Comprehensive two-dimensional gas chromatography/time-of-flight mass spectrometry peak sorting algorithm

Abstract

We report a novel peak sorting method for the two-dimensional gas chromatography/time-of-flight mass spectrometry (GC×GC/TOF-MS) system. The objective of peak sorting is to recognize peaks from the same metabolite occurring in different samples from thousands of peaks detected in the analytical procedure. The developed algorithm is based on the fact that the chromatographic peaks for a given analyte have similar retention times in all of the chromatograms. Raw instrument data are first processed by ChromaTOF (Leco) software to provide the peak tables. Our algorithm achieves peak sorting by utilizing the first and second dimension retention times in the peak tables and the mass spectra generated during the process of electron impact ionization. The algorithm searches the peak tables for the peaks generated by the same type of metabolite using several search criteria. Our software also includes options to eliminate non-target peaks from the sorting results, e.g., peaks of contaminants. The developed software package has been tested using a mixture of standard metabolites and another mixture of standard metabolites spiked into human serum. Manual validation demonstrates high accuracy of peak sorting with this algorithm.

Qualitative and quantitative approaches in comprehensive two-dimensional gas chromatography

“…Recent advances in commercial instrumentation have decreased retention time shift. There have been many reports of retention time shift algorithms and peak alignment methods to correct retention time shift [48,[104][105][106]. Almstetter et al incorporated standards in each sample in order to adjust for retention time shifts in both dimensions [55,107].…”

Features for non-targeted cross-sample analysis with comprehensive two-dimensional chromatography

“…Analyzing human serum with GC ×GC-TOFMS, Oh et al [87] developed a peak sorting method to recognize peaks from the same metabolite in different chromatograms. Their algorithm used several search criteria with retention times and mass spectra, with options to eliminate non-target peaks.…”

Generic Software Frameworks for GC-MS Based Metabolomics

“…Usually, for a one-hour run, the raw data file size exceeds a few Gigabytes. Quite a number of algorithms have been published on alignment of peaks in such four-dimensional (first column retention time, second column retention time, mass, and intensity values) data (Kim et al, 2011;Oh et al, 2008;Pierce et al, 2005;Vial et al, 2009;Zhang, 2010), however only a few methods are available for a more complete typical preprocessing workflow. A compact overview of the available frameworks, their licenses and programming languages is given in Table 3.…”