ADAP-GC 3.0: Improved Peak Detection and Deconvolution of Co-eluting Metabolites from GC/TOF-MS Data for Metabolomics Studies

ADAP-GC is an automated computational
pipeline for untargeted,
GC/MS-based metabolomics studies. It takes raw
mass spectrometry data as input and carries out a sequence of data
processing steps including construction of extracted ion chromatograms,
detection of chromatographic peak features, deconvolution of coeluting
compounds, and alignment of compounds across samples. Despite the
increased accuracy from the original version to version 2.0 in terms
of extracting metabolite information for identification and quantitation,
ADAP-GC 2.0 requires appropriate specification of a number of parameters
and has difficulty in extracting information on compounds that are
in low concentration. To overcome these two limitations, ADAP-GC 3.0
was developed to improve both the robustness and sensitivity of compound
detection. In this paper, we report how these goals were achieved
and compare ADAP-GC 3.0 against three other software tools including
ChromaTOF, AnalyzerPro, and AMDIS that are widely used in the metabolomics
community.