Author Archive

Are your ghost peaks coming from the GC column, or something else?


This is a common GC troubleshooting question.  Since determining the source of the ghost (contamination) peaks can be difficult, I decided to write this post to (hopefully) help our customers.


GC column carryover

When I operated an instrument on a daily basis, it was only a matter of time before something caused ghost peaks in my chromatogram.  So how did I narrow down the source of the ghost peaks?  First, I would cool the injection port.  Then, I would program the GC so that I could simply press the Start Button to acquire data for an analytical analysis without injecting any sample, standard, solvent blank, etc.  In other words, with a cold injection port, and without injecting anything, I would acquire some data while heating the GC oven.  In most cases, there were no ghost peaks in my chromatogram, or if there was, they were much, much smaller.  This told me that the ghost peaks were not a result of my GC column.  However, if the ghost peaks remained, I would trim 1-loop (approximately 0.5-meters) from the inlet side of my capillary column and perform a 10 minute bake-out by setting the GC oven to 20°C less than the column’s maximum isothermal temperature.


Injection port septa

If the GC column is not causing ghost peaks, where should you look next?  One of the most common sources is injection port septa.  I wrote the following post to help identify and fix this issue.

Troubleshooting Injection Port Septa

To test, replace the injection port liner after thoroughly cleaning the injection port.  Then replace your injection port septa and make sure your septum purge is working properly (by measuring the septum purge flow with a flow meter).  Keep the injection port cool and without injecting anything, obtain some data like described in the GC column carryover paragraph above.  This same test can also identify potential off-gassing contamination from the injection port O-ring (if applicable to your instrument).



If the baseline does not contain ghost peaks, heat the injection port and acquire an analytical analysis without injecting anything.  If the baseline still does not contain ghost peaks, inject a solvent blank into a heated injection port.  If you observe peaks, your syringe, blank solvent, and/or rinse vial solvent may be the problem, and you should review the posts below.  Or, your injection port may not be as clean as you think it is.

Troubleshooting GC Syringe Issues

Troubleshooting GC Syringe Issues – Part 2

syringe 2


Vial Septa

Another potential source of ghost peaks is from your sample/standard vial septa.  So how do you test for this?  I used to remove the septa from the vial cap and make an injection (manually or using an autosampler).  Do you still see peaks?  If not, these septa are likely the cause.  If you do, then switch to a septa made from different material and repeat the experiment.  Remember to only inject once from a vial, as piercing the septa multiple times may lead to ghost peaks.



Carrier Gas

If nothing listed above helps you determine the source of the ghost peaks, take a closer look at your instrument and/or carrier gas.  Testing carrier gas is relatively easy; cool your injection port and GC oven temperature to 35°C while letting the carrier gas flow for several hours (do not cool the detector).  With the GC oven and injection port still at 35°C, start acquiring data with the instrument.  Then, increase the injection port and oven temperatures.  If you notice ghost peaks, then suspect the carrier gas.  (Example of a carrier gas filter trap shown below.)



Split Vent line and trap

If you normally operate the GC in splitless mode, you need to check one more thing.  The ghost peaks may actually be coming from the split vent line and/or split vent trap.  Remember that the split vent line is seldom heated, so material (compounds) introduced into it may be condensing out, and vapors may be working their way back into the injection port.  To test, set the injection mode to split (2:1 split should be fine).  Inject a few solvent blanks.  Without letting the instrument switch to splitless mode, acquire data for a sample, standard, or solvent blank.  If the ghost peaks disappear while in the split mode, then the split vent line and/or trap are likely the problem, and both should be replaced.  (Example of a split vent trap shown below.)

split vent 2

I hope something here has helped you identify and fix the source of your ghost peaks.  For additional information on troubleshooting ghost peaks, I suggest you read Jaap de Zeeuw’s blog post Poster on sources for “Ghost-Peaks” in Gas Chromatography which contains links to five articles he has written about ghost peaks.

Thank you.

Broken fused-silica columns – it’s rare, but it does happen.

Once in a while we get a call that one of our GC fused-silica columns has broken, and customers ask if it can be repaired and used.  The answer is “maybe”.


If your column broke while at a high temperature, and the column’s phase has been exposed to oxygen (air), then probably not.  A sure sign of an oxidized phase is high column bleed and/or poor peak shape due to activity.

If it broke while at a low temperature, say 50°C, the column’s phase is probably OK because oxidation occurs very slowly, if at all, at these temperatures.  The only way to know is to repair (as described below) and test the column.


So how should you repair a broken column?  Well, you may not know but when a column breaks, stress fractures are created which travel down the fused-silica tubing.  Therefore, we suggest trimming at least 12 to 18 inches from each broken end using the smooth (flat) edge of a ceramic scoring wafer.  Once trimmed, connect these ends using a glass Press-Tight® Connector, a Vu2-Union Connector, or a MXT-Union Connector.


Once repaired, purge the column with carrier gas as described in this post on How to Condition a New Capillary GC Column.  Of course you don’t need to condition your used column, so inject one of your chemical standards and observe compound peak shape and baseline.  If both look fine, you should be able to use your column.


So why do fused-silica columns break?  If the polyimide coating gets scratched, it creates a compromised section of tubing.  It doesn’t take much for it to break if damaged.  On the rare occasion where the tubing may have a small surface defect, the break almost always occurs here at Restek when we manufacture the column, so very few columns ever leave the factory which break afterwards.  An exception to this statement is very high temperature analysis.  This is why I usually recommend our MXT columns for analytical methods which incorporate oven temperatures greater than approximately 360°C and/or extended final temperature hold times above 340°C for 10 minutes or more.  MXT columns are also recommended when a small coil (outside diameter) is needed and when using portable GC’s.

If your new columns breaks shortly after installation, contact us.  Please have the column catalog number and serial number handy.

I hope this has helped.  If you have any questions, email us at

GC capillary columns for the European Pharmacopoeia methods

Have you ever viewed a European Pharmacopoeia method and tried to figure out which Restek GC capillary column you should use? To make the selection a little easier for our customers, I decided to match the nomenclature listed in the European Pharmacopoeia “Reagents” chapter to the appropriate Restek columns.  I hope you find the table below helpful.  If you have any questions, simply send them to or contact your local distributor.  For HPLC column suggestions for these methods, see HPLC columns for the European Pharmacopoeia methods.  Thank you.



EU Capillary 5

Think twice before purchasing a 3/16” OD packed column

So you may be asking yourself, why the cautionary statement? Well, it’s very simple, many of our customers who purchase 3/16” OD (outside diameter) packed columns have a difficult time installing them into their GC oven.  Why?  Sometimes finding the appropriate fitting/ferrule is difficult.

Let’s say you have a packed column instrument. If your injection port was designed for 1/4” OD columns, then installation is usually not an issue.  Most customers can use a 1/4” x 3/16” OD reducing ferrule, like Restek 20258. To center the column properly (which is recommended if you plan to inject your sample into the packed column) and if you have an Agilent GC with a packed column injection port, you can use our kit 21650, which resembles what is shown in the photo below.  The silver thing that looks like a GC injection port liner is called a “centering sleeve”, and as you may guess, its purpose is to center the packed column in the injection port.



Now let’s look at a few scenarios where installing a 3/16” OD packed column is not so simple. Many modern GC’s have injection ports designed for 1/8” packed columns.  So how does one install the larger 3/16” OD packed column into this smaller injection port?  You will need a short piece of 1/8” OD tubing and a 3/16” to 1/8” reducing compression (straight) union like Swagelok SS-300-6-2. Unfortunately, we do not sell this fitting.  However, we do sell a 1/4” x 1/8” reducing union, Restek 23170.  Simply replace the 1/4” metal ferrule set with ferrule 20258.

What if you have a GC designed for only capillary columns? Normally we would recommend a “pigtail” set-up, like described in this FAQ.  How do I install a packed column into a capillary GC injection port?  However, you would need a 3/16” x 1/16” reducing (straight) union, like Swagelok SS-300-6-1. Unfortunately, we do not sell this fitting either.  However, we do sell a 1/4” x 1/16” reducing union, Restek 23169.  Simply replace the 1/4” metal ferrule set with ferrule 20258.

In summary, before purchasing a 3/16” OD packed column, make sure you have the proper fittings/ferrules available for installation. I briefly mentioned this in my post titled Things to Consider Before Ordering a Packed Column.  To save yourself frustration, do a little homework first to determine if a 3/16” OD column is really your best choice, and if not, consider an alternative OD based upon your particular instrument.


What are these O-rings for that I received with my baseplate trap?

Some of you have noticed that included with several of our baseplate traps are a package of two small O-rings. Technical Service has been informed that these are the O-rings which fit onto the check valves on your baseplate (see red arrows below).  Does this mean that you need to replace these O-rings?  Not necessarily.  Carefully inspect the O-rings on the check valves, and if you do not see any signs of wear (cracks, deformation, etc…), you probably don’t need to replace them.  However, if they do exhibit signs of wear, go ahead and replace them.


 Baseplate 4


If you also need the larger O-rings that are located on the baseplate, at the base of the check valves (as identified by the green arrows), you can obtain those by purchasing Restek catalog number 22023.


Which GC injection port liner to use for gas samples

The answer seems fairly straightforward: Use a narrow internal diameter (ID) liner to keep peak shapes sharp by preventing band broadening; but this isn’t always the correct answer. There has to be enough internal volume in the liner to contain all of the sample.  Let me explain.

Let’s first look at liners when using purge & trap (P&T). All instrumentation that I am familiar with uses a transfer line from the P&T unit to the GC injection port.  In this case, you do want to use a narrow ID liner to minimize dead volume and prevent band broadening, especially for the compounds which will not condense and refocus within the capillary column.


Now let’s look at liners when using headspace (HS). Headspace units can transfer the sample to the injection port two ways:

(1) Using a transfer line (like those used on a P&T unit).

(2) Using a Gas-Tight syringe.


If the headspace unit uses a transfer line, then a small ID liner should be used. However, if a Gas-Tight syringe is used to inject the gas sample directly into an injection port liner, then a larger ID liner is commonly used.  I briefly discussed liner selection for gas samples in the post below.

Liners Every Lab Should Own (in my opinion)

In this post, I stated:

(For splitless and split/splitless injections)

The liner below is Restek 23302.1 Sky® 4.0mm ID Single Taper Inlet Liner , which is typically the best choice for 1-2µL injections of non-polar solvents (like hexane), 0.5-1µL injections of polar solvents (like methanol), and gas injections approximately > 250µL to 1mL.



The liner below is Restek 23315.1 Sky® 2.0mm ID Single Taper Inlet Liner , which is typically the best choice for 1µL or less injections of non-polar solvents (with low expansion volumes), or gas injections less than approximately 250µL.





(Split injections)

If you are are injecting into a liner using a Gas-Tight syringe, and splitting your sample, choose an open-bottom liner (with no gooseneck or other restriction at the bottom), like 23301.1 or 23333.1 (shown below).


.Sky® 4.0 mm ID Straight Inlet Liner  (23303.1)



If you are not using a syringe for sample introduction, but instead the sample is from a purge & trap unit or gas sampling valve, then the liner I usually recommend is 23333.1 (photo below).  Sky® 1.0mm ID Straight Inlet Liner



Please note that these are representative liners for an Agilent GC with a split/splitless injection port; the catalog number of the liner you would select depends upon your specific instrument and injection port.


In summary, liner selection for gas samples will depend on your particular instrumentation and how the sample is introduced into the injection port liner. If your instrument uses a transfer line, then a small ID liner will likely provide you the best chromatography.  If a Gas-Tight syringe is used to inject the gas sample, a larger internal diameter liner will usually provide you the best results.

Verify your GC packed/micropacked column carrier gas flow to obtain reproducible results

Working in technical service has taught me many things, but one of the most important has been “don’t assume anything”. This is especially relevant when it comes to verifying the carrier gas flow through GC columns.  To obtain reproducible results from column to column, this verification should always be done after installing a different packed/micropacked column into your GC oven.


 Packed Column

Setting and verifying the carrier gas flow for packed/micropacked columns is commonly done using an electronic flow meter.  This should absolutely be done with every column installation because each packed/micropacked column has a unique pressure drop. Remember that these columns contain packings which are not of a uniform particle size, but rather contain particles which fall within a specified range.  In addition, particle size distribution within this specified range can vary.  To read more about this topic, please see Understanding packed column mesh size ranges

As far as I know, there is no instrument software that can automatically set the desired flow rate. Even for those GC’s which have inlets controlled by a mass flow controller, it is still is a good idea to measure/verify the flow rate exiting the column.

To set and/or verify the desired carrier gas flow rate when using a packed or micropacked column, you will need a flow meter, electronic or bubble.  Below are a few steps which you may want to follow.


  1. Cool all heated zones and then turn off all GC gases.  Allow the current packed/micropacked column (if one is installed) to depressurize so that its removal from the GC (more specifically, the inlet) doesn’t cause a pressure surge which can expel packing from the column.
  2. Install the new column into the injection port.  Do not connect to the detector at this time.   Do not turn on any heated zones.   Slowly increase the head-pressure just until carrier gas starts exiting from the column (holding a thin strip of tissue paper at the column outlet and observing when it moves is a good indicator).
  3. Attach an electronic flow meter (or soap-bubble flow meter) to the outlet of the column and once again begin slowly increasing the inlet’s head-pressure.   When the desired column flow rate has been obtained, continue to monitor the exiting carrier gas flow rate for five minutes to make sure it is stable.


Very long packed columns, packings with irregular shaped particles, very small mesh sizes, and/or very small internal diameter micropacked columns, require high head pressures to obtain proper carrier gas flow.  As a result, many of these columns are commonly used with valve (switching) systems because obtaining reproducible results using a syringe injection can be difficult (sample loss through a punctured injection port septum is common).

By verifying the column’s carrier gas flow rate when you install a different packed/micropacked column, you should obtain reproducible results every time. Thanks for reading.

Need help in selecting replacement weldments and shell weldments for your Agilent 5890/6850/6890 GC?

When you need a replacement weldment and/or shell weldment for your Agilent 5890/6850/6890 GC, we have the parts. However, selecting the correct catalog numbers can be a little confusing for many of us.  As a result, I decided to try and simplify the selection process below.  I hope you find it helpful.


5890 Weldment catalog numbers are 20265 for stainless and 20267 for Siltek –Treated.




5890 Shell Weldment catalog numbers are 20266 for stainless and 20268 for Siltek-Treated.






6850 & 6890 Weldment:  If your GC has one of the split vent traps shown below (Restek kit 23031, commonly called large canister filter),




and your instrument does have electronic pressure control (EPC), then the associated Restek weldment replacements are 22686 for stainless and 22670 for Siltek-Treated.




If your 6850 and/or 6890 GC has a split vent trap like shown below (Restek 22820, sometimes called a split vent pencil trap or chemical trap),




and your 6850 and/or 6890 does not have EPC, then the weldment catalog numbers are 20265 for stainless and 20267 for Siltek-Treated.  Please note that these are the same weldments used on the 5890 injection ports.


If your 6850 and/or 6890 GC has a split vent trap like shown above (Restek 22820), but it does have EPC, then the Restek weldment replacements are 22674 for stainless and 22672 for Siltek-Treated.




6850 & 6890 Shell Weldment catalog numbers are 22673 for stainless and 22671 for Siltek-Treated.



Did I just break my hydrocarbon trap (22012 and/or 22013)?

Once in a while we (tech service) get a call from a customer who went to refill their hydrocarbon trap (Restek #’s 22012 & 22013) and noticed that when they turn the nut shown below by the red arrow, that the end-cap (shown by the blue arrow) is the part which turns.  It was designed this way to make the refill process much easier, and is not a result of a defect, or anything being broken.

Now that you are aware of this feature, the instruction sheet may make a little more sense.   A few other things you may not know about these traps; they have a black anodized aluminum body, contain Viton O-rings, and have nickel-plated brass end fittings.



SDS (MSDS) for VICI® Mat/Sen® Gas-Specific Purifier Modules

Once in a while we (tech service) get asked for a SDS (MSDS) for VICI® Mat/Sen® Gas-Specific Purifier Modules.  Even though we are not required to provide one with the product, sometimes customers need to know their contents.  Simply click on the links below of the appropriate purifier to obtain your SDS (MSDS).


For the Helium, Hydrogen, and Nitrogen Purifier Module  Helium, Hydrogen, and Nitrogen Purifiers

For the Air Module   Air Purifier


Here are a few other related links (if interested).

Contents inside your baseplate trap

Changes are coming to the MSDS; um, I mean the SDS