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Data Analysis

After firing the SpectroCHIP on the MassArray, the Molecular Diagnostics Laboratory staff will analyze the raw mass spectrometry data utilizing Sequenom’s TYPER Analyzer software. Based upon the mass of the unextended primer for each assay, the software will determine which terminator was added to the primer and will assign a call (A/T/C/G). If no DNA template was present or the initial PCR amplification step failed, only the unextended primer will be detected. The mass spectrum for each assay can be viewed using the Typer Anlayzer Software.

Example Mass Spectrum of a Somatic Mutation Assay

data analysis

The Molecular Diagnostics staff will perform an initial analysis of the data and generate a text file containing the frequency of each allele and call for every assay utilizing the TYPER Analyzer Software. For suspected SNPs or mutations, our scientists will view the mass spectra data to verify the call. If the call is a suspected false positive result, we will make every attempt to note our observations in the text file.

Both the text file containing the frequency data and calls as well as an “.xml” file containing the raw data will be uploaded to the experiment folder in GNomEx. To download the data, open the experiment folder in GNomEx and click the “files” tab and select download files. The “.xml” file can only be opened with the TYPER Analyzer Software. The molecular Diagnostics laboratory has a workstation with the software available for customers who would like to view and analyze their own data.


Due to the complexities of the iPlex Chemistry and mass spectrometry based detection, the Molecular Diagnostics laboratory CANNOT guarantee the accuracy of the data and will not be held liable for false positive or negative results. We strongly encourage users to analyze their own data utilizing the TYPER software. In addition, we CANNOT guarantee every assay will yield useable data due to variables beyond our control, such as DNA quality, primer design, proximal SNPs, etc.