Figure 1. Example of water and soil analysis using GC and LC methods. (Left) Mapping soil VOCs using three green sample extraction techniques and GC–MS (Kaikiti et al., 2024). (Right) Developing a simple robust method for the quantification of PFAS in soil (Akele et al., 2026).
Define the environmental question
List target analytes, transformation products, concentrations of interest and the decision rule. A drinking-water volatile-organic analysis differs from a contaminated-soil polycyclic aromatic hydrocarbon survey or monitoring of polar pesticides in surface water. Use the relevant official method when the result must serve a regulatory purpose, and check its scope, preservation, hold time and quality-control requirements in the current version. Document matrix properties: salinity, suspended solids, organic carbon, moisture, grain size and potential nonaqueous phase. Many contaminants distribute between dissolved, particle-associated and sorbed phases. Whether a result represents whole water, filtered water or dry-weight soil must be explicit. A sample preparation choice changes the measurand if it removes a fraction of the contaminant.
Route analytes to GC or LC
GC is well suited to volatile and many semivolatile organic compounds that tolerate the inlet and separation temperature. Purge-and-trap or headspace approaches can introduce volatile compounds from water; solvent extraction supports many semivolatiles. LC can serve polar, thermally labile or low-volatility targets, with detector selection driven by required sensitivity and specificity. Ion chromatography is a distinct useful branch for inorganic anions in appropriate aqueous samples. Avoid simple rules such as "soil uses GC" or "water uses LC." The same matrix may need several methods. Some polar contaminants are poorly retained by conventional reversed-phase LC and need a different phase, ion-exchange mechanism, derivatization or specialized approach. A GC method may miss nonvolatile transformation products. Choose the pathway compound by compound.
| Analyte behavior | Likely starting platform | Main issue |
|---|---|---|
| Volatile organics | GC with suitable sample introduction | Loss during collection and handling |
| Semivolatile hydrophobics | GC or fit-for-purpose LC | Sorption and extraction recovery |
| Polar, thermally labile organics | LC with appropriate detection | Retention and matrix suppression |
| Inorganic anions | Ion chromatography | High dissolved-salt background |
Preserve water samples correctly
For volatile compounds, minimize headspace and follow method-specific container and preservative requirements. Do not filter or transfer a volatile-organic sample casually; each opening can cause loss. For dissolved-phase analytes, filtration at collection may be specified, while a total concentration study may require retaining suspended solids. Document the choice and timing.
Interferents and field controls
Water can contain natural organic matter, chlorine residual, salts or surfactants that affect analyte stability and extraction. Use field blanks and transport blanks appropriate to the question. Record temperature and receipt conditions. A low detector blank cannot compensate for loss or contamination before the sample reaches the laboratory.
Extract representative soil
Homogenize and subsample soil according to the method, accounting for stones, roots, moisture and spatial heterogeneity. Determine whether concentrations are reported on wet or dry mass. A small aliquot from a contaminated field sample can vary markedly; replicate subsamples reveal this variability. Avoid aggressive drying for volatile targets, since the preparation itself may remove analyte. Solvent extraction, accelerated extraction or other method-specific techniques must be tested for the target and soil type. Strong sorption to organic matter or aged contamination can reduce recovery compared with a fresh spike. Use suitable surrogate compounds and matrix spikes while recognizing that a fresh spike may not perfectly mimic native contamination. The extraction blank detects contamination from solvents, glassware or handling.
Clean extracts without losing targets
Solid-phase extraction can concentrate aqueous analytes and remove interferents; sorbent polarity, pH and breakthrough volume govern recovery. Soil extracts may need sulfur, lipid or humic-substance management. Excessively aggressive cleanup can strip polar transformation products or strongly hydrophobic compounds. Measure analyte in flow-through and wash during development, and compare pre- and post-cleanup spikes. For GC, nonvolatile residues can contaminate inlet and column, changing response over a long sequence. For LC-MS, coeluting humics and salts can suppress ions. Cleanup must improve the actual method outcome, not merely make the extract colorless. Use a guard, blank and sequence checks where they address the identified failure mode.
Build quality controls by stage
Field duplicates assess sampling variation; laboratory duplicates assess subsampling and preparation. Method blanks, surrogates, matrix spikes and calibration checks answer different questions. Define acceptance and corrective action before samples are analyzed. A standard added after extraction does not diagnose collection or extraction loss; an early surrogate can cover more stages if its behavior is relevant. Identity requires retention and detector-specific confirmation according to the selected method. Maintain reporting limits in the actual matrix, not just neat solvent. Dilution can reduce interference but raises the reporting limit. For a complex soil, a negative result may be limited by extraction and cleanup rather than instrument sensitivity.
Connect to site capabilities
The site's water analysis, soil analysis and environmental analysis services are aligned with matrix-specific planning. Custom GC columns and custom LC columns can address a demonstrated selectivity issue. Solid-phase extraction magnetic beads require analyte-specific recovery testing before use in an environmental method. Share the target list, sample source, preservation, regulatory or research objective, matrix load, expected concentration and current chromatograms. Distinguish a new method from a modification of a prescribed method. Site products support a separation; they do not establish official method equivalence without validation.
Match method scope to a real sample
An official analytical method has a defined analyte and matrix scope, plus QC procedures that cannot be summarized as "GC-MS" or "LC-MS." Check extraction, preservation, sample size and performance criteria before claiming equivalence. A method for waste leachate may not establish a drinking-water result, and a soil method modified to include an unusual compound needs verification. Document every departure and its effect on reporting limits. For a water sample with suspended solids, decide whether the target result includes the particle-associated fraction. If the method requires unfiltered whole water, removing particles changes the sample. Conversely, an explicitly dissolved analyte method may call for filtration near collection to prevent later partition changes. Record the field condition, not just the laboratory aliquot. Soil sampling design addresses spatial heterogeneity. A chromatographic method cannot correct a biased field composite. Specify depth, number of increments and relevant land-use history in the sampling plan, then preserve and process the portions as intended.
Investigate retention and breakthrough
An aqueous solid-phase extraction device has finite capacity for both analyte and competing natural organic matter. During development, retain the flow-through and an early wash to measure breakthrough and unintended analyte loss. Adjust sample volume and loading rate within the sorbent's demonstrated range. If the water is turbid, protect the device with a validated prefiltration step or analyze an appropriate whole-water fraction separately. In soil cleanup, a selective sorbent can reduce color while preferentially losing a subset of analytes. Compare total target recovery and instrument response before and after cleanup. A heavily contaminated extract may require dilution; this can bring the detector into range but raises the reporting limit. Note the change in the final report so a nondetect does not imply the original lower threshold was achieved. New cleanup chemistry should be tested against both low and high spikes. High spikes reveal overload and carryover, while low spikes reveal losses near the decision threshold.
Decide whether a second platform helps
An interference suspected in GC-MS can sometimes be addressed through a different column phase, another confirmation ion or a suitable LC method. A polar LC target with poor retention may benefit from an ion-exchange or specialized phase rather than more detector sensitivity. These are method-development choices, not an invitation to switch the instrument without verifying extraction and calibration. Compare the platforms with the same representative sample and a pre-extraction spike. A difference between GC and LC results may arise from different species measured, extraction yields or calibration, not only selectivity. If a component transforms in a hot GC inlet, an LC method may preserve it; if it is extremely volatile, opening a vial for LC preparation may cause more loss. Document analyte stability and the specific result each platform claims.
Control contamination from the workflow
Trace analysis is susceptible to laboratory air, solvents, caps, tubing and carryover. Choose a material blank, field blank and procedural blank that can reveal the relevant source. Glass and polymer containers have different advantages for different analytes; follow method requirements rather than assuming one is universally clean. Keep extraction equipment segregated from high-positive samples. When blanks show a target signal, assess its origin and effect on low-level samples using the predetermined laboratory rule. Do not simply subtract a large blank from every sample. Analyze a blank after a high standard to check instrument carryover separately from field contamination. Store raw chromatograms and manual integrations so results can be audited.
Report meaningful uncertainty
Quantification uncertainty includes sampling, subsampling, extraction, cleanup, calibration and instrumental variation. A single injection standard deviation captures only a small portion. Report dry-weight correction for soil using the measured moisture and stated convention. For water, distinguish concentration per whole sample from a filtered fraction. If an interferent forces a dilution, state the raised reporting limit. When comparing two locations or two seasons, ensure methods and sample definitions match. Apparent trends can reflect a change from whole-water to filtered-water measurements or different soil moisture handling. Use consistent surrogates and QC charts to recognize laboratory drift. A high-quality chromatography result is still tied to the matrix and sample fraction that actually entered the method.
Consider emerging polar contaminants
Some environmental targets are ionic, highly polar or surface active and are poorly described by generic volatile and semivolatile GC panels. Select a dedicated LC or ion-chromatographic method as appropriate, with collection containers and blanks assessed for the particular analyte. A broad chromatographic scan does not establish absence of compounds outside its extraction and detector scope. For extremely low reporting levels, sampling equipment and laboratory materials can contribute background comparable to the target. Build the blank hierarchy before expanding the method, and verify sample stability through transport, storage and preparation.
Connect field decisions with laboratory recovery
A site investigation may compare source, downgradient and background samples. Define whether filtration, preservation and extraction were applied consistently before comparing results. Soil organic carbon and water ionic strength can alter sorption and extraction. If a hot spot is suspected, an extra composite may dilute it; if only a grab sample is taken, it may exaggerate local variability. Analytical replicates cannot replace a defensible field plan. Coordinate the sampling and analytical teams so the laboratory receives the intended fraction, volume and preservation state.
Qualify a new stationary phase
If two target compounds coelute, compare a candidate GC or LC column under the same representative sample conditions. Evaluate critical-pair resolution, recovery, blank carryover, pressure and run time. A new column may improve target separation but expose another interfering pair. Test the complete analyte panel and high-matrix sample, not only two neat standards. The new phase can also shift retention outside established identification windows, requiring documented method verification. For environmental decisions, preserve the original and revised method data for a transparent comparison.
Document extraction boundaries
Environmental chromatograms often describe the portion of a sample that a specific preparation makes available. Name the solvent, extraction time, pH and filtration choice in the report or method reference. If two laboratories use different preparations, differing results need not mean one instrument is faulty. Compare a shared reference and identical subsamples before attributing the difference to site contamination. When a cleanup step discards an insoluble residue, quantify or at least acknowledge that discarded material if it could contain target compounds.
Connect this guide to a chromatography project
Share the sample matrix, target list, analytical goal, existing extraction, chromatograms, required reporting range and instrument configuration. We can help evaluate separation materials and relevant analytical support.
References
- U.S. EPA. Method 8260D, Volatile Organic Compounds by GC/MS.
- U.S. EPA. Method 8270E, Semivolatile Organic Compounds by GC/MS.
- U.S. EPA. Method 300.0, inorganic anions in water by ion chromatography.
- Kaikiti K, Omirou M, Ioannides IM, Agapiou A. Mapping soil VOCs using three green sample extraction techniques and GC–MS. Microchemical Journal. 2024;207:111851. doi:10.1016/j.microc.2024.111851
- Akele ML, Ohlson C, Alghamdi W, et al. Developing a simple robust method for the quantification of PFAS in soil. Talanta. 2026;302:129414. doi:10.1016/j.talanta.2026.129414
