PYQUAN: A rapid workflow around the AMDIS deconvolution software for high throughput analysis of pyrolysis GC/MS data

•This paper describes an approach to automate the analysis of complex py-GC/MS data.•PYQUAN is free and user-friendly software.•It contains visual control during each step of the analysis.•It allows the identification and quantification of peaks with similar mass spectrum less than 10 s apart.•On a regular pc, the quantification of 2000 peaks takes less than 10 min.

Pyrolysis-GC/MS is a powerful technique to characterize soil organic matter. Most samples produce a high number of peaks in chromatograms, many of them overlapping, which complicates data analysis. In order to facilitate the speed and ease of analysis, we have developed an automated workflow that enables us to rapidly identify and quantify peaks from (pyrolysis-)GC/MS data. It is based on identification by the software program AMDIS, followed by peak deconvolution and quantification using our own developed, user-friendly, Python script. Visual inspection of each peak and the possibility to re-quantify individual peaks with adjusted parameters are included in the Python script as well. We applied this workflow to a series of dissolved organic matter samples with increasing glucose concentrations. More than 97% of the peaks were automatically correctly identified and quantified, including compounds with nearly similar spectra and RTs less than 10 s apart.