A method for detecting a plurality of different target nucleic acids in a sample, wherein each target nucleic acid comprises a first target domain adjacent to a second target domain and a third target capture domain located upstream or downstream from said first and second target domains, said method comprising: (a) providing a plurality of ligation substrates each comprising: (i) one of said target nucleic acids; (ii) a first set of ligation probes comprising: a first nucleic acid ligation probe comprising: a first probe domain hybridized to a first target domain of said one target nucleic acid sequence; a 5'-ligation moiety; and a second nucleic acid ligation probe comprising: a second probe domain hybridized to a second target domain of said one target nucleic acid sequence; and a 3' ligation moiety; (b) ligating said first and second ligation probes without the use of a ligase enzyme to form a first plurality of ligation products; (c) hybridizing target capture probes comprising a capture moiety to said third target domain of said target nucleic acids to form target complexes; (d) capturing said target complexes on a surface using said capture moiety; (e) amplifying said ligation products to form amplicons; (f) detecting said amplicons, thereby detecting said target nucleic acids. (a) providing a plurality of ligation substrates each comprising: (i) one of said target nucleic acids; (ii) a first set of ligation probes comprising: a first nucleic acid ligation probe comprising: a first probe domain hybridized to a first target domain of said one target nucleic acid sequence; a 5'-ligation moiety; and a second nucleic acid ligation probe comprising: a second probe domain hybridized to a second target domain of said one target nucleic acid sequence; and a 3' ligation moiety; (i) one of said target nucleic acids; (ii) a first set of ligation probes comprising: a first nucleic acid ligation probe comprising: a first probe domain hybridized to a first target domain of said one target nucleic acid sequence; a 5'-ligation moiety; and a second nucleic acid ligation probe comprising: a second probe domain hybridized to a second target domain of said one target nucleic acid sequence; and a 3' ligation moiety; a first nucleic acid ligation probe comprising: a first probe domain hybridized to a first target domain of said one target nucleic acid sequence; a 5'-ligation moiety; and a first probe domain hybridized to a first target domain of said one target nucleic acid sequence; a 5'-ligation moiety; and a second nucleic acid ligation probe comprising: a second probe domain hybridized to a second target domain of said one target nucleic acid sequence; and a 3' ligation moiety; a second probe domain hybridized to a second target domain of said one target nucleic acid sequence; and a 3' ligation moiety; (b) ligating said first and second ligation probes without the use of a ligase enzyme to form a first plurality of ligation products; (c) hybridizing target capture probes comprising a capture moiety to said third target domain of said target nucleic acids to form target complexes; (d) capturing said target complexes on a surface using said capture moiety; (e) amplifying said ligation products to form amplicons; (f) detecting said amplicons, thereby detecting said target nucleic acids.