MassARRAY Assay Designer 3.1

MassARRAY Assay Designer by Sequenom, Inc. is a specialized software application for creating high‑quality, multiplexed assays for the MassARRAY System. It streamlines the design of PCR and primer‑extension assays for SNP genotyping, somatic mutation detection, and DNA methylation analysis. The software evaluates target sequences, selects primers, and predicts the masses of extension products to ensure clear separation in MALDI‑TOF spectra, helping prevent signal overlap and reducing redesign cycles.

Key capabilities include automated primer selection with constraints for GC content, melting temperature, amplicon length, and secondary structure; checks for nearby variants and repeats; and multiplex optimization to maximize throughput. Users can input sequences or variant lists, review design quality metrics, and generate ready‑to‑run assay panels with export options that integrate into downstream MassARRAY workflows. By combining rigorous quality filters with multiplex‑aware design, MassARRAY Assay Designer helps research and clinical development labs accelerate assay development while maintaining analytical performance and reproducibility.

MassARRAY Assay Designer is developed by Sequenom, Inc.. The most popular version of this product among our users is 3.1.