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The present invention relates to methods, systems, and kits for detecting, quantifying and/or analyzing a fluid sample comprising molecules or particles at low concentration. In certain embodiments, the methods for detection and/or quantifying analyte molecules in a sample comprise capturing a plurality of analyte molecules on a substrate (eg, an array comprising a plurality of reaction vessels). The substrate may then be exposed to additional reaction components such as at least one binding ligand. The substrate may additionally be exposed to a precursor labeling agent molecule, wherein the precursor labeling agent molecule, in some cases, is converted to a labeling agent molecule, which may be detected, either directly or indirectly, which determination may be related to the presence of and/or may be employed to quantify the analyte molecules. Although the various aspects of the present invention may use a …