A method for multiplexed detection of nucleic acid targets in a sample comprising: (a) combining in a chamber a sample, a plurality of primer pairs for priming amplification of nucleic acid targets in the sample, a plurality of first probes immobilized on a plurality of encoded particles such that the identity of each first probe is known from the encoded particle on which it is immobilized, wherein the first probes are optionally labeled with a fluorophore, and a plurality of second probes complementary to the plurality of first probes, wherein the second probes (i) are labeled with a fluorophore or a quencher, and (ii) are not immobilized on the plurality of encoded particles; (b) forming amplification products in the chamber for each of the nucleic acid targets amplified with the plurality of primer pairs; (c) measuring a signal over time from the encoded particles and a signal over time from the label of the second probes hybridized to the first probes immobilized on the encoded particles, wherein the encoded particles are immobilized on a surface of the chamber, and wherein a change in the signal from the label of the second probes hybridized to the first probes immobilized on the encoded particles indicates the presence of the target nucleic acids; and (d) detecting the presence or absence of the nucleic acid targets in the sample based on the change in the signal from the label of the second probes hybridized to the first probes immobilized on the encoded particles; wherein the first probes exhibit less favorable binding and lower melting temperature with the second probes compared to the second probes with the nucleic acid targets, or the first probes exhibit favorable binding of the target sequence compared to the binding kinetics of the target sequence with the second probes. (a) combining in a chamber a sample, a plurality of primer pairs for priming amplification of nucleic acid targets in the sample, a plurality of first probes immobilized on a plurality of encoded particles such that the identity of each first probe is known from the encoded particle on which it is immobilized, wherein the first probes are optionally labeled with a fluorophore, and a plurality of second probes complementary to the plurality of first probes, wherein the second probes (i) are labeled with a fluorophore or a quencher, and (ii) are not immobilized on the plurality of encoded particles; (b) forming amplification products in the chamber for each of the nucleic acid targets amplified with the plurality of primer pairs; (c) measuring a signal over time from the encoded particles and a signal over time from the label of the second probes hybridized to the first probes immobilized on the encoded particles, wherein the encoded particles are immobilized on a surface of the chamber, and wherein a change in the signal from the label of the second probes hybridized to the first probes immobilized on the encoded particles indicates the presence of the target nucleic acids; and (d) detecting the presence or absence of the nucleic acid targets in the sample based on the change in the signal from the label of the second probes hybridized to the first probes immobilized on the encoded particles;