The present disclosure provides methods and systems for detecting multiple different nucleotides in a sample. In particular, the disclosure provides for detection of multiple different nucleotides in a sample utilizing fewer detection moieties than the number of nucleotides being detected and/or fewer imaging events than the number of nucleotides being detected. Disclosed is also a reversibly blocked nucleotide conjugate, which is indirectly labelled with a hapten attached via a linker to the nucleobase, wherein the hapten is detectable by a binding partner-fluorescent moiety conjugate.