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High Pressure Liquid Chromatography (HPLC), Ion Chromatography-Mass Spectrometry (IC-MS), Gas Chromatography (GC),
Gas Chromatography-Mass Spectrometry (GC-MS and GC-MS/MS), and software (Chromeleon CDS, LIMS, and ProteinCenter).

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GC GC-MS Troubleshooting Part I; Top 6 Tips for Fixing a Leak


GC, GC-MS, Troubleshooting, Thermo Scientific

There are many problems that can get you into trouble when using a GC and GC-MS.  For me the most time consuming, costly, and frustrating is the leak.  These things cause no end of problems in your GC-MS system.  They will lower the sensitivity of the method, cause you to lose a lot of carrier gas, could damage your column, and damage the mass spectrometer source.  You can get lucky and find them right away or they can take days to track down (the second is usually my luck).  Many of these will be obvious but when you are the most upset they seem to be forgotten, unless that is only me but I’m guessing it’s not.  GC and GC-MS leak checking can be a little more difficult than on an LC.  With an LC when there is a leak you get a puddle, there isn’t much puddling of carrier gas on a GC.  Sometimes a leak on a GC-MS can be seen in the MS tune page, look for masses 18, 28, 32, 44 and their relative intensities.

  1. Thoroughly check your connections.  If you have recently made any gas connections to the GC check there first.   Here is one of the obvious ones but also can be easily forgotten.  Also, may not have been written in the lab notebook if someone was working on the system just before you (this is the one that I would always blame, even if it was only me using it).
  2. Make sure the septum is seated well and if it is old replace it.  Reports on the number of times septa should be replaced will vary.  I suggest just keeping an eye on it; they will eventually develop holes and will leak.  Personally, I replace them daily with heavy use.  The needle will make a big difference here.  Careful with a bevel tip needle.  They can develop burrs and core the septa, look for other thoughts on this too. 
  3. Checking the bottom of the injector.  There are metal on metal points at the bottom of many injectors.  Make sure these are tightened well (please don’t strip the nuts).  The column ferrule needs to be well seated, meaning not easily moved.  It does not need to be tightened with a large wrench; we certainly do not want to crush the column. 
  4. Column connections.  If you are one of those that likes to connect columns together with press fit connections I applaud you.  It usually takes me three times to get a connection like that to be leak free.  Cut the column flat and straight, take your time.  Give it a little pull to make sure it will stay together (very small pull, we don’t want a good connection coming apart).
  5. Connection to the detector.  Seat the column with the ferrule so that the column does not move.  Do not over tighten here, you can leak carrier gas out and air in to the MS.  If you hear a metal on metal squeaking sound you might have gone too far.
  6. Look to o-rings around the manifold if you had the manifold open for some reason.  I have used laboratory wipes and a very small amount of water to wipe the o-rings.  This just makes sure there is no particle causing a gap and leak.   
One last thought, if helium is your carrier gas use a helium “sniffer” detector.  They can really be useful.  Ok, this is the last thought; use a can of high purity electronic duster for a MS system.  Spray a little and look for ions 69 and 83, for the brand we use.  Just spray a little directly at a connection and wait; then move to the next connection.  If you spray too much you see the masses and know they have a leak but not where.  Please do not use Snoop, it contaminates everything. 
Remember, leaks are frustrating but if you keep your calm and work methodically they can be found and fixed.


Please add my email address to your blog
Posted @ Friday, March 23, 2012 5:17 PM by
You have been subscribed!  
thanks for joining the discussion. 
Posted @ Friday, March 23, 2012 5:26 PM by Sonya Pelia
The catharometer detector used for He leak detection is excellent for hydrogen. 
Argon is good for vacuum leak detection, and you know what's in the cylinder. CO2 is too soluble in flexible seals to be of any use. 
I don't know how to say this politely, but if you are having a lot of trouble with leaks, either you havn't really got your "hand in", or there is something wrong with the design of the seals. 
On the GC side at least, it's best to have a sufficiently small number of people doing it. That way, they get regular practice (principle of surgical operations...). Whatever anyone may say, it's best not to wear gloves; just don't use hand cream & wash your hands using plain soap. 
We had a complicated column switching GC/MS system back in the 1980s (it was published), & I don't remember having much difficulty with leaks - presumably because there was plenty of opportunity to practice and we had a gas detector! 
Instrument makers like to design their own connectors (or they used to). Some of these are/were not very clever, and whenever possible I replaced them with SGE. 
Finally, now I think of it, we had a couple of electronic (thermal) flow monitors in the column switching system. With an ordinary GC everything is controlled by pressure regulators and the readouts are relatively less informative if anything has gone wrong.
Posted @ Saturday, March 24, 2012 4:20 AM by Christopher R Lee
The tips you have provided are basic and classic. It does help to be reminded now and then since this tips are normally handed down by word of mouth. I have heard SGE provides good products for this type of problems. 
Posted @ Saturday, March 24, 2012 1:30 PM by Agnes C. Torres
Thank you Eric for your information on leak problem. 
You commented on the abundance of 18, 32 and 44 peaks. Although my auto tune does not show any significant 18 or 32 (only 0.25%) peaks but during the analysis 32 and 44 ions are highly abundant, mainly 90 % of the total background peaks. Do you think that it is normal? 
Posted @ Sunday, March 25, 2012 11:09 AM by hooshang
I like the comment about gloves. I tend to use gloves when putting a source together. You are right though, using clean hands with no creams can be just as good as gloves and it is certainly a lot easier.  
To the comment on the intensities of the ions. First check the vacuum reading. I would be curious what samples and compounds you analyzing.
Posted @ Sunday, March 25, 2012 1:39 PM by Eric
Hi all, 
For me, i would use Ar to spray around the MS or the transfer line to detect m/z 40. For turbopump leakage point, i would prefer to use methanol and rub around the O ring and check for sudden increase fore pressure reading.
Posted @ Wednesday, March 28, 2012 10:14 PM by Richard Ong
Good day to all! Thank you for your theory! All of the above is true. 
One of the problems of leaks in the GC Inlet is leaking. 
This problem is eliminated by holding Leak test. 
You turn off the injector (remove column) and setting the pressure cuts off gas to the balloon through the gearbox. If within 10 minutes of pressure drop, then a leak in the system. 
Check all gas line to the point of connection of the column to the injector. 
The reasons are many (bad connections, leaks in the gas trap, a faulty gas flow control valve, the old septa, a broken liner, etc.). 
Interesting to look for leaks in the detector. 
A huge amount of nitrogen comes out of the filter, if not properly prepared. In each case, after replacing the new filter does not connect the gas line to the chromatograph. At first pass through the filter carrier gas removal from the filter of residual nitrogen. 
When the ions with m / z 18, 28, 32, 44 leaks in the system, the old filter, or the recently opened analyzer. In two recent cases to properly replace the filter and wait for a good vacuum system. 
Check the leakage detector with acetone. 
Locations of possible leaks - seal the side boards, calibration valve, a place connecting tube triode, calibration valve vent, transfer line. I sprayed a small amount of acetone from a syringe on the sealing compound and looking for a surge abundance of ions 43 mass without opening the calibration valve. 
If leakage is found, the trace amount of L-apiezon lubricate seals, carefully wiping the remnants of a lint-free cloth. This procedure helps prevent leaks and create a good vacuum. 
Posted @ Monday, April 16, 2012 4:27 AM by
Posted @ Monday, February 10, 2014 7:45 AM by
Hi Katrin 
What kind of information would you like? Do let us know. 
best regards 
Posted @ Tuesday, February 11, 2014 4:06 AM by Sonya Pelia
the abundance of the 40m/z in the air water spectrum. 
what is the cause, or long term effect? 
the 18m/z and 32m/z have low intensity. leak check @3E5gain shows 0nly 2% leak.
Posted @ Friday, April 04, 2014 4:46 AM by yvonne
Dear Yvonne, 
Thank you for visiting our blog and also your question. I have forwarded to GC expert and expect to hear back shortly. 
best regards 
Posted @ Friday, April 04, 2014 10:01 AM by Sonya Pelia
Hello everyone, 
I have the same probleme as Yvonne: 
- abundance of the 40m/z in the air water spectrum. 
It appears on both GCMS in my laboratory since I change the gas bottle helium 6.0. I've also changed the gas filter. 
Thank you for your answer. 
Best regards 
Sothany from France
Posted @ Wednesday, May 14, 2014 5:01 AM by Sothany
Subscribe via email
Posted @ Friday, May 30, 2014 10:39 AM by Fatima Khan
Hi Fatima, 
I have subscribed you to the blog.  
Best regards 
Posted @ Monday, June 02, 2014 10:33 AM by Sonya Pelia
Hi Malta 
Thanks for visiting our blog and commenting. Much appreciated. 
Glad we could help. 
Best regards 
Posted @ Thursday, July 03, 2014 8:24 AM by Sonya Pelia
what is ion 44?
Posted @ Wednesday, July 16, 2014 2:17 AM by kim elm
Hi Kim, 
Thank you for visiting our blog and commenting. Much appreciated. 
Best regards, 
Posted @ Wednesday, July 16, 2014 11:50 AM by Tanya Tran
Hello guys, 
I am using Shimadzu GC/MS system. Recently there was power trip. When I started the instrument I am not able to build the vacuum system as the instrument showing "High Vacuum Error". I have change the backing pump, tightened the column ends, got new septum and I am runing of ideas now ! 
Can anybody suggest what should I do
Posted @ Thursday, July 17, 2014 4:54 PM by Sanat
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Posted @ Monday, July 21, 2014 12:38 AM by EUPHEMIA
Hello Euphemia, 
We are glad you enjoy our blog! Thank you for visiting and commenting. Much appreciated. 
Best regards, 
Posted @ Monday, July 21, 2014 12:22 PM by Tanya Tran
the abundance of the 40m/z in the air water spectrum.  
what is the cause? 
It appears on both GCMS in my laboratory since I change the gas bottle helium and the gas filter.
Posted @ Thursday, August 14, 2014 2:39 PM by Saul
Hi Saul, 
m/z 40 is almost certainly argon coming from the new gas filter. Argon or nitrogen is typically used as a purge gas for the filters, and it takes a long time for it to be removed. Not to worry though because argon is non-reactive, so it won’t damage the column or cause unwanted reactions in the source, and at such low concentrations relative to helium its presence won’t affect your chromatography. So my recommendation is to ignore it and it will eventually go away, but if it really bothers you, you can disconnect the filter from the GC and blow helium through it at high flow to remove the argon (this still might take an hour or more).  
Best regards, 
Posted @ Thursday, August 14, 2014 3:30 PM by Jason
i have a gcms  
when a run tune in ms without the gc and close the interface line by closed nut  
the tune is stoped and there no leak  
i change the forline pumb still problem 
change the side board still problem 
change the log amp board still problem  
note: this ms not connect any gases  
clean ion source and change the intrance lens  
change all o-ring  
change the interface line  
my question: 
why is the tune is not stable in afternoon ok pass but not good and in med night is not pass
Posted @ Tuesday, April 07, 2015 3:00 AM by mahmoud
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