NEW INSTRUMENT NEWS!

Funded by NSF EAR-IF, our new Thermo 1610GC – GCIsolink II – ConfloIV – Delta Q  is here!!! (March 2024)

Installation was completed by 28th March 2024, and method and protocol development is underway.  Qtegra is quite glitchy (so many reboots!) and we are looking forward to the promised software update in April, that will improve aspects of workflow. At the moment methods have to be built from scratch when making minor modifications, which is a frequent headache when optimizing methods for inlet and GC conditions. We are currently running standards and are excited to establish robust methods and workflows and to begin generating data. Here is Disha Baidya with her first compound specific carbon isotope measurement – and the first sample run on the new system – from Woranso-Mille, Ethiopia.

Funded by NSF EAR-IF, our new Thermo ISQ7610-NoVPI, with GC, FID and AS is here!!! (Oct 2023)

Installation took >3 weeks, rather than 3 days, plus another couple of weeks for applications training and development, in total ~half of the semester – setting up lab instrumentation takes time! Now things are running well (end of October 2023). Here’s the proud team responsible for getting the first methods, workflows and kinks of a new system worked out – we did it!! Samples and number crunching fun is happening!!

Instrumentation in the Feakins lab

GC-IRMS – Gas Chromatography Isotope Ratio Mass Spectrometry
We now use a brand new 2024 Thermo Scientific 1610GC equipped with a Rxi®-5ms (30m x 0.25mm, film thickness 1mm); a PTV inlet; a TriPlus autosampler; connected via GC Isolink II with parallel combustion furnace (at 1000 °C) and pyrolysis furnace (at 1420 °C) together with a Conflo IV to a Delta Q mass spectrometer. Combustion is used for the analysis of 13C/12C and pyrolysis is used for the analysis of D/H.

GC-MS/FID – Gas Chromatography – Mass Spectrometry – Flame Ionization

We now use a brand new 2023 Thermo 1610GC equipped with a AS1610 programmable injector, a Rxi®-5ms column (30m x 0.25mm, film thickness 0.25mm); an FID flame ionization detector; and connected to a ISQ7610 (intelligent single quadrupole) mass spectrometer. The MS provides mass spectral information for biomarker identification and FID provides quantification.

We used to use (2008-2023, retired 2023 at ~25 yrs old) a Agilent 6890 GC equipped with a Rxi®-5ms (30m x 0.25mm, film thickness 0.25mm); and a 7683 programmable injector connected to an Agilent 5973 MSD mass spectrometer and an FID flame ionization detector. The Agilent GC-MS provides mass spectral information for biomarker identification and FID provides quantification.

Preparative facilities in the Feakins lab

Freeze-drying sediments
New, summer 2023! We have a Labconco benchtop 2.5L freeze dryer with an oil-free scroll pump.

We have a Virtis 2k freeze dryer, including secondary cold trap (organic clean) to dry sediment and plant tissue prior to solvent extraction.

Cryogenic Vacuum Line Extraction
We have a vacuum line and offline batch distillation apparatus, to enable efficient extraction of plant leaf waters.

Solvent Extraction
We use Accelerated Solvent Extraction (ASE) by Dionex Corporation, which completes solvent extraction and filtration under high temperature (100°C) and pressure (1500psi).

Virtual Tour of the Lab

Dornsife video: Tap the Past to Map the Future (3 mins)

Method development

Resources that we have developed for compound specific isotopic analysis are shared here.

Protocols for lignin methoxy quantification

  1. Zeisel method for methoxy cleavage and liquid-liquid extraction of product for quantification. SOP1
  2. Lignin phenol calibration for quantification of methoxy in lignin substrates. SOP2

If you use these protocols, please cite:

Lee, H., X. Feng, M. Mastalerz, and S. J. Feakins (2019), Characterizing lignin: Combining lignin phenol, methoxy quantification, and dual stable carbon and hydrogen isotopic techniques, Organic Geochemistry, 136, 103894.

How to derivatize fatty acids for CSIA work?

To derivatize fatty acids e.g. long chain n-alkanoic acids for GC work we methylate the fatty acids to fatty acid methyl esters. To do so, we use HCl and methanol*, for more information, read a paper by Hyejung Lee and co-authors Lee et al., 2017, RCM.

*Purchase a batch of GC-grade methanol for derivatization (4L), bottle it in aliquots (we use 500 mL bottles) and teflon tape to seal. Mark it for isotope use only, not general lab use. Find out the isotopic composition of the methyl in the methanol by derivatizing a known standard.  Phthalic acid of known isotopic composition can be acquired from A. Schimmelmann, U. Indiana (many OG stds here). But wait, it’s not that easy!!

Methylation of phthalic acid requires more care and skill, and slightly different protocols, than long chain (e.g. leaf wax) FAME preparation, see Hyejung’s protocol accompanying her paper that should guide you to success. NB. Beware evaporation of your PAME product. Good luck!!

Then you can correct your FAME CSIA data for the added methyl group to determine the value of the FA. It is all in the paper: full RCM article here.

Make your own combustion reactor

Video: How to pack your own combustion reactor for the GC Isolink3 mins
by Sarah Feakins

Parts list (Excel file) – parts we order to pack our own combustion reactors as well as other common consumables for the PTV-GC-Isolink

Explanation:
The GC Isolink from Thermo has a computer controlled furnace to heat the pyrolysis and combustion reactors. Here we provide an isl script that can be opened and run in workspace that will heat/cool the HTC reactor at a slow rate. The goal is to minimize the development of leaks at solder points, leaks at fittings and microcracks in the reactor. The rate, and set-point temperature can be modified in the script. The script could be modified for the combustion reactor.

Details on how to save and run scripts in Isodat:

*Please note that you use and implement the scripts and these instructions at your own risk.*

  1. Save the files in the same directory along with Thermo ISL scripts C:\Thermo\Isodat NT\Global\ISL\GC Isolink.
  2. Open the ISL script in workspace set the temperature in the script to the target temperature (endT) and then click ‘! Run’ tab.
  3. Leave the script open in workspace. Switch over to Instrument control and you can see the temperature ramp happening (slowly) in the GC Isolink window.

ISL Scripts for Isodat software

For the GC Isolink:

  • //========================================================================
//ISODAT NT SCRIPT LANGUAGE (ISL) : HTC_Temp_Up
//========================================================================
//
//  History list
//    
//  Author      				Date        			Reason      					changes
//  ---------------------------------------------------------------------------------------------------------------------
//
//  Copyright Thermo Fisher Scientific, 2006 
//
//  Michael Cheetham				9/3/2010		initial			automate slow heating of HTC oven
//  MIC						10/13/2010		minor tidying
//  THIS SCRIPT COMES WITH NO WARANTY!
//-------------------------------------------------------------------------------------------------------------------------
include "lib\stdisl.isl"
//-------------------------------------------------------------------------------------------------------------------------
script HTC_Temp_up
{
	switches (EXCLUSIVE-)
}
//-------------------------------------------------------------------------------------------------------------------------
main()
{
	// WARNING: this script will take about 2.5 hours to run with the current temperature ramp
	// it can be safely aborted at any time: however you will need to take care of the reactor (ensure you leave it at a sensible temperature)
	number currT;	// the current temperature of the reactor
	number startT; // the starting temperature of the reactor
	number endT; // the ending temperature of the reactor
	number wait; // the delay between 1C increments in ms

	wait = 9000; // defined to be 200 degrees in 30 minutes
	endT = 1430; // current operating temperature 9/3/10

	startT = _Get("GC IsoLink Node/HTC Temp Get");  // start from the actual current temperature, not the set point

	_UserInfo("Current HTC temp : %2.0f",0,0, startT); 

	for (currT=startT;currT<=endT;currT++;)
	{
	    _Set("GC IsoLink Node/HTC Temp"`, currT);
	    _UserInfo("Current HTC temp : %2.0f",0,0, currT); 
	    _Delay(wait);
	}
	
  _UserInfo("finished setting HTC temperature to %2.0f",0,1,endT);

}	
//--------------------------------------------------------------------------------------------------------------------------
  • //========================================================================
//ISODAT NT SCRIPT LANGUAGE (ISL) : HTC_Temp_Down
//========================================================================
//
//  History list
//    
//  Author      				Date        			Reason      					changes
//  ---------------------------------------------------------------------------------------------------------------------
//
//  Copyright Thermo Fisher Scientific, 2006 
//
//  Michael Cheetham				9/3/2010		initial			automate slow heating of HTC oven
//  MIC						10/13/2010		minor tidying
//  THIS SCRIPT COMES WITH NO WARANTY!
//-------------------------------------------------------------------------------------------------------------------------
include "lib\stdisl.isl"
//-------------------------------------------------------------------------------------------------------------------------
script HTC_Temp_down
{
	switches (EXCLUSIVE-)
}
//-------------------------------------------------------------------------------------------------------------------------
main()
{
	// WARNING: this script will take about 2.5 hours to run with the current temperature ramp
	// it can be safely aborted at any time: however you will need to take care of the reactor (ensure you leave it at a sensible temperature)
	number currT;	// the current temperature of the reactor
	number startT; // the starting temperature of the reactor
	number endT; // the ending temperature of the reactor
	number wait; // the delay between 1C increments in ms

	wait = 9000; // defined to be 200 degrees in 30 minutes
	endT = 400; // current standby temperature 9/3/10

	startT = _Get("GC IsoLink Node/HTC Temp Get");  // start from the actual current temperature, not the set point

	_UserInfo("Current HTC temp : %2.0f",0,0, startT); 

	for (currT=startT;currT>=endT;currT--;)
	{
	    _Set("GC IsoLink Node/HTC Temp"`, currT);
	    _UserInfo("Current HTC temp : %2.0f",0,0, currT); 
	    _Delay(wait);
	}
	
  _UserInfo("finished setting HTC temperature to %2.0f",0,1,endT);

}	
//--------------------------------------------------------------------------------------------------------------------------
  • //========================================================================
//ISODAT NT SCRIPT LANGUAGE (ISL) : Comb_Temp_Up
//========================================================================
//
//  History list
//    
//  Author      				Date        			Reason      					changes
//  ---------------------------------------------------------------------------------------------------------------------
//
//  Copyright Thermo Fisher Scientific, 2006 
//
//  Michael Cheetham				9/3/2010		initial			automate slow heating of oven
//  Sarah Feakins 					12/11/2011	modified for Comb oven
//  THIS SCRIPT COMES WITH NO WARANTY!
//-------------------------------------------------------------------------------------------------------------------------
include "lib\stdisl.isl"
//-------------------------------------------------------------------------------------------------------------------------
script Comb_Temp_up
{
	switches (EXCLUSIVE-)
}
//-------------------------------------------------------------------------------------------------------------------------
main()
{
	// WARNING: this script will take about 2.5 hours to run with the current temperature ramp
	// it can be safely aborted at any time: however you will need to take care of the reactor (ensure you leave it at a sensible temperature)
	number currT;	// the current temperature of the reactor
	number startT; // the starting temperature of the reactor
	number endT; // the ending temperature of the reactor
	number wait; // the delay between 1C increments in ms

	wait = 9000; // defined to be 200 degrees in 30 minutes
	endT = 1000; // current operating temperature 1000C, 12/11/2011

	startT = _Get("GC IsoLink Node/Comb Temp Get");  // start from the actual current temperature, not the set point

	_UserInfo("Current Comb temp : %2.0f",0,0, startT); 

	for (currT=startT;currT<=endT;currT++;)
	{
	    _Set("GC IsoLink Node/Comb Temp"`, currT);
	    _UserInfo("Current Comb temp : %2.0f",0,0, currT); 
	    _Delay(wait);
	}
	
  _UserInfo("finished setting Comb temperature to %2.0f",0,1,endT);

}	
//--------------------------------------------------------------------------------------------------------------------------
  • //========================================================================
//ISODAT NT SCRIPT LANGUAGE (ISL) : Comb_Temp_Down
//========================================================================
//
//  History list
//    
//  Author      				Date        			Reason      					changes
//  ---------------------------------------------------------------------------------------------------------------------
//
//  Copyright Thermo Fisher Scientific, 2006 
//
//  Michael Cheetham				9/3/2010		initial			automate slow heating of oven
//  Sarah Feakins 					12/11/2011	modified for Comb oven
//  THIS SCRIPT COMES WITH NO WARANTY!
//-------------------------------------------------------------------------------------------------------------------------
include "lib\stdisl.isl"
//-------------------------------------------------------------------------------------------------------------------------
script Comb_Temp_down
{
	switches (EXCLUSIVE-)
}
//-------------------------------------------------------------------------------------------------------------------------
main()
{
	// WARNING: this script will take about 2.5 hours to run with the current temperature ramp
	// it can be safely aborted at any time: however you will need to take care of the reactor (ensure you leave it at a sensible temperature)
	number currT;	// the current temperature of the reactor
	number startT; // the starting temperature of the reactor
	number endT; // the ending temperature of the reactor
	number wait; // the delay between 1C increments in ms

	wait = 9000; // defined to be 200 degrees in 30 minutes
	endT = 400; // current standby temperature 12/11/2011

	startT = _Get("GC IsoLink Node/Comb Temp Get");  // start from the actual current temperature, not the set point

	_UserInfo("Current Comb temp : %2.0f",0,0, startT); 

	for (currT=startT;currT>=endT;currT--;)
	{
	    _Set("GC IsoLink Node/Comb Temp"`, currT);
	    _UserInfo("Current Comb temp : %2.0f",0,0, currT); 
	    _Delay(wait);
	}
	
  _UserInfo("finished setting Comb temperature to %2.0f",0,1,endT);

}	
//--------------------------------------------------------------------------------------------------------------------------