PFAS Column Selection for LC and GC: Method Compatibility and Solvent Considerations

Abstract

Reliable characterization of PFAS at trace levels depends on selecting chromatographic setups that minimize background artifacts and deliver consistent retention and resolution. This article explains how phase chemistry, particle design, and instrument hardware influence the separation of PFAS with different polarities, chain lengths, and structural variants. It provides practical guidance on choosing C18, mixed-mode, phenyl-hexyl, HILIC, and GC phases, along with recommendations for solvent verification, additive selection, and delay-column use to enhance data quality. These considerations support robust PFAS workflows across drinking water, environmental, and other complex sample types.

Section Overview

• Column Selection Overview
• Importance of Column Selection: Bleed, Selectivity, and Chain-Length Resolution
• Matching Column Chemistry to Analyte Properties
• Column Chemistry Options
• Practical LC setup
• Solvent and Additive Selection
• Isomer Resolution Tips
• GC Considerations
• Mini Decision Guide (LC)
• Related Products

At a Glance

• Use low-bleed columns equipped with PFAS-inert hardware to minimize background artifacts.^2,5
• Select column chemistry, length, and particle technology according to the analyte characteristics, sample matrix, and required resolution.^1,2
• Confirm solvent purity using PFAS-tested methanol or acetonitrile, and employ volatile buffers. Include system blanks and install delay or guard columns before sample analysis.^1,3
• Maintain the system configuration consistent with the intended method, whether for regulatory compliance or screening, and document all modifications.
• Install a PFAS delay column to capture system-derived PFAS and early eluting background peaks, verifying its effectiveness through system blank analyses.⁴

Column Selection Overview

The choice of columns and solvents is crucial for achieving low-ppt sensitivity while avoiding background artifacts. Regulatory method details can be found here. This page should be used to select LC or GC chemistries, column dimensions, and mobile phases appropriate for the target PFAS profile and sample matrix.^1,2

Importance of Column Selection: Bleed, Selectivity, and Chain-Length Resolution

• Bleed and background: Fluorinated species originating from the stationary phase or column hardware can increase baseline noise. Use low-bleed columns combined with PFAS-certified inert hardware to minimize such interference.^2,4
• Selectivity and isomers: Homologs and positional isomers require effective separation. High-efficiency columns provide improved selectivity, particularly for phenyl-hexyl and longer compounds.
• Chain-length retention: Ultra-short chain PFAS compounds tend to elute near the void volume on conventional C18 phases, while long-chain PFAS require sufficient retention and resolution to ensure accurate quantification.

Matching Column Chemistry to Analyte Properties

• Ultrashort-chain PFAS (≤ C3): These highly polar compounds exhibit weak retention on conventional C18 columns. Improved retention can be achieved using mixed-mode or hydrophilic interaction liquid chromatography (HILIC) phases.¹
• Short-chain PFAS (C4–C6): These strongly polar compounds often show poor retention on standard C18 phases, leading to limited resolution and matrix interferences. Mixed-mode columns that combine hydrophobic and anion-exchange functionalities enhance both retention and selectivity for these analytes.
• Long-chain PFAS (> C6): These compounds are strongly retained on C18 phases. Columns with lengths of 100–150 mm and sub-3 µm particle sizes are recommended to achieve higher resolution.
• Head groups: Carboxylate and sulfonate functional groups respond well to mild ammonium buffers, such as acetate or formate, which help stabilize peak shape and improve ionization efficiency.

Column Chemistry Options

• Reversed-Phase C18 Columns: These are the standard choice for EPA Methods 537.1 and 533, providing strong hydrophobic interactions for PFAS separation. Modern designs incorporating core-shell particles and metal-free hardware improve separation efficiency while reducing PFAS adsorption and contamination risks.
• Mixed-Mode Columns: These columns integrate C18 hydrophobicity with embedded anion-exchange functionalities, enabling simultaneous interactions with the fluorinated tails and ionized head groups of PFAS. This dual interaction enhances both retention and selectivity, particularly for ultra-short-chain PFAS such as trifluoroacetic acid (TFA) and difluoroacetic acid (DFA), which typically elute early on conventional C18 phases.
• Phenyl-Hexyl Columns: These aromatic stationary phases provide π–π and dipole interactions that facilitate the separation of PFAS isomers and complex mixtures. They deliver high-efficiency separations with minimal ion suppression, making them suitable for simultaneous analysis of short- and long-chain PFAS.
• Hydrophilic Interaction Liquid Chromatography (HILIC) Columns: These columns are well suited for polar and ionizable PFAS compounds that exhibit limited retention in reversed-phase systems, such as ultra-short chains. Phases containing quaternary ammonium groups offer a combination of HILIC and weak anion-exchange mechanisms, improving both separation and ionization efficiency under high-organic mobile phase conditions, such as acetonitrile-rich environments.

Practical LC setup

• Delay column: A PFAS delay column should be installed upstream of the analytical column to trap system-derived PFAS and early-eluting background compounds. This improves baseline cleanliness and minimizes false positives.
• Column dimensions and particle size: Column lengths between 50 and 150 mm provide a balance between resolution and runtime. Longer columns enhance the separation of isomers and homologs but can increase backpressure. Sub-3 µm or core-shell particles are recommended to achieve higher efficiency.
• Inner diameter and solvent use: For LC–MS, a 2.1 mm inner diameter is a reliable standard. Smaller diameters (approximately 1.0–2.1 mm) support lower flow rates, reduce solvent consumption, and can enhance ESI sensitivity when the system is optimized for microflow operation.⁵
• Hardware: Use metal-free flow paths whenever possible, and incorporate both guard and delay columns to protect the analytical column and capture system-derived PFAS contaminants.⁴
• System blanks: Perform solvent and system blank runs regularly, ensuring that the early-eluting region remains free of contamination before initiating sample analysis.^1,2

Solvent and Additive Selection

Solvents

• Use LC–MS grade water, methanol, and acetonitrile, and verify each lot with method blanks prior to PFAS analysis. EPA drinking water methods 533, 537.1, and the screening method 8327 emphasize minimizing PFAS background from solvent supplies and require routine blank verification.^1,2
• Using verified PFAS-tested solvents, vial caps, liners, and SPE consumables reduces the risk of quality control failures and minimizes rework. EPA methods mandate demonstrating acceptable background levels whenever new supply lots are introduced.

Additives

• Use volatile LC–MS/MS-compatible additives that align with the target method, such as weak organic acids or ammonium salts, while avoiding non-volatile buffers. Method 8327 specifies an acetic acid in methanol/water background check and highlights potential contamination from laboratory supplies. Drinking water methods 533 and 537.1 require field and laboratory blanks, along with method quality controls, to confirm acceptable background levels in reagents and mobile phases.^1,3
• For solid-phase extraction (SPE) elution in drinking water methods, methanol containing a small percentage of ammonium hydroxide is specified. Ammonium hydroxide should be reserved for SPE use as directed by the method and not employed as a mobile-phase additive in LC analysis.

Isomer Resolution Tips

• Increase column length and efficiency by using sub-3 µm or core-shell particles to improve separation of closely eluting isomers.
• Use phenyl-hexyl stationary phases when isomer discrimination is critical, as their π–π and dipole interactions enhance selectivity.
• Optimize gradient slopes around critical pairs and verify the separation performance using reference standards.

GC Considerations

• Applicability: Gas chromatography (GC) is suitable for analyzing volatile and semivolatile PFAS precursors, particularly fluorotelomer alcohols (FTOHs), as well as other highly volatile fluorinated compounds. It complements LC–MS/MS, which is primarily used for ionic PFAS. EPA guidelines differentiate semivolatile or polar PFAS (addressed under OTM45, using LC–MS/MS after filter or PUF sampling) from volatile, nonpolar fluorinated compounds (addressed under OTM50, using canister sampling with GC–MS).⁶
• Column choice: Nonpolar stationary phases containing 5% phenyl and 95% dimethyl polysiloxane, such as “5ms” type columns, are commonly used for FTOH analysis due to their stable and reproducible performance.
• Sampling interface: Sampling media should be selected according to compound volatility, using sorbent tubes or canisters as specified in the method. Sample losses can be minimized by adhering to method-specific handling, cleanup, and storage procedures.⁷

Verification of PFAS-Free Consumables

Due to the ubiquitous presence of PFAS and the sensitivity of current analytical methods, all consumables—including columns, solvents, buffers, and hardware—should be verified PFAS-free. Guard columns or delay columns can reduce system-derived PFAS contamination and improve data reliability.

Mini Decision Guide (LC)

• Ultrashort or short-chain emphasis, or unknown PFAS: Use mixed-mode or HILIC columns to improve retention of highly polar compounds. Include a delay column to capture system-derived PFAS and verify the early-eluting region using blanks.^2,4
• Broad drinking water suites: Select low-bleed C18 columns for compliance with EPA methods. Consider phenyl-hexyl columns when isomer resolution is required.¹
• Multimatrix or expanded PFAS lists (e.g., PFEAs, FTS): Use longer columns combined with high-efficiency particles to achieve adequate resolution. A mixed-mode column can serve as an adjunct to improve retention of early-eluting analytes.^1,2

Do's & Don'ts

• Do: Use metal-free flow paths, PFAS-tested solvents and caps, and incorporate guard and delay columns. Perform routine system and solvent blanks to confirm baseline cleanliness.^1,2,4
• Don’t: Rely exclusively on conventional C18 columns for ultrashort-chain PFAS. Avoid non-volatile buffers, and do not assume system hardware is PFAS-inert without proper verification.²

Discover More

• PFAS: Definition, Classification, Sources, Impact, & Detection
• PFAS Analysis Methods: Regulatory Alignment, QA/QC, and Contamination Control
• PFAS Sample Prep by Matrix

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