SIMAT: GC-SIM-MS Analysis Tool
M. R. Nezami Ranjbar
Selected Ion Monitoring
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?
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
The SIMAT paper is freely available on BMC Bioinformatics. Please cite SIMAT as:
The package is available on Bioconductor,
where it can be installed by running the commands below in R:
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.
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.
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:
|Contact: Please send comments or questions to nranjbar AT vt DOT edu by including "SIMAT" in the subject.|