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Table of Contents
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GC3-Natural Gas Analysis Advanced User Guide

Manual Information

Author(s):

C. Bennight

Reviewer(s):

L. Brandt, C. Neal, K. Marsaglia

Editor(s):

K. Graber, L. Peters

Management Approval (Name, Title, Date):

D.J. Houpt, Supervisor of Analytical Systems, 9/24/2010

Audience:

Research Specialists, Laboratory Technicians

Origination date:

5/12/2008

Current version:

Version 1.0 09/24/2010

Revised:


Domain:

Chemistry

System:

Gas Chromatography

Keywords:

Hydrocarbons, headspace gas, methane, ethane

Changes to User Guide

Summarize requested modifications to this user guide in an e-mail and/or annotate the PDF file and e-mail change requests to techdoc@iodp.tamu.edu.

User Guide Contents

Topic

See page…

Introduction

Instrument Installation & Setup

GC3 & NGA Startup

LIMS Data Upload

Maintenance & Troubleshooting (HP6890GC)

Introduction

Overview

The absolute quantity of hydrocarbons combined with the potential for trapping and accumulating hydrocarbons is the primary safety risk during shipboard operations. Gas monitoring via gas chromatography (GC) analysis is a means of quanitfying the risk posed by these factors. Figure 1 depicts the safe ranges for gas concentrations (C1/C2) vs. temperature.
Image Added
Figure 1. Risk Assessment for Drilling Safety (IODP).


Hydrogen sulfide (H2S) is another significant risk factor for individuals working in the area. Early detection of H2S is accomplished by emergency monitors on the drill floor, and later quantification is performed on the natural gas analyzer (NGA).

Hydrocarbon Generation

Hydrocarbon generation in sediments results from thermal decomposition (maturation) of biogenic organic matter (e.g., Tissot and Welte, 1984). C1–C4 hydrocarbons may be generated in significant quantities in sediment via two processes:

  • Biogenic: biogenic hydrocarbons are typically characterized by methane. They are produced in a sulfate-free environment via the reduction of dissolved bicarbonate.
  • Thermogenic: thermogenic hydrocarbons are produced in sediments in direct proportion to temperature. C5 and other heavy hydrocarbons almost always result from thermal generation of hydrogen-rich organic matter. Typically, a temperature of ~100°C or greater is required for these products to become significant.


The evolution of sedimentary biogenic organic matter under increasing burial depth and consequent temperature rise is divided into three stages:

  • Diagenesis
  • Catagenesis
  • Metagenesis

Diagenesis

Diagenesis refers to the biological, physical, and chemical alteration of sedimentary organic matter that occurs at low temperature (<50°C) in relatively recently deposited sediments (Peters et al., 2005).

Catagenesis

Catagenesis, the principal zone of oil formation, refers to a temperature range of 50°C~150°C. Liquid and gaseous hydrocarbons together with organic compounds with heteroatoms (oxygen, sulfur, and nitrogen) are released from the kerogen (Figure 2), so the catagenesis stage is called the "oil window."

Metagenesis

The last stage of sedimentary organic matter alteration is metagenesis. Dry gases (mainly methane) are derived from liquid hydrocarbon accumulation in the crust (Figure 3). C1–C4 hydrocarbons may be generated in significant quantities in sediment via biogenic and thermogenic processes.


Image Added
Figure 2. Hydrocarbon Formation Pathways in Geological Situations (Rullkotter, 1993).
Image Added
Figure 3. Hydrocarbon Generation Resulting from Burial of Organic Matter during Geologic Time.


Hydrogen Sulfide

Sulfate reducing bacteria produce H2S in euxinic sediments (Raiswell and Berner, 1985). Biogenic alteration of organic matter may occur in a relatively shallow part of the sediment. Thermochemical sulfate reduction of sulfate by hydrocarbons in reservoirs occurs under high temperature (>127°C ~ 140°C) (e.g., Orr, 1974; Worden et al., 1995).

References

Orr, W.L., 1974. Changes in sulfur content and isotopic ratios of sulfur during petroleum maturation. Study of Big Horn Basin Paleozoic oils. Bull. AAPG, 58:2295-318.
Peters, K.E., Walters, C.C., and Moldowas, J.M., 2005. Origin and preservation of organic matter. The Biomarker Guide. Cambridge University Press, 3-17.
Raiswell, R., and Berner, R.A., 1985. Pyrite formation in euxinic and semi-euxinic sediments. Am. J. Sci., 285:1616-1620.
Rullkotter, J., 1993. The thermal alternation of kerogen and the formation of oil. In: Engel, M.H., and Macko, S.A. (Eds.), Organic Geochemistry. New York: Plenum Press, 377-396.
Tissot, B.P., and Welte, D.H., 1984. Petroleum Formation and Occurrence (2nd ed.), Heidelberg: Springer-Verlag.
Worden, R.H., Smalley, P.C., and Oxtoby, N.H., 1995. Gas souring by thermochemical surface reduction at 140°C. Bull. AAPG, 79:854-863.

Theory of Method

The hydrocarbon monitoring system consists of two instruments that monitor gases in core headspace and core void samples:

  • GC3: Agilent 6890 gas chromatograph (GC) with a flame ionization detector (FID). This instrument measures C1–C6 hydrocarbons.
  • NGA: Agilent 6890 GC with an FID and a thermal conductivity detector (TCD). This instrument measures C1–C6 hydrocarbons as well as N2, O2, CO2, CS2, and H2S gases.

GC3

The GC3 is used to determine the concentrations of the following light hydrocarbon gases:

  • Methane (CH4)
  • Ethene (C2H4)
  • Ethane (C2H6)
  • Propene (C3H6)
  • Propane (C3H8)

The GC3 instrument has a 1/6-inch VALCO union injector with a 2 µm stainless steel screen and a 10 port VALCO valve that is electrically switched (Figure 4). An 80/100 mesh 8 ft HaySep "R" packed column (2.0 mm ID x 1/8 inch OD) is installed in the oven.


Image Added
Figure 4. Schematic of Sample Gas Line in the GC3.


NGA

The NGA is used to determine the concentrations of nonhydrocarbon gases along with hydrocarbons from C1 to C7. The analytes measured on this instrument are:

  • Nonhydrocarbons
  • Nitrogen (N2)
  • Oxygen (O2)
  • Carbon dioxide (CO2)
  • Carbon disulfide (CS2)
  • Hydrogen sulfide (H2S)
  • Hydrocarbons
  • Methane (CH4)
  • Ethene (C2H4) + Ethane (C2H6)
  • Propene (C3H6) + Propane (C3H8)
  • n-Butane (C4H10)
  • iso-Butane (CH3–C3H7)
  • n-Pentane (C5H12)
  • iso-Pentane (CH3–C4H9)
  • n-Hexane (C6H14)
  • iso-Hexane (CH3–C5H11)
  • n-Heptane (C7H16)
  • iso-Heptane (CH3–C6H13)


The TCD flow path contains the following columns (Figure 5):

  • 6 ft x 2.0 mm ID stainless steel column packed with Poropak T (50/80 mesh)
  • 3 ft x 2.0 mm ID stainless steel column packed with molecular sieve 13x (60/80 mesh)
  • 6 ft x 2.0 mm ID stainless steel column packed with 80/100 mesh HaySep R (acid wash)


The FID flow path has a 60 m x 0.25 mm ID with 0.25 µm film thickness DB-1 capillary column.
Image Added
Figure 5. Schematic of a Sample Gas Line in the GC-NGA.


Instrument Installation & Setup

Agilent 6890 GC Specifications

Oven specifications

Range



Maximum temperature

450°C

Temperature program

Up to 6 ramps

Maximum run time

999.99 min

Temperature ramp rate

0°–120°C/min

Dimensions

50 cm × 58.5 cm × 50 cm

Weight

112 lb (50 kg)

Heat dissipation

7681 BTU/hr max

Operating temperature

20°–27°C

Operating humidity

50%–60%

Gases

The GC requires that hydrogen and air are connected to the marked fittings on the back of the instrument. The type of makeup gas must be identified in the method file.

  • Air, compressed (Zero-Air +): >50 psi
  • Helium, compressed (99.9995% +): >50 psi
  • Hydrogen, compressed (99.9995% +): >50 psi

GC3 Method: GC390FR.M

h7.Injector

  • Injection source: manual
  • Injection location: front

h7.Oven

  • Initial temperature: 90°C
  • Maximum temp: 250°C
  • Initial time: 0.50 min
  • Equilibration time: 1.00 min
  • Port temp: 100°C
  • Post time: 0.00 min
  • Run time: 8.60 min (run time will automatically be changed based on ramp setting)

  • Temperature program:

    Ramp

    Rate (°C/min)

    Final Temperature (°C)

    Final Time (s)

    1

    30.00

    100

    0.00

    2

    15.00

    110

    4.50

    3

    50.00

    150

    1.80

    4

    0.00 (grey lightbulb)




    h7.Front Inlet

  • Initial temp: 120°C (lightbulb)
  • Flow: 30.6 mL/min (lightbulb)
  • Gas type: helium


h7.Column 1

  • Packed column (model #: Restek PC3970)
  • HaySep "R" 80/100, 2.00 mm ID x 1/8 inch OD, 6 ft
  • Max temperature: 225°C
  • Mode: ramped flow
  • Initial flow: 30.0 mL/min
  • Initial time: 2.70 min
  • Post flow: 0.0 mL/min
  • Inlet: front
  • Outlet: front detector
  • Outlet pressure: ambient

  • Temperature program:

    Ramp

    Rate (°C/min)

    Final Temperature (°C)

    Final Time (s)

    1

    100.00

    40

    3.00

    2

    10.00

    30

    0.30

    3

    100.00

    60

    0.00


    h7.Column 2 (not installed)
    h7.Front detector (FID)

  • Temperature: 250°C (always on)
  • Hydrogen (H2) flow: 40.0 mL/min (on if FID temperature is >150°C, auto control)
  • Air flow 400.0 mL/min (on if FID temperature is >150 °C, auto control)
  • Mode*: constant makeup flow
  • Makeup flow*: 25.0 mL/min
  • Makeup gas type*: nitrogen (*Makeup flow: none; makeup gas: none)
  • Flame: on (auto on when FID temperature reaches 150°C)
  • Electrometer: on
  • Lit offset: 1.0


h7.Back detector: no detector
h7.Signal 1

  • Data rate: 5 Hz
  • Type: front detector
  • Save data: On
  • Zero: 0.0 (grey lightbulb)
  • Range: 0
  • Fast peaks: off
  • Attenuation: 0

h7.Signal 2

  • Data rate: 20 Hz
  • Type: front detector
  • Save data: Off
  • Zero: 0.0 (grey lightbulb)
  • Range: 0
  • Fast peaks: off
  • Attenuation: 0


h7.Column comp 1 & 2

  • Derive from front detector


h7.Auxillary pressure 3, 4, & 5

  • Gas type: helium
  • Initial pressure: 0.00 psi (grey lightbulb)


h7.Valves

  • Valve 5 switching off

h7.Post run time: 0.00 min
h7.Time table for valve control

  • 0.01 min—Valve 5 on; 6.00 min—Valve 5 off

GC3 Sample Flow Schematics

Standby Mode

Green line shows helium carrier gas flow when GC3 is in standby mode.

  • Inlet—injector port—V6—V7—V9—V8—column—V1—V10—FID


Image Added
Figure 6. GC3 in Standby Mode.


Injection Mode


He carrier (green) and sample (red) gas flows during injection mode. Sample gas fills the 25 µL sample loop.

  • Sample gas: injector—V3—V2—V5—V4—vent
  • Carrier gas: Inlet—injector port—V6—V7—V9—V8—column—V1—V10—FID


Image Added
Figure 7. GC3 in Injection Mode.


Run Mode

He carrier (green) and sample (red) gas flows during the sample run. When the valve is turned, helium coming from the inlet pushes the sample gas trapped in the sample loop.

  • Sample gas: column—FID
  • Carrier gas: V5—V2—V1—column—V8—V7—V9—V10—FID


Image Added
Figure 8. GC3 in Run Mode.


NGA Method: NGA_CS.M

Injector

  • Injection source: manual
  • Injection location: front

Oven

  • Initial temp: 50°C
  • Maximum temp: 300°C
  • Initial time: 2.00 min
  • Equilibration time: 1.00 min
  • Port temp: 50°C
  • Post time: 0.00 min
  • Run time: 14.80 min (run time will be changed based on ramp setting)

  • Temperature program:

    Ramp

    Rate (°C/min)

    Final Temperature (°C)

    Final Time (s)

    1

    8.00

    70

    0.00

    2

    25.00

    200

    5.10

    3

    0.00 (grey lightbulb)

    NA

    NA

    Front Inlet

  • Flow: 21.0 mL/min (lightbulb)
  • Gas type: helium

Back inlet

  • Initial temp: 80°C (lightbulb)
  • Initial time: 0.00 min
  • Cryo: off
  • Cryo type: compressed air
  • Pressure: 20.75 psi (On)
  • Gas type: helium

  • Temperature program:

    Ramp

    Rate (°C/min)

    Final Temperature (°C)

    Final Time (s)

    1

    0.00 (grey lightbulb)

    NA

    NA

    Column 1: Not installed

           Column 2

  • Capillary column (model #: Agilent 122-1062)
  • Agilent DB-1 (dimethylpolysiloxane) 60.0 m x 0.25 mm diameter x 0.25 µm film thickness
  • Max temperature: 325°C
  • Mode: constant flow, 2.0 mL/min
  • Inlet: back inlet
  • Outlet: back detector
  • Outlet pressure: ambient


Front detector (FID)

  • Temperature: 250°C (always on)
  • Hydrogen (H2) flow: 40.0 mL/min
  • Air flow 400.0 mL/min
  • Mode*: constant makeup flow
  • Makeup flow*: 50.0 mL/min
  • Makeup gas type*: helium
  • Flame: On
  • Electrometer: on
  • Lit offset: 2.0


Back detector (TCD)

  • Temperature: 200°C (always on)
  • Reference flow: 45.0 mL/min (lightbulb)
  • Mode: constant makeup flow
  • Makeup flow: 3.0 mL/min
  • Makeup gas type: helium
  • Filament: on
  • Negative polarity: off


Signal 1

  • Data rate: 5 Hz
  • Type: back detector
  • Save data: on
  • Zero: 0.0 (grey lightbulb)
  • Range: 0
  • Fast peaks: off
  • Attenuation: 0


Signal 2

  • Data rate: 5 Hz
  • Type: front detector
  • Save data: on
  • Zero: 0.0 (grey lightbulb)
  • Range: 0
  • Fast peaks: off
  • Attenuation: 0


Column comp 1

  • Derive from front detector


Column comp 2

  • Derive from back detector


Thermal AUX 1 & 2

  • Use: valve box heater
  • Initial temp: 110°C

  • Initial time: 0.00 min

    Ramp

    Rate (°C/min)

    Final Temperature (°C)

    Final Time (s)

    1

    0.00 (grey lightbulb)

    NA

    NA

    AUX pressure 3

  • Gas type: helium

  • Initial time: 4.50 min

    Ramp

    Rate (°C/min)

    Final Temperature (°C)

    Final Time (s)

    1

    30.00

    22.20

    0.00

    2

    1.10

    27.50

    0.00

    3

    0.00 (grey lightbulb)

    NA

    NA

    Aux pressure 4 & 5

  • Gas type: helium
  • Initial pressure: 0.00 psi (grey lightbulb)



Valves (1 to 4, initial): Switching off

  • Valve control time program

    Time (min)

    Valve control

    0.00

    valve 1: off


    valve 2: off


    valve 3: off


    valve 4: off

    0.01

    valve 4: on


    0.07

    valve 1: on


    valve 2: on

    1.80

    valve 3: on

    1.83

    valve 4: off

    8.50

    valve 3: off

    9.10

    valve 1: off


    valve 2: off

    NGA Sample Flow Schematics

    Standby Mode

    He gas flow for standby mode (green lines).
  • Line 1: Aux-3—V1-4—V2-5—V2-3—capillary column—V2-4—V2-1—FID
  • Line 2: Aux-4—sample inlet—V1-2—V1-3—V1-6—V1-1—V3-3—V3-4—V3-1—V4-3—V4-2—V4-5—V4-4—Vent
  • Line 3: Front inlet—V3-5—V3-6—HaySep R column—V3-8—V3-7—V4-9—V4-8—TCD
  • Line 4: Back inlet—V4-6—V4-7—MolSieve column—V4-1—V4-10—Vent


Image Added
Figure 9. NGA in Standby Mode.


Injection mode

He carrier gas (green line) and sample gas (red line) flows in the NGA in injection mode. Sample gas fills the sample loops connected to V1 (25 µL), V3 (1 cm3), and V4 (0.5 cm3). He flushes the separation columns.
He gas flow (green):

  • Line 1: Aux-3—V1-4—V1-5—V2-3—V2-2—capillary column—V2-4—V2-1—FID
  • Line 3: Front inlet—V3-5—V3-6—HaySep R column—V3-8—V3-7—V4-9—V4-8—TCD
  • Line 4: Back inlet—V4-6—V4-7—MolSieve column—V4-1—V4-10—Vent


Sample gas flow (purge; red):

  • Sample inlet—V1-2—V1-3—V1-6—V1-1—V3-3—V3-4—V3-1—V3-2—V4-3—V4-2—V4-5—V4-4—Vent


Image Added
Figure 10. NGA in Injection Mode.


Run Mode at 0.01 min (open Valve V4)


He (green) and sample gas (red) flows in the NGA 0.01 min after start of run. Sample gas remains in the sample loop connected to V1 (25 µL) and V3 (1 cm3). After V4 opens, He returning from the back inlet pushes the sample gas out of the sample loop and into the molecular sieve column. Separated elements are detected by TCD.
He gas flow:

  • Line 1: Aux-3—V1-4—V1-5—V2-3—V2-2—capillary column—V2-4—V2-1—FID
  • Line 2: Aux-4—V1-2
  • Line 3: Front inlet—V3-5—V3-6—HayeSep R column—V3-8—V3-7—V4-9—V4-10—Vent
  • Line 4: Back inlet—V4-6—V4-5


Sample gas flow (purge):

  • V1-2—V1-3—V1-6—V1-1—V3-3—V3-4—V3-1—V3-2—V4-3—V4-4—out


Sample gas flow with He:

  • V4-5—V4-2—V4-1—MolSieve column—V4-7—V4-8—TCD


Image Added
Figure 11. NGA in Run Mode: 0.01 min after starting run.


Run Mode at 0.07 min (open Valves V1 and V2)


He (green) and sample gas (red) flows in the NGA 0.07–1.79 min after start of run. Sample gas remains in the sample loop connected to V3 (1 cm3). After V1 and V2 open, He from Aux-3 pushes the sample gas out of the sample loop connected to V1 (25 µL) and into the capillary column (60 m) through V2, where it passes into the FID.
He gas flow:

  • Line 1: Aux-3—V1-4
  • Line 2: Aux-4—V1-2
  • Line 3: Front inlet—V3-5—V3-6—HaySep R column—V3-8—V3-7—V4-9—V4-10—vent
  • Line 4: Back inlet—V4-6—V4-5—V4-2—V4-1—MolSieve column—V4-7—V4-8


Sample gas flow (purge):

  • V3-4—V3-1—V3-2—V4-3—V4-4—out


Sample gas flow with He:

  • V4-8—TCD
  • V1-3—V1-6—V1-5—V2-3—V2-4—capillary column—V2-2—V2-1—FID
  • V1-1—V3-3


Image Added
Figure 12. NGA in Run Mode: 0.07–1.79 min after starting run.


Run Mode at 1.80 min (open Valve V3)


He (green) and sample gas (red) flows in the NGA 1.80–1.82 min after start of run. After V3 opens, He from the front inlet pushes the sample gas out of the 1 cm3 sample loop into the HaySep column.
He gas flow:

  • Line 1: Aux-3—V1-4—V1-3—V1-6—V1-5—V2-3—V2-4
  • Line 2: Aux-4—V1-2—V1-1—V3-3—V3-2—V4-3—V4-4—out
  • Line 3: Front inlet—V3-5—V3-4
  • Line 4: Back inlet—V4-6—V4-5—V4-2—V4-1—MolSieve column—V4-7—V4-8—TCD


Sample gas flow with He:

  • Capillary column—V2-2—V2-1—FID
  • B3-4—V3-1—V3-8—HaySep R column—V3-6—V3-7


Image Added
Figure 13. NGA in Run Mode: 1.80–1.82 min after starting run.


Run Mode at 1.83 min (close Valve V4)

He (green) and sample gas (red) flows in the NGA 1.83–8.49 min after start of run. After V4 closes, He from the back inlet flushes the molecular sieve column (backflush). Gas samples separated by the HaySep column enter the TCD through V4.
Helium gas flow:

  • Line 1: Aux-3—V1-4—V1-3—V1-6—V1-5—V2-3—V2-4—capillary column—V2-2—V2-1—FID
  • Line 2: Aux-4—V1-2—V1-1—V3-3—V3-2—V4-3—V4-2—V4-5—V4-4—out
  • Line 3: Front inlet—V3-5—V3-4—V3-1—V3-8


Sample gas flow with He:

  • HaySep R column—V3-6—V3-7—V4-9—V4-8—TCD

Backflush:

  • Line 4: Back inlet—V4-6—V4-7—MolSieve column—V4-1—V4-10—vent


Image Added
Figure 14. NGA in Run Mode: 1.83–8.49 min after starting run.


Run Mode at 8.50 min (close Valve V3)

He gas (green) and sample gas (red) flows in the NGA 8.50–9.09 min after start of run. After V3 closes, He from the front inlet flushes the HaySep column and the line leading to the TCD (backflush).
He gas flow:

  • Line 1: Aux-3—V1-4—V1-3—V1-6—V1-5—V2-3—V2-4—capillary column—V2-2—V2-1—FID
  • Line 2: Aux-4—V1-2—V1-1—V3-3—V3-4—V3-1—V3-2—V4-3—V4-2—V4-5—V4-4—out
  • Line 3: Back inlet—V4-6—V4-7—MolSieve column—V4-1—V4-10—vent


Backflush:

  • Line 3: Front inlet—V3-5—V3-6—HaySep R column—V3-8—V3-7—V4-9—V4-8—TCD


Image Added
Figure 15. NGA in Run Mode: 8.50–9.09 min after starting run.


Run Mode at 10.0 min (close Valves V1 and V2)

He (green) and sample gas (red) flows in the NGA 9.09–10.0 min after start of run. After V1 and V2 close, He flow returns to standby mode.
He gas flow:

  • Line 1: Aux-3—V1-4—V1-5—V2-3—V2-2—capillary column—V2-4—V2-1—FID
  • Line 2: Aux-4—V1-2—V1-3—V1-6—V1-1—V3-3—V3-4—V3-1—V3-2—V4-3—V4-2—V4-5—V4-4—out
  • Line 3: Front inlet—V3-5—V3-6—HaySep R column—V3-8—V3-7—V4-9—V4-8—TCD
  • Line 4: Back inlet—V4-6—V4-7—MolSieve column—V4-1—V4-10—vent


Image Added
Figure 16. NGA in Run Mode: 9.09–10.0 min after starting run.


GC3 & NGA Startup

Overview

The chromatography application ChemStation controls GC data acquisition and processing. It can be run either online or offline. Offline mode can be run without communication with the GCs, so it is useful for reintegrating or reprocessing chromatograms. Online mode requires communication with the GC.


Starting up GC3/GC-NGA and ChemStation


Start ChemStation software and load the appropriate method for the analysis (see Starting up ChemStation and GC Ovens).


Condition the GC (see Conditioning the GC). If the GC has been turned off for longer than a week, then bake the column for 8 hr with gas flowing (manually set the oven temperature to 175°C for GC3 or 275°C for NGA).


Run a calibration curve (see GC3/NGA User Guide).


Run a calibration verification standard (see GC3/NGA User Guide)


Run a test sample (see GC3/NGA User Guide)

Starting up ChemStation and GC Ovens


Turn on the GC. WARNING: Before turning on the GC, make sure the gas lines are open.
The 6890 GC performs a comprehensive self-evaluation and shows real-time diagnostics on the screen. Warning, Fault, or Bad Main Board & Fatal Error messages require troubleshooting before moving to the next step (see Maintenance & Troubleshooting (HP6890GC)).


Turn on the PC.


Click the GC3 Online or NGA Online icon to start ChemStation. The Method and Run Control window opens. At startup, ChemStation uses the method last used (shown on the main screen). In addition, the GC LCD shows the loaded settings from ChemStation.
Settings changed on the GC using the GC control panel are also made to ChemStation, and parameter changes entered into ChemStation are made to the GC. ChemStation will prompt to save changes.


To load a different method in Chemstation:

  • Click Method > Load Method, select the method from the list, and press OK or
  • Click the Method tab on the left side of the window and select a method to load

The system automatically loads the new method selected in ChemStation to the appropriate GC. Oven and detector temperatures may increase immediately after a new method is loaded, and the FID will ignite when the detector temperature reaches 150°C. Sometimes, the GC beeps because the FID flame is out, especially after a long idle period. See Maintenance & Troubleshooting (HP6890GC).

GC3 Methods

Method Title

Definition

GC390FR.M

Standard operation method since November 2007.

def_gc.m

Default for ChemStation. This method must be kept in the Method folder permanently.

cbt.m

Default method for training.

estd_ex.m

Default method for training.

istd_ex.m

Method created onshore to make conditions for GC3.

NGA Methods

Method title

Definition

NGA_CS

Standard operation method since November 2007.

NGA_308

Method for IODP phase 1, Expedition 308.

def_gc.m

Default for ChemStation. This method must be kept in the Method folder permanently.

cbt.m

Default method for training.

estd_ex.m

Default method for training.

istd_ex.m

Method created onshore to make conditions for GC3.

Conditioning the GC


To condition the GCs, in the Main menu click RunControl > Sample Info.


Fill in the following fields:

  • Operator name: your last name
  • Sample name: "cond" for conditioning
  • Comment: "Conditioning"
    Click OK to close window and save information.

Prepare laboratory air (5000 µL) and inject it into the GC when the ChemStation software shows Ready.


Press the Start button on the GC control panel to start the run.


Confirm the chromatogram on the screen shows no peaks. If peaks are present, the system contamination must be found (injector, detector, sample loop, etc.).

LIMS Data Upload

Overview

Data is uploaded from the GC3 and NGA in one of two modes:

  • Automatic mode: files are uploaded as soon as the run completes
  • Manual mode: the user selects upload from the menu


Automatic Upload

Data is uploaded from the GC3 and NGA via a multi-step process:

  1. When the run is complete, a macro (GC3_LIMS.MAC or NGA_LIMS.MAC) is automatically called, as configured in the method file. The macro copies information from the method directory to C:\LIMS\NGA\data or C:\LIMS\GC3\data.
  2. An in-house program called MegaUploadaTron (MUT) monitors the data folder locations and when a file is copied in initiates the next steps of the upload process.
  • The file is opened and read, and data points are uploaded to LIMS
  • The data files are compressed (zipped) and uploaded as well
  • LIMS analysis codes are GC3, NGAFID, and NGATCD
  1. After the upload to LIMS is complete, MUT moves the data files to an archive directory at C:\DATA\GC3\archive or C:\DATA\NGA\archive.
  2. If an upload error occurs, the files are not archived and MUT will report the error in the main window (only).

Manual Upload

If MUT is not running when the GC finishes, files will queue in the data directory for manual upload.

Maintenance & Troubleshooting (HP6890GC)

Overview

Use the Status and Info keys on the GC keypad as a first check when something goes wrong.

Leak Checking

When checking for leaks, check both parts of the system:

  • External leaks: gas cylinders, gas purifiers/traps, regulator fittings, supply shutoff valves, GC supply fittings.
  • GC leaks: inlets, purge vents; column connections to inlets, detectors, valves, splitters, adapters, and unions.


For safe leak-checking and flow measurement:

  • Purge flowmeters with inert gas after measuring a flammable gas (such as hydrogen).
  • Measure gases individually.
  • Turn off detectors while measuring gas flows.

Column Size and Carrier Gas Flow Rate

Column type

Column ID

Carrier gas flow rate (mL/min)

 



Hydrogen

Helium

Packed

1/8 inch


30


1/4 inch


60

Capillary

50 µm

0.5

0.4


100 µm

1.0

0.8


200 µm

2.0

1.6


250 µm

2.5

2.0


320 µm

3.2

2.6


530 µm

5.3

4.2

These flow rates at normal temperature and pressure (25°C and 1 atm) are recommended for all column temperatures.
For capillary columns, flow rates are proportional to column diameter and are 20% lower for helium than for hydrogen.




6890GC Messages


Message

Description/Cause

Troubleshooting

Not Ready

"Not Ready" LED lights (a component of the GC is not ready to begin a run)

  • Press Status key for explanation
  • Check for leaks in gas lines
  • Check gas supply delivery pressure
  • Check that oven, inlet, and detector temperatures are not too far apart

Method Mismatch

A loaded method contains parameters that do not match the GC's current configuration

  • If the parameter is set from the keyboard, method will overwrite current parameter and display a message that the parameter has been replaced
  • If the parameter depends on hardware, the method will be ignored and the current setpoints will remain. A message will indicate the method parameter is being ignored.

Follow ChemStation instructions
After method update, open Method parameter to check new setting; edit method if needed

Warning

A serious problem exists.

  • GC will not stop or prevent a run
  • GC emits 1 beep and displays warning message
  • Warning appears at run start
  • Warning is not recorded in run log

Press Status key to view explanation

Shutdown

Shutdown occurs/numbered error message is displayed

Pop-up message briefly explains the nature of the problem

Faults

Hardware problem requires user intervention

  • GC emits no beep or a single beep
  • Ready LED does not light
  • Error message appears

Press Status button for more information

Bad Main Board & Fatal Errors

Main board has malfunctioned; must be replaced

See



Bad Mainboard/Fatal Error Messages

Anchor
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RTF36313337363a203348656164

Common Chromatography Problems

Problem

Cause

Troubleshooting

No peaks on chromatogram

Acquisition aborted

Confirm the method is correct


Bad cable or connection

Check cables between GC and PC, detectors and GC


Leak in sample line

  • Purge test injectors and detectors
  • Check sample loop and columns for leaks


FID flame out

See FID flame out/will not light


TCD filament break

Measure TCD filament resistance (~10 ohm)


Column break

Check column installation

Retention times inconsistent

Column flow has changed

  • Check for leaks at inlet, liner, column connections
  • Check carrier gas supply pressure
  • Check column installation
  • Check method


FID jet contaminated

Remove jet and clean


Injector port temperature wrong

Check method


Oven temp program changed

Check method


Column overload

Inject less sample

Extra peaks on chromatogram

Contamination in system

  • Clean sample loops and injector port with solvent
  • Check gas trap indicators and expiration dates
  • Verify carrier/detector gas purity
  • Check gas supply tubing and fittings
  • Click Start on the control panel of GC without injection to confirm column contamination


Contaminated syringe

  • Clean syringe and vials with solvent
  • Click Start on the control panel of GC without injection, then inject laboratory air

Noisy baseline/random spiking

Leaks

  • Check for leaks at column fittings


Contamination

  • Verify purity of carrier/detector gases
  • Inspect the jet for contamination
  • Verify column has been conditioned


Electrical problem

  • Column is installed too high in detector
  • Electronic interference in laboratory

Common Hardware Problems

Problem

Cause

Troubleshooting

FID flame out/will not light

Detector gas flow incorrect

  • Check that gas lines are open
  • Check the gas system for leaks
  • Check air/hydrogen flow rates/mix
  • Check column flow rate
  • Check column/detector fitting for leaks


FID temperature too low

Wait 15–20 min for conditioning
Press Front Detector on the GC control panel and light the flame manually

FID flame out/will not light

Bad igniter

Remove heater/sensor assembly from the FID and measure resistance of heater and sensor. Replace ignitor if resistance is too high or too low:

  • Heater resistance = ~22 ohm
  • Sensor resistance = ~109 ohm


Jet dirty or partially plugged

Remove jet and clean


Flame will not stay lit

Check dessicant state in the hydrogen generator

Oven cannot attain or maintain setpoint temperature

  • Oven flaps
  • Oven fan
  • Oven heater
  • Oven temperature sensor

Contact service representative










Bad Mainboard/Fatal Error Messages

Message

Comment

Main FPGA Failure

Contact vendor representative

Static RAM Failure


Boot ROM Checksum


ROM #2 or #3 Checksum

EEPROM 2 or 3 malfunction

Incorrect ROM #2 or #3

EEPROM 2 or 3 installed in wrong position

ROM #2 or #3 wrong version

EEPROM 2 or 3 does not match other EEPROMs

DMA FPGA Failure

Contact vendor representative

DRAM Failure


Exception Vector


Bus Error


Address Error


Illegal Instruction


Divide by Zero


No 512Hz Interrupt



Shutdown Messages

Message number

Message

Explanation/Troubleshooting

1

Oven shut off

  • Oven flap malfunction
  • Thermal leaks (missing insulation)
  • Excessive oven load
  • Heater electronics malfunction

2

Oven cryo shutdown

Timeout

3, 5

Inlet pressure shutdown

Inlet does not reach setpoint

4, 6

Inlet flow shutdown


5, 8

Front detector fuel gas shutdown

Gas unable to reach/maintain setpoint in time allowed

6, 9

Front detector air/ref shutdown


7, 10

Front detector makeup shutdown


8, 9, 10

Pres aux shutdown

Pneumatics aux module cannot maintain setpoint

9

Multiposition valve not switching

  • Valve disconnected
  • Valve stuck
  • Switching time too short

10

Can't reach setpoint of multiposition valve

  • Valve position incorrect
  • Invert BCD setpoint incorrect

11, 12

Inlet cryo shutdown

Timeout

12, 14

Aux cryo shutdown


13, 14

Inlet heating too slowly

  • Temperature sensor failure
  • Zone heater defective

Warning Messages

Message number

Message

Explanation/Troubleshooting

100

Oven sensor missing


101, 102

Invalid heater power

Invalid heater power for front detector, inlet, or aux 1 or 2

103, 104

Signal buffer full

  • PC network down
  • PC cable disconnected
  • PC turned off
  • PC entered power saver mode
  • PC data collection stopped
  • GC hardware problem

105

Analog out data loss

Possible data loss

106

Signal data loss


107, 108

Detector config changed

Correct method to match hardware

109, 110

Inlet config changed


111, 112

Column config changed


113, 114, 115

Aux method changed


116

Log overflow

Capacity = 50 entries

117, 118

Inlet calibration deleted

Returned to default calibration

119, 120

Detector calibration deleted


121

Aux calib deleted


122

Comm data overrun

Possible data loss

123

Comm data error


124

Comm abnormal break

Check connection

125

Sampler data overrun

Possible data loss

126

Sampler data error


127

Sampler abnormal break

Check connection

128, 129

Inlet flow calibration fail

Contact vendor representative

130, 131

Aux cryo disabled

Reconfigure cryo

132–137

Sampling end problem

Setpoint conflicts with sampling end time parameter


Fault Messages

Message number

Message

Comments

200, 201

Faulty pneumatics board


202

Hydrogen shutdown

  • Check gas supply pressure
  • Check for leaks
  • Check for broken column
  • Check for stuck valve stuck

203–207

Signal DSP fault


208–211

Out signal path test failed


212, 213

Detector electrometer out of spec


214, 215

Detector flame out

  • Check hydrogen/air flow rates
  • Check for leaks at detector/column fitting
  • Check jet

216–219

TCD filament open or shorted

  • Check wire connections
  • Check cell temperature sensor
  • Replace TCD cell

220, 221

Thermal shutdown

  • Check electrical supply to GC
  • Check zone control electronics
  • Possible shorted temperature sensor
  • Possible shorted heater

222–224

Oven temperature fault


225–228

Detector temperature fault


229–232

Inlet temperature fault


233–236

Aux temperature fault


237, 238

Line interrupt fault


239, 240

Mux ADC thermal shutdown


241

Invalid line sense


242–244

Pneu aux module invalid constants


245–249

Obsolete EEPROM


250–254

Wrong module


255–258

Invalid module


259, 260

Detector module/board mismatch


261

MIO board defective


262, 264

RS232 defective


263

GPIB defective


265–269

Invalid pids


270–274

Invalid checksum


275–279

Invalid constants from factory calibration


280–284

I/O failure


285, 286

Detector offset adjustment failed


Archive Version

LMUG-GC3-NGAAUG2011-230220-1905-146.pdf