obtaining an image; iii) removing said optical signal signature produced by the hybridization of said set of decoder probes; iv) repeating steps (i) through (iii) for other subsequences of said detection reagents, thereby producing a temporal order of optical signal signatures corresponding to the plurality of pre-determined subsequences, wherein the temporal order of the optical signal signatures corresponding to said plurality of pre-determined subsequences of said detection reagent identifies a subpopulation of the detection reagents and is unique for each subpopulation of the detection reagents; and d. comparing said temporal order of the optical signal signatures with different identifiers of said at least one probe reagent, wherein an agreement between the temporal order of the optical signal signatures and a particular identifier of said at least one probe reagent identifies the analyte in the sample.