Issue 5, 2024

Open-source Python module to automate GC-MS data analysis developed in the context of bio-oil analyses

Abstract

GC-MS (Gas Chromatography-Mass Spectrometry) is widely used to measure the composition of biofuels and complex organic mixtures. However, the proprietary GC-MS software associated with each instrument is often clunky and cannot quantify compounds based on similarity indices. Beyond slowing individual research group's efforts, the lack of universal free software to automatically process GC-MS data hampers field-wide efforts to improve bio-oil processes as data are often not comparable across research groups. We developed “gcms_data_analysis,” an open-source Python tool that automatically: (1) handles multiple GCMS semi-quantitative data tables (whether derivatized or not), (2) builds a database of all identified compounds and relevant properties using PubChemPy, (3) splits each compound into its functional groups using a published fragmentation algorithm, (4) applies calibrations and/or semi-calibration using Tanimoto and molecular weight similarities, and (5) produces multiple different reports, including one based on functional group mass fractions in the samples. The module is available on PyPI (https://pypi.org/project/gcms-data-analysis/) and on GitHub (https://github.com/mpecchi/gcms_data_analysis).

Graphical abstract: Open-source Python module to automate GC-MS data analysis developed in the context of bio-oil analyses

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Article information

Article type
Paper
Submitted
26 Sep 2023
Accepted
24 Mar 2024
First published
09 Apr 2024
This article is Open Access
Creative Commons BY license

RSC Sustain., 2024,2, 1444-1455

Open-source Python module to automate GC-MS data analysis developed in the context of bio-oil analyses

M. Pecchi and J. L. Goldfarb, RSC Sustain., 2024, 2, 1444 DOI: 10.1039/D3SU00345K

This article is licensed under a Creative Commons Attribution 3.0 Unported Licence. You can use material from this article in other publications without requesting further permissions from the RSC, provided that the correct acknowledgement is given.

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