I think you are having problems during removal of the esters. You must take special care when removing the esters from the rest of the reaction mixture.

how do you do it?

Another possibility is that your columnis is not in good condition.

Could you  show me a chromatogram?

I have to agree with Veymar. Can you please post chromatograms with and without the "junk" so we can compare the results? This would help us a lot in helping you.

Also, could you please post a brief synopsis of your derivatisation with all the key steps (volumes, times etc. are not relevant)? Maybe there is something that sticks out in helping to explain your current problem.

Thanks,

Sabine

If you're derivatizing, we typically had a very difficult time with residual derivatizing agent when we can drugs-of-abuse via GC/MS.  The residual derivatizing agent would foul the liner and column, but since running the MS in SIM mode you're blind to it for a while, but it's only a matter of time before the extra material you're injecting becomes a problem.

As above

Also cut the first 6 inches from your column and deactivate your glass liner.

Run a conditioning temperature ramp program a few times until a steady base line is achieved

Our derivation steps for red blood cells is to take the red blood cells and add to a vial and then add BF3 and EMD Hexane with an ISTD in it. Heat at 100C for 10minutes, cool for 10minutes and then add de-ionized water. We then remove the hexane layer and run that on our GC.

Here are the chromatograms. I have attached 2 samples and 2 blanks.  Each set has 1 with junk and 1 without junk in it.  The junk came between 9 and 9.5 minutes which is were our Trans-linoleic Acid FAME came off. 

Hi Jeremy,

Could you please post the chromatograms in maybe gif, jepg or similar?

Thanks,

Sabine

I sure can do that. They are as jpegs.

Hi John,

We typically get between 1500 and 2500 injections per column.   By inlet do you mean the whole injection port?  Only thing we do in the injection port is change out the glass liner, septum and O-ring about every 200-300 injections.  I asked our lab manager if we ever done inlet cleaning and they are unsure on how to go about doing that.  Any tips or tricks to it?  Or any guides out there?  I looked online and it just comes up with stuff on the glass liner and occasionally something about the gold seal in the port.

Jeremy,

I agree with the comments above regarding getting rid of your "junk" in respect to chopping the column but also good inlet care as it the "peaks" you see seem to be coming from there. It is just unfortunate that it happened when you changed the lot of the BF3.

Take out the column and cut off about 10 cm on either side of the column.

Before refitting the column, replace the inlet liner (check how dirty the glass wool is: if it is very dirty, i.e. you can see actual specs or discolouration, you will have to change it more often than 200-300 samples) as well as the septum (that may need changing more frequently than 200-300 samples also!).

The gold seal does not typically need very frequent replacement. However, they can cause "junk" to appear in your chromatogram. The seals are not very expensive and really easy to replace once the column and liner are taken out. If you take it out and find it not be "nice and shiny" it certainly requires replacement.

Once you have refitted everything, give the whole inlet a really good bake-out; my suggestion would be about 20C above your typical inlet temp for about 3 hours. This should really clean out the inlet.

Good luck!

I talked with our lab manager about it some more today and showed him all the responses and he brought up the fact that we do not see all the junk peaks when we just run just EMD Hexane through our GC and that all the GC we run (currently 7, all at Shimdazu GC-2010 plus) started to get the same junk at the same time.  He thinks it isn't an inlet issue but said it doesn't hurt to try and clean one out and see if it helps any.  So we will schedule that sometime here.  I attached a chromatogram of an EMD Hexane run.  The "blanks" I attached before were ones we run on GC's without any sample besides our chemical reagents added to them so they were not technically blank.