Fully automated non-targeted GC-MS data analysis

Abstract

Non-targeted analysis is applied in many different domains of analytical chemistry such as metabolomics, environmental and food analysis. In contrast to targeted analysis, non-targeted approaches take information of known and unknown compounds into account, are inherently more comprehensive and give a more holistic representation of the sample composition. 

Besides chromatographic techniques coupled to high resolution mass spectrometry such as LC-HRMS, gas chromatography with unit resolution mass spectrometry is still regularly utilized for non-targeted profiling or fingerprinting. This is mainly due to high separation power of GC and a wide availability and low costs of quadrupole mass spectrometers. 

Although several non-targeted approaches have been developed, data processing still remains a serious bottleneck. Baseline correction, feature detection, and retention time alignment can be prone to errors and time-consuming manual corrections are often necessary. We therefore developed an automated strategy to non-targeted GC-MS data avoiding feature detection and retention time alignment. The novel automated approach includes segmentation of chromatograms along the retention time axis, multiway decomposition of transformed segments followed by a supervised machine learning pipeline based on gradient boosted tree classification on the decomposed tensor [1, 2]. 

In order to make this novel data analysis strategy available to scientists without programming background, we developed a convenient browser based application. For the here presented interactive browser application the open source Python packages Bokeh and HoloViews were used. The application will be online freely available soon. 

[1] J. Vestner, G. de Revel, S. Krieger-Weber, D. Rauhut, M. du Toit, A. de Villiers, Toward automated chromatographic fingerprinting: A non-alignment approach to gas chromatography mass spectrometry data. Acta Chimica Acta 911 (2016) 42-58 
[2] K. Sirén, U. Fischer, J. Vestner, Automated supervised learning pipeline for non-targeted GC-MS data analysis. Analytica Chimica Acta: X 1 (2019) 100005

DOI:

Publication date: June 19, 2020

Issue: OENO IVAS 2019

Type: Article

Authors

Jochen Vestner, Kimmo Sirén, Pierre Le Brun, Ulrich Fischer

Institute for Viticulture and Oenology, DLR Rheinpfalz, Breitenweg 71, D-67435 Neustadt, Germany
Institut National Supérieur des Sciences Agronomiques de l’Alimentation et de l’ Environnement, Agrosup Dijon, 6 boulevard Docteur Petitjean, 21000 Dijon, France
Department of Chemistry, University of Kaiserslautern, Erwin-Schroedinger-Strasse 52, D-67663 Kaiserslautern

Contact the author

Keywords

metabolomics, non-targeted, GC-MS, exploratory data analysis 

Tags

IVES Conference Series | OENO IVAS 2019

Citation

Related articles…

Influence of climatic conditions on grape composition of Tempranillo in La Mancha DO (Spain)

The aim of this work was to analyze the variability in grape composition of the Tempranillo cultivar related to climatic conditions, in La Mancha Designation of Origin. Grape composition (sugar content, total acidity, pH, malic acid, and total and extractable anthocyanins) recorded during ripening, were analysed for the period 2000-2019. The weather conditions at daily time scale, recorded during the same period, were also evaluated. The relationships between grape parameters with climatic variables related to temperature and to water deficits, referring different periods between phenological events along the growing cycle, were evaluated using regression analysis. High variability in grape composition was observed in the period analysed. Total acidity varied between 3.7 and 7.3 gL-1 while malic acid varied between 1.2 and 4 gL-1. The extractable anthocyanins ranged between 526 and 972 mgL-1, and total anthocyanins ranged between 922 and 1388 mgL-1, being the lowest values recorded in the hottest year (2017). Total acidity decreased 0.77 gL-1 for an increase of 100 GDD, while malic acid decrease in 0.42 gL-1 for the same GDD increase, being the period between veraison and harvest the one that seemed to have higher influence on acidity. In addition, it was confirmed that increasing water deficits decreased acidity. Total and extractable anthocyanins increased in about 210 and 105 mgL-1, respectively, with an increase of 100 GDD from veraison to harvest, and the increase in water deficits favour the increase of anthocyanins, both total and extractable anthocyanins. Total and extractable anthocyanins concentration increased in 35 and 22 mgL-1 per an increase of 10 mm in the water deficit. These results can be of interest to understand the potential changes that grapes composition may suffer under future warmer climates.

Better understand the soil wet bulb formation with subsurface or aerial drip irrigation in viticulture

The gradual change in rainfall patterns experienced in the south of France vineyards, especially around the Mediterranean sea, means that the vines are increasingly subject to summer drought. The winegrowers developped the use of irrigation techniques to ensure the maintenance of competitive yields in the production of wines under Protected Geographical Indication label. In practice, drip irrigation pipes can be installed above the ground or buried into the soil as well as at different distances from the vine row. The objective of this study was to examine the profiles of the wet bulbs of the soil obtained from two drip irrigation systems : aerial drip located under the vine row and subsurface drip placed in the middle of the inter-row. This experiment took place over two consecutive seasons (2020-2021) on a 3.4 ha Viognier plot in the Mediterranean region (PGI Oc, France) on sandy clay soil. The annual rainfalls were less than 400 mm. Soil water content probes were installed at different depths (20 – 40 – 60 – 80 cm) and at different lateralities from the vine row (30 – 60 – 90 – 120 cm) to control the formation of the soil wet bulb during irrigation. The mapping and the analysis of the data allowed a better understanding and differentiation of the water percolation when irrigating with subsurface or aerial drip. For the same amount of water and without differences of vine water status, it is shown that in a subsurface drip irrigation situation, the size of the wet bulb formed is larger than in aerial drip irrigation system.

austrianvineyards.com: online viewer of all designations of Austrian wine

To digitally record and present all the origins of Austrian wines in the same perfect and clear way was the motivation for the Austrian Wine Marketing Board (Austrian Wine) to start with the project in 2018. In June 2021 the results were presented to the public in an online viewer showing all the designations of Austrian wine, available at https://austrianvineyards.com in a largely barrier-free manner. The online viewer provides tailored individual maps fitted to the respective zoom level. The smallest unit of wine-origins in Austria is called Ried and is displayed in a plot-specific manner highlighting areas under vine. Information on the Ried include administrative district, winegrowing municipality, cadastral municipality, large collective vineyard site, specific winegrowing region, generic winegrowing region, winegrowing area and, in many cases, an illustrative picture. Complementary data on the size, elevation (minimum-maximum), orientation (in 8 sectors plus flat) and gradient (minimum, maximum, average) are based on the area under vine according to the EU’s Integrated Administration and Control System. Additional information covers climate data. The diagrams are taken from the monthly breakdown of data in the annals of the Central Institute for Meteorology and Geodynamics, Austria provide a display of values for air temperature, precipitation, and sunshine hours for the reference year and the long-term average. Seasonal aggregated data on temperature, precipitation, and sunshine hours complete the display. Short descriptions with emphasis on geology and soil, field name in historical maps, etymology of the denomination, and main planted variety complements the available information for the main designations in the online viewer. These descriptions are compiled by winegrowers, geologists, historians, and journalists. All the information and data can be extracted to a pdf-file. Printed vineyard maps are also available. Missing content regarding wine origins in Styria will be completed in winter 2021/22.

Mobile device to induce heat-stress on grapevine berries

Studying heat stress response of grapevine berries in the field often relies on weather conditions during the growing season. We constructed a mobile heating device, able to induce controlled heat stress on grapes in vineyards. The heater consisted of six 150 W infrared lamps mounted in a profile frame. Heating power of the lamps could be controlled individually by a control unit consisting of a single board computer and six temperature sensors to reach a pre-set temperature. The heat energy applied to individual berries within a cluster decreases by the squared distance to the heat source, enabling the establishment of temperature profiles within individual clusters. These profiles can be measured by infrared thermography once a steady state has been reached. Radiant flux density received by a berry depending on the distance was calculated based on a view factor and measured lamp surface temperature and resulted to 665 Wm-2 at 7cm. Infrared thermography of the fruit surface was in good agreement with measurements conducted with a thermocouple inserted at epidermis level. In combination with infrared thermography, the presented device offers possibilities for a wide range of applications like phenotyping for heat tolerance in the field to proceed in the understanding of the complex response of plants to heat stress. Sunburn necrosis symptoms were artificially induced with the aid of the device for cv. Bacchus and cv. Sylvaner in the 2020 and 2021 growing season. Threshold temperatures for sunburn induction (LT5030min) were derived from temperature data of single berries and visual sunburn assessment, applying logistic regression. A comparison of threshold temperatures for the occurrence of sunburn necrosis confirmed the higher susceptibility of cv. Bacchus. The lower susceptibility of cv. Sylvaner did not seem to be related to its phenolic composition, rendering a thermoprotective role of berry phenolic compounds unlikely.

Estimating bulk stomatal conductance of grapevine canopies

In response to changes in their environment, grapevines regulate transpiration using various physiological mechanisms that alter conductance of water through the soil-plant-atmosphere continuum. Expressed as bulk stomatal conductance at the canopy scale, it varies diurnally in response to changes in vapor pressure deficit and net radiation, and over the season to changes in soil water deficits and hydraulic conductivity of both soil and plant. It is necessary to characterize the response of conductance to these variables to better model how vine transpiration also responds to these variables. Furthermore, to be relevant for vineyard-scale modeling, conductance is best characterized using data collected in a vineyard setting. Applying a crop canopy energy flux model developed by Shuttleworth and Wallace, bulk stomatal conductance was estimated using measurements of individual vine sap flow, temperature and humidity within the vine canopy, and estimates of net radiation absorbed by the vine canopy. These measurements were taken on several vines in a non-irrigated vineyard in Bordeaux France, using equipment that did not interfere with ongoing vineyard operations. An inverted Penman-Monteith equation was then used to calculate bulk stomatal conductance on 15-minute intervals from July to mid-September 2020. Time-series plots show significant diurnal variation and seasonal decreases in conductance, with overall values similar to those in the literature. Global sensitivity analysis using non-parametric regression found transpiration flux and vapor pressure deficit to be the most important input variables to the calculation of bulk stomatal conductance, with absorbed net radiation and bulk boundary layer conductance being much less important. Conversely, bulk stomatal conductance was one of the most important inputs when calculating vine transpiration, further emphasizing the need for characterizing its response to environmental changes for use in vineyard water use modeling.