I would like to share a GC troubleshooting journey with you all in case it may help some other non-expert GC-MS users or maybe some well-experienced scientists as well. Because I have failed hard with this like an amateur :).
Among other unwanted ions, ion 73m/z (accompanied with ions 147, 207, 221 and so) which corresponds to the one and only Dimethylpolysiloxane, one of the most popular ones since -as you well know- it is the main component of most septums and methyl silica columns. When I first encountered bleeding signals (belongs to 73, our protagonist) in my chromatograms I knew what it was, because I had worked with the column quite a long time and it is expected from them to be degraded by time. On the other hand, I had always been careful with the conditions, and that had to be helped with the life-cycle of the column. Nevertheless, as expected, I changed the column and let it be conditioned over the night. When I continued to work with the instrument the other day, yes, the same peaks with the same ions occurred in my chromatogram once again.
If you are not familiar with the issue entirely let me clarify it; this re-occurring is quite overwhelming because you might have just ruined your brand new column too because bleeding signals may also occur with the help of a leakage. Oxygen and humidity coming from the atmosphere and/or from a low-quality carrier gas can also break the integrity of the stationary phase of your capillary column. So I checked all the possible leaking points with the help of a hand-held device but I couldn’t find any. The problem is with these type of high-end instruments, they consist of hundreds of pieces and there are so much to consider. Most of the time the end-user doesn’t bother at all and gives a call to the instrument’s support unit. Well, obviously, this doesn’t apply to me.
Then, the septums I have were actually quite old and it was possible that they started to decay. I replaced them with the new ones and started the instrument all over again. Still the same problem, our hero; Dimethylpolysiloxane. The liner was new and was replaced not long time ago. I cleaned it anyway and I pump the MS again and; Dimethylpolysiloxane. You can understand that almost every single time I had to vent and re-pump the instrument and it is a very time-consuming process, therefore, exhausting both physically and mentally. Though there were tiny little pieces of the septum in the glass wool of the liner which can be considered as a usual phenomenon because the needle can pluck some pieces from the septum of your vial and/or injection port if it is old and lost its sharpness. In this case glass wool steps in and detain these type of impurities to protect the column.
Then I thought; what if something wrong with that detaining mechanism? So I replaced the liner since it is hard to re-load the wool and, for me, was unnecessary. So I pump down the instrument again and once again; 73 and the other musketeers (Dimethylpolysiloxane).
Everything, almost everything was replaced and checked repeatedly, even the Helium was replaced with ultra-pure one, but the problem was still there. There was no other spare column so I was stuck with the contaminated/bleeding ones. Then an idea came to my mind and I vent the MS and remove the column and started to investigate the inlet part with a magnifier. Yes, there were tiny little rascals, lying inside of the column. They were septum pieces and they came to this far passing through the wool filter, vaporizing after 200 C in the oven and causing annoying repetitive signals. I simply bought a new column since even removing these particles can not be enough to get rid of ghost ions.
Regards.
GC-MS contamination Troubleshooting:
It is always a good idea to have a spare (brand new) column on hand. Consider it to be a troubleshooting tool as well as a spare. Contamination issues are frequently sourced to columns (after all, in many cases they are the most restrictive part of the flow path). Relative to your time, materials and operation costs ($$$), columns are inexpensive consumable items. Time and materials are worth far more than the column. Cutting away a bad section (if advisable) or replacement of the suspect column may be the fastest solution to get back up and running again.
Maintaining a spare column for all common applications is something that we used to teach professionally in our GC-MS classes (no longer offered), but is always worth reminding others, as you have learned and done, too. Good job.
Mr. Akkaya,
First of all, the method of mass spectrometry (MS) is absolute (or exact) method for qualitative, quantitative and 3D structural molecular information about the analytes in chemometric terms.
It powerful capability of chemical analyses can be revealed, however, within the framework of our (mine and my co-author's theory according to the shown authorship of the papers) innovative quantitative stochastic dynamic concept and model formulas for quantification of the experimental measurable variable 'intensity' accounting for precisely the fluctuations of the MS variables (both m/z- and 'intensity' values of the MS peaks,) due to the stochastic nature of the mass spectrometric phenomena.
Please, consider references [1-3].
Therefore, if you would like to proof of your claim that the MS peaks at m/z 73, 147, 207, 221 belong to analyte dimethylpolysiloxane, there is needed to carry out a parallel analysis of pure dimethylpolysiloxane according to reference [1] or [2]. The results according to our theory should be absolutely identical with those of the sets of MS peaks at m/z 73, 147, 207, 221 observed experimentally in the questionable samples.
Please, bear in mind that we have obtained an absolute reproducibility of our model formulas within replicase of six measurements studying carbohydrates in mixture, obtaining coefficient of linear correlation /r/ = 1. Please, consider reference [3], in the latter context.
Our method has been tested on analyte concentration levels at pg.(mL)-1 and ng.(L)-1 showing /r/ = 0.99997-1.
[1] Steroids, 164 (2020) 108750
Stochastic dynamic mass spectrometric quantification of steroids in mixture — Part II; Bojidarka Ivanova, Michael Spiteller
[2] B.Ivanova, M. Spiteller, Stochastic dynamic mass spectrometric approach to quantify reserpine in solution, (2020) in press.
[3] Bioorganic Chemistry, 93 (2019) 103308
A mass spectrometric stochastic dynamic diffusion approach to selective quantitative and 3D structural analyses of native cyclodextrins by electrospray ionization and atmospheric pressure chemical ionization methods
Bojidarka Ivanova, Michael Spiteller
What is the stationary phase of the column you are using? 73, 207, 281, 381 (I believe) are all common siloxanes originating from polydimethylsiloxane based stationary phases. Even with an air tight system you'll still see these are background and even distinct peaks if you are looking low enough. Otherwise, what is the problem they are causing? Do you think your background is too high?
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