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GC2 PFT Analysis: User Guide
Rev. 376 | June 2018 – V.Percuoco
Draft 6/7/2011; Rev. 1/2/1014; Rev. 371T | July 2017 – D.Houpt


Table of Contents

Introduction


The major concern in shipboard microbiological study is whether microbes from the drilling fluid are introduced into the recovered core material during coring. Therefore, it is critical to verify whether recovered cores are contaminated. Perfluorocarbon tracer (PFT) can be used to quantify the amount of contamination due to drilling fluid. It is strongly recommended that this test be routinely conducted when coring for microbiological studies.
PFTs are chemically inert and can be detected with high sensitivity. The JRSO has two chemicals it uses as chemical tracers to monitor potential contamination of sediment and rock samples on the JOIDES Resolution.

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The GC2 system comprises an HP 6890 gas chromatograph (GC) with a micro-electron capture detector (µECD).
The GC inlet is operated in splitless mode. PFT gas samples obtained using the headspace extraction method may be injected manually after incubation for 30 minutes at 85 70 deg. C, or can be injected by the Gerstel autosampler (whose incubator oven should be set to 70°C for 600 seconds). The injection port liner assembly is connected to a megabore column (Rt-Alumina BOND/KCl, 50 m, 0.53 mm ID, 10 µm thickness), and then to a µECD detector, which requires both carrier (helium) and makeup gases (nitrogen).

Ensure the syringe installed in the autosampler has the Teflon-tipped plunger (Figure 6).



Figure 6: Different syringes used by the Gerstel Autosampler. The rubber plunger of the syringe shown on top causes significant sample carryover, likely due to tracer penetrating pore spaces within the rubber. It is best to use the syringe with the teflon-tipped plunger shown on bottom.

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The µECD cell contains 63Ni, a radioactive isotope emitting high-energy electrons (β-particles) with a nominal radioactivity of 10 mCi. These undergo repeated collisions with carrier gas molecules, producing ~100 secondary electrons for each initial β-particle.
Further collisions reduce the energy of these electrons into thermal range. These low-energy electrons are then captured by suitable sample molecules, which reduces the total electron population within the cell. Therefore, with higher sample concentration the conductivity of an existing gas will drop noticeably, which is recorded by the µECD outcoming signal detector.
(Note that the raw signal represents a drop in electron current signal, flipped over to positive peaks through the GC electronics and software.)

Sample Preparation & Analysis

PFT is pumped into the drilling fluid during coring. When core is delivered to the deck, small core samples are placed in headspace vials, sealed, and heated before headspace analysis on the GC2. The presence of a PFT peak from a sample from the interior of a core indicates core contamination from drill fluid, which may contain contaminating microbes.

Sample Collection

Sediment samples are collected from the edge and center of the core on the catwalk immediately after cores are retrieved. The sample from the outer edge is used to confirm successful delivery of the tracer to the core, whereas the interior sample is used to estimate the quantity of intrusion of drill water into the core. Because the exterior of the core liner is coated with drilling fluid, contact with the liner should be avoided while collecting core samples for PFT analysis.

Unconsolidated Sediments
  1. After cutting the core liner, break up sediment core by pulling sections apart rather than cutting with a knife to ensure that the tracer is not dragged through the core with the knife.
  2. Cut the Luer end off 5 mL plastic syringes (one for each sample to be collected).
  3. Collect one plug sample (~3 cm3) using a cut-off syringe from the outer edge of the sample along the core liner.
  4. Collect another plug sample (~3 cm3) using another cut-off syringe from near the center of the core.
  5. Immediately extrude each sample into a 20 mL headspace vial and seal with gas-tight PFTE -lined cap and septa.
Consolidated Sediments
  1. After cutting the core liner, place the core on a fresh sheet of aluminum foil.
  2. Pare the exterior of the core using hammer, chisel, and tongs. Before using these tools, pass them through a flame torch to remove any PFT contaminant.
  3. Collect one sample (~3 cm3) from the outer edge of the sample along the core liner.
  4. Collect another sample (~3 cm3) from near the center of the core.
  5. Immediately place each sample into a 20 mL headspace vial and seal with gas-tight PFTE-lined cap and septa.
Igneous Rock

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Preparing and Running Calibration Standards


Image Added


  1. Use a dedicated syringe for each concentration of tracer. See labels on syringes. Do not use labeled syringes for any other purpose.
  2. If suspecting contaminated syringes, rinse syringes with methanol (fill syringes with Optima Methanol three times and discard contents, separate plunger and syringe, place segregated on clean foil) and bake them in the oven at 70°C for 12 hours to drive off any possible trace of PFT.
  3. Prepare dilutions of PFT as per the instructions above.
  4. In the Agilent Open Lab program, choose Method and Run Control.
  5. Choose the latest PFT method file and wait until the Ready message is lit. Do not raise the detector temperature without sufficient nitrogen quality and flow!
  6. If injecting manually, incubate the standards in the 70°C oven for 30 minutes beforehand, as if they were samples. The Gerstel oven should be set to the same temperature.
  7. Set up a Gerstel autosampler sequence for the calibration standards, or inject each level manually, beginning from the most dilute to the highest concentration. (The samples should be injected by the Gerstel or manually, the same as the standards.)


Image Added


Allow the gas chromatograph to return to the Ready state before injecting the next standard; repeat until all of the standards have been run (for both PFMCH and PFMD, if both PFTs are expected to be used).


Approving Calibration


  1. Navigate to Calibration > Data Analysis and open the calibration files.
  2. Enter required parameters into the Calibration table and view calibration curve and correlation coefficient.
  3. If calibration is acceptable, continue with sample analysis.

Sample Preparation & Analysis


PFT is pumped into the drilling fluid during coring. When core is delivered to the deck, small core samples are placed in headspace vials, sealed, and heated before headspace analysis on the GC2. The presence of a PFT peak from a sample from the interior of a core indicates core contamination from drill fluid, which may contain contaminating microbes.


Sample Collection


Sediment samples are collected from the edge and center of the core on the catwalk immediately after cores are retrieved. The sample from the outer edge is used to confirm successful delivery of the tracer to the core, whereas the interior sample is used to estimate the quantity of intrusion of drill water into the core. Because the exterior of the core liner is coated with drilling fluid, contact with the liner should be avoided while collecting core samples for PFT analysis.


Unconsolidated Sediments




  1. After cutting the core liner, break up sediment core by pulling sections apart rather than cutting with a knife to ensure that the tracer is not dragged through the core with the knife.
  2. Cut the Luer end off 5 mL plastic syringes (one for each sample to be collected).
  3. Collect one plug sample (~3 cm3) using a cut-off syringe from the outer edge of the sample along the core liner.
  4. Collect another plug sample (~3 cm3) using another cut-off syringe from near the center of the core.
  5. Immediately extrude each sample into a 20 mL headspace vial and seal with gas-tight PFTE -lined cap and septa.


Consolidated Sediments


  1. After cutting the core liner, place the core on a fresh sheet of aluminum foil.
  2. Pare the exterior of the core using hammer, chisel, and tongs. Before using these tools, pass them through a flame torch to remove any PFT contaminant.
  3. Collect one sample (~3 cm3) from the outer edge of the sample along the core liner.
  4. Collect another sample (~3 cm3) from near the center of the core.
  5. Immediately place each sample into a 20 mL headspace vial and seal with gas-tight PFTE-lined cap and septa.

Sample Analysis

Sample analysis includes the following steps:

  • Prepare GC and syringes
  • Prepare standards and run calibration curve
  • Approve calibration
  • Run samples
  • Analyze results

Nitrogen Gas Purity

Important! The nitrogen gas supply to the Agilent 6890 GC-µECD must be of sufficient purity to protect the 63Ni source, so before the detector is brought to operating temperature, be sure that no significant nitrogen demands are being made throughout the laboratory. For example, if the microbiologists are using the "Berkley bucket" technique to flush nitrogen through a container, do not proceed.
If time-critical measurements must be made without waiting for other usage to go down, talk to the Laboratory Officer about hooking up a UHP nitrogen tank from the reserve tanks in the hold.

Preparing GC and Syringes

  1. Check nitrogen gas availability, delivery pressure = 50 psi.
  2. Change septum on GC.
  3. Clean and bake all syringes at 85°C for at least 10 minutes (the longer the better, up to 24 hours). Place clean aluminum foil on a metal tray. Remove the needles, plungers and valves from each syringe to increase exposure of syringe surfaces. Ensure each syringe and its components are segregated-each should be reassembled exactly as it was disassembled. Verify that Teflon end on syringe plungers are not missing—this is especially important for the 10 µL SGE cemented-needle syringes (Figure 5).

Preparing and Running Calibration Standards

  1. Rinse syringes with methanol and bake them in the oven at 70°C for 12 hours to drive off any possible trace of PFT.
  2. Prepare dilutions of PFT as per the instructions above.
  3. In the Agilent Open Lab program, choose Method and Run Control.
  4. Choose the latest PFT method file and wait until the Ready message is lit.
    1. Again! Do not raise the detector temperature without sufficient nitrogen quality and flow!
  5. If injecting manually, incubate the standards in the 85°C oven for 30 minutes beforehand, as if they were samples. The Gerstel oven should be set to the same temperature.
  6. Set up a Gerstel autosampler sequence for the calibration standards, or inject each level manually, beginning from the most dilute to the highest concentration. (The samples should be injected by the Gerstel or manually, the same as the standards.)
  7. Allow the gas chromatograph to return to the Ready state before injecting the next standard; repeat until all of the standards has been run (for both PFMCH and PFMD, if both PFTs are expected to be used).

Approving Calibration

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Igneous Rock


  1. Immediately after the core liner is split in the core lab, choose pieces of core for PFT analysis.
  2. Place several small pieces of rock from the exterior of the core into a 20 mL headspace vial and seal with gas-tight cap and septa.
  3. Alternatively, wipe the interior of the core liner with a cotton swab and place the swab into the 20 mL headspace vial and seal with gas-tight cap and septa.
  4. Remove PFT from the surface of the rock before sampling the interior. Rinse the exterior with water or methanol, then hold the piece with tongs under the flame of a handheld propane torch until it appears dry.
  5. After cleaning, hold the rock on a fresh sheet of aluminum foil and pare away the exterior using a cleaned hammer and chisel or the hydraulic rock splitter. Use cleaned tongs to handle the rock pieces.
  6. After each paring, pass tools through the flame of the torch and place rock pieces on fresh aluminum foil.
  7. When the entire exterior of the rock is removed, crush the interior of the rock in a mortar.
  8. Immediately place an aliquot of the crushed rock into a 20 mL headspace vial and seal with gas-tight cap and septa.


Sample Analysis


Sample analysis includes the following steps:


  • Prepare GC and syringes
  • Prepare standards and run calibration curve
  • Approve calibration
  • Run samples
  • Analyze results


Nitrogen Gas Purity


Important! The nitrogen gas supply to the Agilent 6890 GC-µECD must be of sufficient purity to protect the 63Ni source, so before the detector is brought to operating temperature, be sure that no significant nitrogen demands are being made throughout the laboratory. For example, if the microbiologists are using the "Berkley bucket" technique to flush nitrogen through a container, do not proceed.
If time-critical measurements must be made without waiting for other usage to go down, talk to the Laboratory Officer about hooking up a UHP nitrogen tank from the reserve tanks in the hold.


Preparing GC and Syringes


  1. Check nitrogen gas availability, delivery pressure = 50 psi.
  2. Change septum on GC.
  3. Clean and bake all syringes at 85°C for at least 10 minutes (the longer the better, up to 24 hours). Place clean aluminum foil on a metal tray. Remove the needles, plungers and valves from each syringe to increase exposure of syringe surfaces. Ensure each syringe and its components are segregated-each should be reassembled exactly as it was disassembled. Verify that Teflon end on syringe plungers are not missing—this is especially important for the 10 µL SGE cemented-needle syringes (Figure 5).


Running Samples (Manual Injection)

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Both PFMCH and PFMD are considered to be non-hazardous by US and EU classifications under normal conditions.


Chemical Hazards:


  • Incompatible substances: oxidizing agents, strong acids, strong bases
  • Emits toxic fumes (HF) under fire conditions

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