Preparing for GC Analysis—A Definitive Checklist

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LCGC North America

LCGC North America, LCGC North America-04-01-2020, Volume 38, Issue 4

In-depth knowledge of GC setup is a significant advantage for the user. Here, a checklist is provided for preparation of a GC or GC–MS system prior to analysis work- referencing the actions, checks, tools, and consumable items that might be required.

My fellow LCGC author John Hinshaw recently published an excellent article on the items in the gas chromatography (GC) toolkit and the uses for those tools (1). Inspired by John’s article, I wanted to produce a checklist for preparation of a GC or gas chromatography–mass spectrometry (GC–MS) system prior to analysis, referencing the actions, checks, tools, and consumable items that might be required. I write this having recently been involved in several troubleshooting exercises where more in-depth knowledge and a pragmatic approach to GC setup would have been a significant advantage for the user.

Check that gases are of the correct purity (99.999%+)

Turn on the cylinders. If cylinder bottle pressure is below 30 psi, replace it. If the line pressure (second regulator stage or gauge at the bench) is below 80 psi, increase the line pressure with cylinder or bench regulator.

Verify gas traps

Verify that the correct gas traps are installed, and not exhausted, and check when they were last replaced.

Is the GC column fit for purpose?

Has it been properly stored (out of sunlight with column ends capped)? How did it perform last time it was used? Check records.

Remove the inlet septum cap

Ensure you have the correct septum in terms of bleed profile and temperature. Use pinch-nose plastic tweezers to avoid scratching the metal surfaces of the inlet. Avoid applying excess torque pressure on the septum by following manufacturer’s guidelines for the inlet closure and septum nut tightening. Failure to do this will lead to septum coring and splitting.

Open the inlet

Inspect the inlet liner and check for cleanliness, including solid debris, discoloration, and dark patches of burned-on matrix contaminants. Ensure that inlet surfaces and seals are included in medium-term maintenance and replacement schedules.

Replace nuts and ferrules on each end of the column

Quarter a used inlet septum and slide one quarter onto both detector and inlet ends of the column, carefully removing any septum shards retained in the head of the column. These will be used to maintain the correct distance between the ferrule and the tip of the column on installation.

Trim and inspect column ends

Trim the ends of the column and inspect with a magnifier or low-power microscope to ensure the cut is straight and there are no rough edges. The quality of the column cut is directly related to peak shape and quantitative reproducibility, therefore good column cutting technique is essential.

Note your manufacturer’s recommended column insertion distance (inlet and detector)

Wipe the outer column surface of the column ends with a solvent suitable for removing contamination from fingerprints (isopropyl alcohol is a popular choice). Adjust the nut and ferrule position and hold in place with the quarter septum from two steps earlier.

Insert the column into the inlet


Tighten the ferrule and gently pull the column to check if the fitting is tight enough. Grip the column and continue to tighten about an eighth of a turn until the column can’t be moved. Repeat with the detector connection.

Input key information

Input into the instrument: column dimensions, carrier gas type, required flow rate, and whether constant flow or constant pressure is to be used. Verify column flow at the detector using an electronic flow meter.

Switch on the inlet and detector heaters, and the detector gas flows

Ignite the detector if it is flame-based.

Purge dissolved oxygen

Purge dissolved oxygen by allowing carrier to flow through the column at ambient temperature for 10–30 min depending upon column dimensions. This step is important and should not be omitted. Failure to purge the phase may lead to unnecessary column damage and increased thermal equilibration times.

Set the oven settings

Set the oven to the conditioning temperature –10 °C above the maximum oven temperature of your method or at the gradient upper temperature limit of the column, whichever is lower. Allow to thermally condition for the period recommended in the guide below

Cool the oven

Cool the oven to starting temperature of your analysis.

Load the test method into the GC and data system

Check the split flow at the split outlet port using an electronic flow meter. Check the septum purge flow using an electronic flow meter. Perform at least one full temperature program according to your analytical method.

Perform a test

Perform a test injection or system suitability test to check method performance.


  • J.V. Hinshaw, LCGC North America, 37(9), 676–683, (2019).

Tony Taylor is the Chief Scientific Officer of Arch Sciences Group and the Technical Director of CHROMacademy. Direct correspondence to: