MassARRAY system occupies an important position in SNP typing, and it is a cost-effective mid-to-high-throughput SNP typing detection system on the market. This technology has been widely used in genetic mutation detection, routine genetic analysis, linkage studies, and subsequent validation of GWAS studies. Various applications such as SNP, DNA methylation, gene expression quantification, and sequence alignment can be analyzed by MassARRAY.

CD Genomics uses the MassARRAY system to provide you with efficient and cost-effective SNP genotyping.

The principle and process of MassARRAY technology

The MassARRAY system is based on MALDI-TOF mass spectrometry. The PCR amplified product was added with SNP sequence-specific extension primers to extend 1 base at the SNP site. The prepared sample analytes are then co-crystallized with the matrix of the chip. The crystal is placed into the vacuum tube of the mass spectrometer and then excited by an instantaneous nanosecond (10-9 s) laser. Due to the energy absorbed by the matrix molecules through radiation, energy is accumulated and heat is rapidly generated, thereby sublimating the matrix crystals. Nucleic acid molecules will desorb and transform into metastable ions, and the ions generated are mostly single-charged ions. These individual charged ions obtain the same kinetic energy in the acceleration field and are separated according to their mass charge ratio in the non-electric field drift region. The smaller the ion mass, the faster it reaches the detector.

The principle and process of MassARRAYFigure 1. The principle and process of MassARRAY. (Busó et al, 2016)

Advantages of MassARRAY service

  • Reliable and accurate: This method is based on the combination of PCR and mass spectrometry. The principle is classic and simple, and the instrument is stable and sensitive. The test standard is quality change.
  • High sample throughput: This method can perform multiple detection of 384 samples on a single chip, and each reaction well can achieve up to 40 reactions, and can analyze up to 100,000 genotypes per day.
  • More flexible: NGS must gather enough sample numbers to make full use of the amount of data obtained on each machine. From the perspective of data amount, Massarray does not have the minimum sample number required for a single test. Ability to quickly and easily modify an existing panel.
  • Low cost per SNP.
  • MassARRAY system can be used to analyze SNP, DNA methylation, gene expression quantification, and sequence alignment.

Workflow of MassARRAY service

Workflow of MassARRAY service

Sample Requirements

  • Tissue sample (≥ 100mg)
  • Cultured cells in vitro (≥ 106 cells).
  • Genomic DNA* (For each SNP-plex reaction, 5-10 μl of 25-50 ng/uL genomic DNA is required). OD260/280 = 1.7 ~ 2.0, no degradation or RNA contamination.
  • Whole blood (≥ 0.2ml).
  • Saliva (≥ 0.5ml).
  • Formalin-fixed, paraffin-embedded (FFPE) samples are available.
  • *DNA can be submitted to 96-well or 384-well plates with at least two open holes for every 384 negative controls.

Want to know about other Non-NGS gene mutation detection methods?


  1. Busó E J, Iborra M. Sequenom MassARRAY Technology for the Analysis of DNA Methylation: Clinical Applications//Epigenetic Biomarkers and Diagnostics. Academic Press, 2016: 137-153.
  2. Ellis J A, Ong B. The MassARRAY® System for targeted SNP genotyping//Genotyping. Humana Press, New York, NY, 2017: 77-94.
* For Research Use Only. Not for use in diagnostic procedures.

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