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5 Simple Pictures Which Reveal Problems With Your GC Analysis – And How to Fix Them!

A picture paints a thousand words.  The art of GC troubleshooting often lies in being able to recognize a problem from the evidence presented in the chromatogram or baseline appearance.  In this short series of articles, we present simple GC pictures which show you how to recognize the issues, deal with the causes, and prevent them from happening again.

1) Baseline Spikes
Baseline Spikes

What type of spike do you have?  Zoom into the chromatogram and look at the noise - do the peaks have Gaussian shape and a peak width, if not then the likely cause is electrical noise.  Electrical noise can be caused by a poorly smoothed electrical supply to nearby electrical equipment, this can be overcome by fitting a power scrubber to the supply, isolating any equipment giving rise to the problem, removing it to a different area of the laboratory or placing it on a different ring circuit.

If the peaks have width and occur in a homologous series then column bleed is to blame, to fix this the column can be reconditioned, however, if the bleed profile does not improve you may need to trim the column to remove any contaminated/damaged stationary phase (approximately 5% of the column length) and recondition.

Column bleed (Figure 1) is the elution of degradation products of the stationary phase causing a background signal in the GC detector.  All columns produce bleed products, although bleed is inherently worse for more polar stationary phases, thicker films, and older columns.  A rising baseline during temperature programming is often attributed to column bleed, however, it may also be caused by septum bleed products, sample matrix bleed, changes in the carrier flow (mass-flow sensitive detectors only) etc.  Bleed is characterized by a bleed profile - a temperature program that ramps to the column top operating temperature and holds for 10-15 minutes.

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Figure 1: GC column bleed.

If the peaks have a Gaussian shape, no apparent homologous series, and random peak heights the column may be mounted too high in the FID, coming into contact with the flame, this causes the polyimide coating to flake and peel off into the detector giving the baseline spikes.

2) Tailing Solvent Peak (Splitless Injection)
Baseline Spikes

A tailing solvent peak during splitless injection is indicative of a poorly optimized splitless time.  Too long a splitless time gives solvent peak tailing as not enough of the solvent is vented away and instead enters the column.  Whereas, too short a splitless time results in loss of early eluting analytes.  Monitoring the peak area of an early eluting peak and plotting this against splitless time until a consistent peak area is observed will give the optimum splitless time (5-10 seconds can be added to further optimize this time).

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Figure 2: Optimizing splitless injection - purging the inlet.

3) Tailing Analyte Peaks
Baseline Spikes

If some, but not all analyte peaks are tailing this would indicate a chemical problem.  The most likely cause of chemical tailing is secondary interactions of polar analytes with active sites, typically silanol groups, in the inlet liner, on glass wool in the liner, or at the edges of a poor column cut. 

When all analyte peaks tail this would identify a physical problem (unless all analytes have similar chemistries, i.e. they are all basic).  For example, a poor column cut can expose surface silanol species that basic analytes can interact with causing tailing, or it can result in turbulent eddies at the column inlet which causes analytes to be held up prior to entering the column leading to tailing.  Re-cutting the column and examining the cut under a microscope to unsure it is smooth and at 90° to the column wall will resolve this issue.

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Figure 3: GC column installation.

4) Chair Shaped Peaks
Baseline Spikes

If all peaks are affected a physical issue rather than a chemical one is to blame.  Chair shaped peaks can be caused by a poor column cut.  If the chair shaped peak is accompanied by a broad solvent peak which exhibits a sudden vertical cut-off this would point to the column being installed too high in the inlet.

Ensure that guidelines for column insertion distances are followed closely. Use the septum to keep the nut and ferrule at the correct position on the column whilst inserting the column.  Note that you MUST consult your GC system manufacturer to find out what the correct column connection length (either L1 or L2) that must be used (Figure 4).

If the column is incorrectly positioned broad peaks or incorrect peak area ratios will be seen due to the increase in dead volume, incorrect sampling of analytes into the column, or analyte degradation.

Setting the column insertion depth

Figure 4: Setting the column insertion depth (L).

Incorrect GC column positioning

Figure 5: Incorrect GC column positioning is the source for a multitude of GC peak shape and quantitation problems.

5) Shifting Baseline Position
Baseline Spikes

This is a different phenomenon to baseline drift.  Here a shift between the start and end of the solvent peak is seen which suggests that the gas flow is changing during the injection cycle, which affects the response of mass-flow sensitive detectors to impurities in the carrier gas.  This could be due to leaks during, before, or after injection caused by a cored or leaking septum, therefore, check your septum regularly for damage.

Septa integrity

Figure 6: Septa integrity versus injection number (N).


There may be other causes of these problems, so for further troubleshooting tips visit the CHROMacademy GC Troubleshooter »

Watch the associated webcast here and check out some of our other great CHROMacademy content…

Webcasts & Tutorials

GC Troubleshooting Masterclass »

Troubleshooting GC Separations - Retention Time, Efficiency, and Peak Shape Issues »

Troubleshooting GC Separations - Selectivity, Resolution, and Baseline Issues »

Quick Guides

GC Column Installation and Conditioning Guide »

Chromatography Troubleshooting Tips »

GC Column Maintenance - Prevention is Better than Cure »

10 Common GC Mistakes »

Troubleshooting Videos

Practical GC Troubleshooting Video - Peak Splitting »

Practical GC Troubleshooting Video - Peak Tailing »

Practical GC Troubleshooting Video - Peak Area Reproducibility »

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Dr. Dawn Watson

This article was written by Dr. Dawn Watson.

Dawn received her PhD in synthetic inorganic chemistry from the University of Strathclyde, Glasgow. The focus of her PhD thesis was the synthesis and application of soft scorpionate ligands. As well as synthetic skills, this work relied on the use of a wide variety of analytical techniques, such as, NMR, mass spectrometry (MS), Raman spectroscopy, infrared spectroscopy (IR), UV-visible spectroscopy, electrochemistry, and thermogravimetric analysis.

Following her PhD she spent two years as a postdoctoral research fellow at Princeton University studying the reaction kinetics of small molecule oxidation by catalysts based on Cytochrome P450. In order to monitor these reactions stopped-flow kinetics, NMR, HPLC, GC-MS, and LC-MS techniques were utilized.

Prior to joining the Crawford Scientific and CHROMacademy technical team she worked for Gilson providing sales and support for the entire product range including, HPLC (both analytical and preparative), solid phase extraction, automated liquid handling, mass spec, pipettes, and laboratory consumables.

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