Differential analysis of soil using the Orbitrap Exploris GC 240 mass spectrometer and Compound Discoverer software

Importance of the topic

Environmental soils can harbor a diverse array of volatile and semi-volatile contaminants such as PAHs, PCBs, dioxins, and pesticides. Comprehensive non-target screening is essential for reliable environmental monitoring and risk assessment. High-resolution accurate mass (HRAM) GC-MS expands detection capabilities beyond targeted analyses and uncovers unexpected contaminants.

Goals and Overview of the Study

This study evaluates the Thermo Scientific™ Orbitrap Exploris™ GC 240 mass spectrometer and Thermo Scientific™ Compound Discoverer™ software for differential analysis of soil extracts. Three soil samples (labeled D, L, and M) collected near Bremen, Germany, were compared to demonstrate non-target profiling, statistical discrimination, and compound identification workflows.

Methodology and Used Instrumentation

Sample Preparation:

• 2 g soil extracted with acetonitrile, liquid–liquid partitioned into hexane
• Direct injection of hexane extracts without clean-up
• Triplicate EI analyses interspersed with pooled QC injections

Instrumentation and Acquisition:

• Orbitrap Exploris GC 240 MS coupled with TRACE 1610 GC and TriPlus RSH SMART autosampler
• Full-scan EI (m/z 50–550, resolving power 120 000)
• Positive and negative chemical ionization (PCI, NCI) for molecular ion confirmation
• Data-dependent ddMS2 scans for MS2 spectra in PCI mode

Data Processing:

• Compound Discoverer workflows for EI and PCI data
• Spectral deconvolution, library searches (NIST 2020, HRAM GC-Orbitrap Contaminants) and elemental composition prediction
• QC correction, missing value imputation, and background compound marking
• Statistical tools: PCA, Volcano plots, Box-Whisker charts

Main Results and Discussion

PCA fully separated the three soil groups and demonstrated tight replicate clustering. Volcano plots highlighted compounds enriched in each soil pairwise comparison. Key findings included:

• Detection of polyaromatic hydrocarbons (pyrene, fluoranthene, perylene) with highest levels in sample M (residential area with fireplaces)
• Accurate identification of pyrene (EI search index > 890; mass error < 0.2 ppm) and confirmation via PCI molecular ions and ddMS2 data
• Identification of a hexachlorinated PCB congener by characteristic isotopic patterns in EI and strong response in NCI

Statistical charts facilitated rapid selection of discriminating features and comparison of peak areas across samples.

Benefits and Practical Applications

• Non-target screening without need for analytical standards or targeted methods
• High resolving power and mass accuracy for confident formula assignment
• Combined EI and CI enhances structural confirmation and adduct detection
• Automated workflows accelerate data processing and statistical evaluation

Future Trends and Potential Applications

Ongoing developments may include expanded high-resolution spectral libraries, integration with machine learning for compound classification, field-deployable HRAM GC-MS systems, and broader environmental or industrial applications such as metabolomics, food safety, and forensic analysis.

Conclusion

The Orbitrap Exploris GC 240 coupled with Compound Discoverer software offers a powerful HRAM GC-MS solution for non-target environmental analyses. It delivers sensitive detection, accurate mass assignments, and robust statistical workflows for comprehensive soil contaminant profiling.

Reference

• Thermo Fisher Scientific Technical Note 10730 (2021) “Mass resolving power of 240,000: for confident compound identification”