Chromatography Forum

Hi,
I have a problem in my GC-MS. I am using 5890GC and 5971MSD. I found there is always a peak around 40min even when I run blank. So I condition the column, cut it, change the linear and septa. When I re-run it, it is even worse, I find a huge peak around 28min (acturally it is not a peak, it is more like a bump), and many peaks after 30, the peak at 40min is still there. If I run temp. program (blank) for several times, the extraneous peaks are gone. Next day, when I re-run it, all the problems come over again. It is looks like septa bleed from my knowledge. But I change it to new bought septa, nothing changed. By the way, recently I use the same kind of septa, I don't have any problem before. From last week, the problems are always there. What wrong and any suggestions? I appreciate your help.

Go back to your original brand of septa.

Ask your vendor if they have any complaints about the newest lots of septa.

It certainly sounds like you have identified the problem.

Bluesky,

Another possibility might be flashback into the injector pneumatics form an earlier dirty sample, bleeding into the injector over time, would give the same type of indications as septum bleed maybe. Just my 2 pennies worth.

Regards,
Mark

Thank you for your reply.
Mark, if it is flashback into the injector pneumatics from an earlier dirty sample, the problem will be gone after I change the septa and liner, right? Or what should I do to get rid of it? By the way, I already conditioned the colum, but the problem is still there.

If you have flash products upstream in your pneumatics they will not go away quickly or with a simple septum injection liner replacement.

This is caused by trying to inject too large a sample to be vaporized in too small a space in the injector. The vaporized cloud expands back into the pneumatics where it may sit in a cold spot and slowly bleed into your injector port and collect onto your septa.

You could also have contaminated gas as your problem ( a new cylinder? or regulator?)

You have a system contamination problem. Now you just have to find where it is coming from. If you have other injection ports and other detectors showing the same problem this will help identify the source of your contamination.

chromatographer1, thank you so much.

Unfortunatly, this is the only GC-MS in my lab. I will try my best to figure out what's the problem.

If it is because of flash products upstream in the pneumatics, how to clean it?

Thanks again.

I have seen this problem with 5890s and 6890s. After multiple injections over a space of about 6 months there can be a build up of material on the split line weldment. This is a "cold" part of the injection port so the majority of anything that goes up there tends to stay there. Maybe I am running very tarry samples but I think that there can be some polymerisation of analytes in the gas phase following an injection, which then condense in the port. It can come off in small amounts if the liner is overloaded and flashback occurs.
The only cure is to strip out the entire welment assembly (not too bad a job as long as you let the system cool down first!) and clean it in a suitable solvent. I find a good cleaning regime is to put the weldment into a beaker full of DMF and place in an ultrasonic bath for about 30 minutes. I usually replace the split line and trap at the same time. The weldment is available from Agilent so it is useful to have a spare to swap over quickly whilst the dirty one is cleaned.
Best of luck.
GCguy

GC Guy covered the Agilent GC situation well. Other brands of GC may have different problems. It entails taking apart your pneumatics and replacing or cleaning the contaminated parts.

I have had to clean and replace a lot of parts if the gas cylinder was contaminated with junk accidently put into the gas cylinder, flow controllers, traps, lines, etc.

If often is easier and cheaper to replace than to clean.

Good luck

Since you are using a GCMS system, what are the major masses that appear in the peaks? If I knew that I could give a more definitive answer to the question.

Thank you all.

Ron, the major masses for the bump peak are 76,105,177,149(base peak), and the major masses for the second peak (symmetrical peak) are 91 (base peak), 117. Any suggestion? Thanks.

The 149 base peak is a phthalate, and the other is probably a light aromatic. It is doubtful either one is coming from the septum. Phthalates come from many sources, but a common source is sample vials, or from solvents stored too long in a container with a plastic cap. The aromatic is probably from the solvent or something in the air.