The LCGC Blog: Preparing for GC Analysis—A Definitive Checklist


I wanted to produce a checklist for preparation of a GC or GC–MS system prior to analysis, 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 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 a more in-depth knowledge and pragmatic approach to GC set-up would have been a significant advantage for the user.


If cylinder bottle pressure less than 30 psi, replace it 

If the line pressure (second regulator stage or gauge at the bench) is below 80 psi, increase line pressure with cylinder or bench regulator



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

Replace the inlet septum



Inspect the inlet liner and check for cleanliness, including solid debris, discoloration, and dark patches of burned-on matrix contaminants

If in doubt, replace the liner– check that the liner geometry and packing is appropriate for your method

Use a fresh liner O-ring as necessary

Replace the inlet bottom seal if necessary (follow manufacturer’s instructions)

Ensure that inlet surfaces and seals are included in medium term maintenance and replacement schedules.





The quality of the column cut is directly related to peak shape and quantitative reproducibility, therefore good column cutting technique is essential



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 pace with the ¼ septum from step 6




Repeat with the detector connection

Verify column flow at the detector using an electronic flow meter



Ignite the detector if it is flame-based



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


Allow to thermally condition for the period recommended in the guide below




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







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

Tony Taylor is Group Technical Director of Crawford Scientific Group and CHROMacademy. His background

is in pharmaceutical R&D and polymer chemistry, but he has spent the past 20 years in training and consulting, working with Crawford Scientific Group clients to ensure they attain the very best analytical science possible. He has trained and consulted with thousands of analytical chemists globally and is passionate about professional development in separation science, developing CHROMacademy as a means to provide high-quality online education to analytical chemists. His current research interests include HPLC column selectivity codification, advanced automated sample preparation, and LC–MS and GC–MS for materials characterization, especially in the field of extractables and leachables analysis.

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