Chlorinated phenols contaminate GC column or mass spec?

Discussions about GC-MS, LC-MS, LC-FTIR, and other "coupled" analytical techniques.

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Hi All,
I am analyzing chlorinated phenols with BSTFA derivatization using a GC-MS. The GC column is Agilent J&W DB-1701 and EI-MS. After tens of injections, I noticed that the signal intensities are dropping and one of the chlorinated phenols cannot be detected any more.
When I switch to another same type GC-MS, I could see all of them again. This suggests that the chlorinated phenols are contaminating somewhere in the GC-MS system. But I have no idea where. Any suggestions about the contamination and precaution for this contamination are appreciated! Thanks.
Simon001 wrote:
Hi All,
I am analyzing chlorinated phenols with BSTFA derivatization using a GC-MS. The GC column is Agilent J&W DB-1701 and EI-MS. After tens of injections, I noticed that the signal intensities are dropping and one of the chlorinated phenols cannot be detected any more.
When I switch to another same type GC-MS, I could see all of them again. This suggests that the chlorinated phenols are contaminating somewhere in the GC-MS system. But I have no idea where. Any suggestions about the contamination and precaution for this contamination are appreciated! Thanks.


Could it be the BSTFA that is contaminating the instrument?

We analyze for chlorinated phenols such as 2-Chlorophenol or 2,3,6-Trichlorophenol by GCMS all the time without derivatization using a DB-5 phase column. If the inlet becomes contaminated with a lot of high boiling material like heavy oils we can lose some of these analytes but just changing the inlet liner and removing a few centimeters of column will correct it. Pentachlorophenol is normally the first analyte to be lost, others are less sensitive to contamination.
The past is there to guide us into the future, not to dwell in.
I cleaned the ion source, replaced the liner, septum, glod plate, and the guard column, but the problem was not fixed. I have just replaced the analytical column, hope this can resolve the issue.

About the contamination of BSTFA, I do not have specific idea, as I have just started working on this method.
Just to follow up - I am analyzing 3 tetrachlorophenols (TCPs) and pentachlorophenol (PCP), using pentachlorophenol-13C6 (PCP-13C6) as an internal standard. I could see three TCPs, but PCP and PCP-13C6 are missing.
Contamination of the inlet by high boiling compounds like heavy oils or fats are what I usually see that causes loss of PCP. Often it does not return after inlet maintenance and we have to replace the guard column after removing about 10cm of the analytical column since these compounds can make it past the guard and contaminate the first few cm of the phase coating of the analytical column. A few times we have had samples that contaminate the entire column and it required replacement before PCP would return, but that is not normal.
The past is there to guide us into the future, not to dwell in.
@James_Ball: Thanks for your response. I replaced the analytical column and seems that the PCP signal comes back.
I don't think its the chlorination per se. I ran PCB's and Pesticides routinely on a dual column (DB-5 & DB-1701) with ECD detection and had no problems. Of course I had the very strong chromic acid cleanup for the PCB oils and a routine cleanup for the MeCl extracted PCB's and Pest. samples.

James-Ball response about heavy oils and fats is probably most appropriate.
LALman wrote:
I don't think its the chlorination per se. I ran PCB's and Pesticides routinely on a dual column (DB-5 & DB-1701) with ECD detection and had no problems. Of course I had the very strong chromic acid cleanup for the PCB oils and a routine cleanup for the MeCl extracted PCB's and Pest. samples.

James-Ball response about heavy oils and fats is probably most appropriate.


@LALman: Thanks for the suggestion. I believe the contamination is from the matrix I am working on (meat samples). But I measured the GC injection solution (i.e. BSTFA (with 1% TMCS) derivatization of the chlorophenols in ACN), the pH is between 3-4, i.e. the samples is acidic. I do not know if this high acidic sample also has negative effect on the DB 1701 comlumn I am using.
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