Quantitative Gene Expression Analysis

MassARRAY Compact

Company Profile

SEQUENOM is committed to providing the best genetic analysis products that translate genomic science into superior solutions for molecular medicine and biomedical research. The cornerstone of SEQUENOM's approach is the Company's proprietary MassARRAY® system, a high-performance DNA analysis platform, which efficiently and precisely measures the amount of genetic target material and variations. The system is able to deliver reliable and specific data from complex biological samples and from trace amounts of genetic target material.

Contact Info

3595 John Hopkins Court, San Diego, CA 92121-1331
Phone (858) 202-9000 Fax (858) 202-9001

Mendelssohnstrasse 15D, D-22761, Hamburg, Germany
Phone (+49) 40-899676-0 Fax (+49) 40-899676-10


Quantitative Gene Expression Analysis Overview

MassARRAY QGE from Sequenom combines Competitive PCR with MALDI-TOF mass spectrometry (MS) analysis to offer a highly accurate, sensitive, and high-throughput method for the quantitative analysis of gene expression in multiple samples. MassARRAY QGE is scalable, allowing you to perform assays without compromising, accuracy, sensitivity, or reproducibility, thus solving the “multi-plate replication gap” seen with other quantitative gene expression technologies. In addition, the MassARRAY method does not use chemiluminescence, fluorescence or other secondary-labeling approaches, allowing unambiguous multiplexing and the inclusion of multiple normalization standards in each assay.

MassARRAY QGE is the method of choice over real-time PCR for validation of microarray data, for the investigation of coding and noncoding transcripts – and whenever sensitivity and accuracy are required in transcription analysis.

  • Instrumentation The foundation of the MassARRAY system is the MassARRAY MALDI-TOF mass spectrometer. Several system options are available depending on throughput requirements. Sequenom developed the MassARRAY MALDI-TOF MS Analyzer systems to specifically meet the requirements of moderate to high throughput quantitative genetic analysis. Accurate analysis is ensured by the configuration of the MassARRAY MS optics and the 384-pad SpectroCHIP. The mass of each primer extension product is resolved using the Time-of-Flight (TOF) tube on the MassARRAY MALDI-TOF MS. The separated masses are analyzed in the MS using MassARRAY QGE software.


  • Software The accuracy, sensitivity and automation of the MassARRAY QGE system are enabled and optimized by the MassARRAY software. The software includes AssayDesigner for PCR and hME primer and competitor oligonucleotide design and Typer™ software for data analysis, management and reporting functions. The QGE software package contains full data analysis and management capabilities built on an Oracle data management system.


  • Reagents The MassARRAY QGE method uses robust, familiar biochemistry: Competitive PCR and the hME primer extension reaction. The oligonucleotides used in these assays are unlabeled synthetic oligonucleotides that can be ordered from your own supplier or through Assays-by-Sequenom. In addition, Sequenom can serve as a your source for process-tested enzymes and reagents, or you can continue to use your current trusted suppliers for quality reagents. (Check with us for process approved reagents and enzymes.)

QGE Screen Shot
MassARRAY QGE data collection and analysis is fully software supported. The user interface can be formatted by each user to display different views pertaining to data analysis. Experiment data is exportable as a text file for analysis in third party gene expression software.


Conc Chart
MassARRAY QGE quantifies cDNA over a wide concentration range with a low RSD, independent of concentration.

Download Application Notes

Features and Benefits

Competitive PCR
• Internal standard in every assay • High precision, CV <3%
• Wide dynamic range; nM to aM
• Relative and absolute quantitation capable
• Short amplicons enable use of trace and degraded
• RNA samples
Separate PCR and Analysis Steps
• End-reaction assay methodology
• Quantitation independent of PCR kinetics
• Highest sensitivity – measures single molecule range
• Sensitive down to 1 – 10 cell range
• Measure as low as 10% change in relative gene expression
• Automated for higher throughput
• Multiple assay plates can be standardized and normalized
Mass Spectrometry Analysis 
• TOF tube provides HPLC-like product separation
• for every assay
• Single assay multiplex genes of interest and normalizing
• HKG genes
• All genes of interest can be analyzed – any organism
• Uses unlabeled oligonucleotides
• Multiple plate technology – ideal for microarray validation
Flexible Assay Design
• Complete user control
• AssayDesigner software
• Validated assays through Assays-by-Sequenom option
• Allele-specific gene expression analysis
• Analyze transcription of individual members of multigene
• families
• Analyze alternate splice-sites
• Take advantage of exon-exon junction sequence
• information for mRNA specificity

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