SIMAT: GC-SIM-MS Analysis Tool

By: M. R. Nezami Ranjbar

Selected Ion Monitoring

Gas chromatography coupled with mass spectrometry (GC-MS) is one of the promising technologies for qualitative and quantitative analysis of small biomolecules. Because of the existence of spectral libraries, GC-MS instruments can be set up efficiently for targeted analysis. Also, to increase sensitivity, samples can be analyzed in selected ion monitoring (SIM) mode. While many software have been provided for analysis of untargeted GC-MS data, no specific tool does exist for processing of GC-MS data acquired with SIM.

What is SIMAT?

SIMAT is a tool for analysis of GC-MS data acquired in SIM mode. The tool provides several functions to import raw GC-SIM-MS data and standard format mass spectral libraries. It also provides guidance for fragment selection before running the targeted experiment in SIM mode by using optimization. This is done by considering overlapping peaks from a library provided by the user. Other functionalities include retention index calibration to improve target identification and plotting EICs of individual peaks in specific runs which can be used for visual assessment.

SIMAT Capabilities:

  • Processing gas chromatography coupled with mass spectrometry data acquired in selected ion monitoring (SIM) mode.
  • Peak detection and identification.
  • Similarity score calculation.
  • Retention index (RI) calibration.
  • Reading NIST mass spectral library (MSL) format.
  • Importing netCDF raw files.
  • EIC and TIC visualization
  • Providing guidance in choosing appropriate fragments for the targets of interest by using an optimization algorithm.


    The SIMAT paper is freely available on BMC Bioinformatics. Please cite SIMAT as:

    Nezami Ranjbar M.R., Di Poto C., Wang Y., Ressom H.W., "SIMAT: GC-SIM-MS data analysis tool," BMC Bioinformatics, 2015, 16:259.



    R package:

    The package is available on Bioconductor, where it can be installed by running the commands below in R:



    Example Data Sets

    QC Runs:

    A set of 5 quality control (QC) runs are provided. These runs acquired using SIM mode. A list of targets in MSL format is also included. The list can be used to find the corresponding peaks in the runs. The data set, i.e. raw netCDF files and the list of targets, can be downloaded as a single archive.

    Standard Mixtures:

    A set of 39 runs consist of 3 replicates of 13 levels of 5 spiked-in internal standards acquired in SIM mode. Starting from the highest concentration to the lowest, each level is half of its predecessor. Also, one full scan run is included for quality control purpose. Therefore, the list of targets, includes the 5 standards and is provided in MSL format. The data set, i.e. raw netCDF files and the list of targets, can be downloaded as a single archive.

    Code Examples

    A list of examples can be found in this PDF document. For more, please refer to the examples included in the help files of the functions which can be accessed through R help retrieval after installing the package. To dowload and use data sets in R:

    # download an example data set
    URL <- ""
    destfile <- ""
    download.file(url = URL, destfile = destfile)

    # unzip the data set

    # read CDF files <- readCDF(path = "./ExampleDataSet_1")

    # get the list of targets in a file with MSL format from Example Data Set 1
    Targets1 <- readMSL("Targets_1.MSL", path="./ExampleDataSet_1")

    # read target table information form file
    target.table <- getTargetTable( = "TargetTable.txt", path = "./ExampleDataSet_1")

    # read RItable from file
    RItable <- getRIStandard( = "RIStandards.csv", path = "./ExampleDataSet_1")
    Contact: Please send comments or questions to nranjbar AT vt DOT edu by including "SIMAT" in the subject.