SIMAT

SIMAT is an R package for quantitative analysis of targeted analytes in gas chromatography-selected ion monitoring-mass spectrometry (GC-SIM-MS) data. It provides a comprehensive set of tools to facilitate the analysis process, including:

1. Fragment selection: SIMAT guides users in choosing optimal fragments for targeted analytes using an optimization algorithm that selects the most appropriate fragments from overlapping chromatographic peaks based on a pre-specified library of background analytes.

2. Data visualization: The package allows users to visualize total ion chromatograms (TIC) of runs and extracted ion chromatograms (EIC) of analytes of interest, facilitating data interpretation and quality control.

3. Retention index calibration: SIMAT enables retention index (RI) calibration, which is essential for accurately identifying analytes.

4. Data import: Raw GC-SIM-MS data can be imported in netCDF or NIST mass spectral library (MSL) formats, making it compatible with various instruments and data formats.

5. Data preprocessing: SIMAT implements various functions and algorithms to perform GC-SIM-MS data preprocessing, ensuring data quality and consistency.

SIMAT offers an alternative to existing software tools like AMDIS and MetaboliteDetector for accurately detecting targets and estimating their relative intensities in GC-SIM-MS data.