TaqMan® Multiplex Real-Time (qPCR) Solutions

New multiplex qPCR solution helps you get more data from your samples

Multiplex qPCR is a simple, efficient, and cost effective solution for overcoming the challenges of limited samples and costly analysis. Successful multiplex qPCR enables the amplification of more than one target in a single reaction using different reporters with distinct fluorescent spectra and making it possible for you to use less of your precious samples in each experiment.

We are proud to offer a complete multiplex qPCR solution that enables you to perform up to a 4-plex reaction for gene expression and a duplex reaction for genotyping analysis. Our solution includes up to four dyes optimized to work together with minimal spectral overlap, a TaqMan™ custom probe with a new QSY™ quencher, a range of qPCR master mixes, and spectral calibration plates. These, combined with our custom services and real-time PCR instruments and software, decrease the amount of time required to optimize your multiplex qPCR.

Add more color to your gene expression & genotyping experiments ›
TaqMan QSY Probes flyer

Learn more about the nonfluorescent  QSY quencher available for multiplexing projects.

Benefits to multiplexing

Multiplex qPCR allows you to get more information out of a single reaction. This is particularly important when your sample input is limited or when you need to minimize sample-analysis costs. 

Multiplexing provides a way to reduce reaction costs by as much as 40%. The relative costs for the multiplex reaction are much closer to those for a singleplex reaction and offer substantial savings when compared to the costs of performing 4 singleplex reactions independently. 

Design your own multiplex qPCR primers and probes

The TaqMan Multiplex solution consists of five components: 

ABY™ and JUN™ dyes, combined with FAM™ and VIC™ dyes, provide a set of four dyes whose spectral wavelengths are closely aligned with the filter channels found on Applied Biosystems™ instruments.

multiplex qPCR
Figure 1: Fluorescence emission spectra of different dyes used for multiplex qPCR.

The TaqMan quencher, QSY, is now available for optimal high-level multiplexing with best performance in 3 and 4-plex reactions. 


Applied Biosystems™ TaqMan™ Multiplex Master Mix, TaqPath™ 1-Step Multiplex Master Mix* , and TaqPath™ ProAmp™ Master Mixes* are formulated to allow all amplifications to proceed despite the competition between reactions. They contain Mustang Purple™ dye, a passive reference dye that is used for normalization in place of ROX™ dye. No-ROX versions are also available.

Multiplexing Master Mix

Calibration plates are available in different formats, and are suitable for use with the following real-time PCR systems: the QuantStudio™ instrument portfolio, the ViiA™ 7 system, and the 7500 and 7500 Fast real-time PCR systems. 

TaqMan QSY Assays use JUN and ABY dyes to measure the expression of the GAPDH and RNase P genes. These assays are also available in a primer-limited format for your convenience. Run control assays and experimental assays in the same well. 

Workflow to develop and optimize your multiplex reaction

Determine your probe options 

When starting a new project, we recommend designing your assays using TaqMan QSY probes and the FAM, VIC, ABY, or JUN reporter dyes. See the TaqMan Multiplex Optimization guide for design recommendations and advice on optimizing your multiplex qPCR experiments.

Redesign and order assays, primers, and probes

Redesign: Use Primer Express™ software and TaqMan Multiplex Optimization guide recommendations to design primers and TaqMan QSY probes, or contact Custom Services to redesign your assays (additional fees apply). 

Reorder: We recommend ordering primers and probes separately, as individual oligonucleotides and probes, to facilitate the optimization of your multiplex qPCR experiments. 

Contact Custom Services if you need information to reorder assays with alternate dyes, or if your require assistance to redesign your assays with TaqMan QSY probes (additional fees apply). 

Choose and order the appropriate master mix 

Use TaqMan Multiplex Master Mix or for 1-step reactions choose TaqPath 1-Step Multiplex Master Mix .


Once you have the reagents necessary for your multiplex qPCR experiment, you can use the TaqMan Multiplex Optimization guide to optimize your gene expression and genotyping experiments. 

*For Laboratory Use. General purpose reagent.