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How to Quickly Locate the Source of Your Background Contamination

Contaminations of any compound during solid phase extraction can ruin good results and be frustrating to identify where it occurs. Therefore, quickly locating the source of background contamination is important for labs to minimize disruption to routine analysis and obtain reliable results. Luckily, we have a simple test to help isolate the contamination on the SPE-03. The same approach can be used for manual extraction.

What are the possible routes of contamination?

Background contamination can come from many different sources in the lab including containers, standards, solvents, SPE equipment, analysis instrument, pressurized nitrogen and even the surrounding air. Our protocol homes in on the four main areas that are involved in the SPE process, without the need for performing time-consuming blank extractions.

A quick contamination check on the SPE-03

Without doing any full sample extractions, the protocol below delivers elution solvent through different parts of the SPE-03 and is collected for analysis. Nitrogen drying of the SPE cartridge is also included to quantify any contaminants from the lab's nitrogen supply.


  1. Run the "clean sys" method using the cleaning solvent, eg. Methanol. This will remove carry over from previous extractions.

  2. Keep 4 used SPE cartridges on the left side and place 4 new SPE cartridges on the right side of the SPE-03

  3. Enable only “samples 5 to 8” on the touch screen to reduce solvent usage

  4. Place 4 fraction tubes in positions 5 to 8 of fraction tray


  1. Run our "Contamination Check" method, during which 3 groups of fractions will be collected in about 20 minutes. No samples need to be extracted. Group 1 - solvent that goes through the inner (solvent and cartridge) lines Group 2 - solvent that goes through the inner lines + sample lines Group 3 - solvent that goes through the inner lines after nitrogen drying of cartridges.

  2. Directly pipet 8mL of your elution solvent from the solvent bottle into a fraction tube as control


  1. Evaporate and analyze all 3 fraction groups + 1 control.

  2. Compare the contamination levels from the 3 locations as well as control to determine if the solvent, nitrogen source, inner lines or sample lines are responsible for contamination

PFAS Case Study

A lab using the SPE-03 with MOD-005 (Minimal-Teflon option) mentioned that they were seeing around 60 ppt of PFBA in their blank extracts. The level was unprecedented for this compound as the minimal-Teflon option typically gives <0.1 ppt for PFAS analytes. The above protocol was performed, which yielded the following results.

As described in the above section, each fraction group consists of 4 sample positions on the extractor. Fraction group 1 corresponds to the inner lines. Fraction group 2 corresponds to the inner + sample lines. Fraction group 3 corresponds to the inner lines after nitrogen drying of SPE cartridges. The control shows the background within the solvent source.

From the results, it was found that the methanol source contained about 17 ppt of PFBA. This is significant for PFAS applications and would contaminate any other components of the system. The solvent lines (fraction group 2) had slightly higher levels, likely from deposits through previous methanol cleaning steps. The effects of deposition was most evident on fraction group 3, which has the combined background of solvent and sample lines. Since methanol is used for cleaning the sample lines prior to each run, more contamination is built up as the residual solvent evaporates from the sample tubing and bottle adapter caps. The nitrogen source (fraction group 3) was not clear a contributor in this case.

After identifying the source, care was taken to isolate the methanol from other lab activities that involved high concentrations of PFAS.

Common sources of contamination

From our experience, solvents and reagent water are the most common contributors to background. This can be resolved by verifying each reagent batch or changing suppliers. In some cases, PFAS was introduced into the system through the nitrogen source or lines. A pre-conditioned WAX cartridge attached to the SPE-03 nitrogen inlet has worked well as a filter.

Carry over from high concentration field samples is another factor. However this is easy to identify since labs are aware of these samples and the contamination often manifests itself as traces of long-chain and sticker compounds.

The minimal-Teflon option of the SPE-03 has not resulted in any PFAS contamination above method limits. Testing of inner and sample lines is still performed to give a comprehensive assessment of system background and provide clues to other sources of contamination.

Applying the protocol to vacuum manifold

A similar approach can be used to determine contamination when using manual extraction.

  1. Set up extractor with 4 new SPE cartridges

  2. Clean SPE cartridges with 10 mL of methanol

  3. Draw and collect 8 mL of methanol through SPE cartridges as fraction group 1

  4. Connect sample lines or reservoir

  5. Dispense 8 mL of methanol in 4 sample bottles and draw through the sample lines or reservoir to be collected as fraction group 2

  6. Perform 5 minutes of air drying

  7. Repeat step 3 to collect fraction group 3

  8. Pipet 8 mL of solvent directly from the solvent bottle as the control

  9. Analyze all 3 fraction groups + control to determine whether contamination is coming from the solvent source, surrounding air, manifold or sample line/reservoir/bottle


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