i had been lazy writing/posting some chemical stuff for a while that's why this blog had been growing some moss and organisms particular to stagnation.
anyways, despite the [pseudo]writer's writers' block, this year had been motivatingly dynamic, well, at least, chemistry-wise. :)
well, i almost got started with my masters in soil science, but, fortunately, i underwent a very drastic career turn. i am now endowed to aroma in rice and my job also calls for my contribution in the quality evaluation program in rice. everything is exciting that i almost got no time to write my adventures in chemistry.
last may, i started with my new group doing research on rice grain quality. t'was a sudden shift from environmental aspect of rice research to the 'more direct' aspect, i.e. cereal chemistry rice chemistry.
i was also given the chance to continue some aroma research on rice and to plant aromatic lines in our experiment station's quarantine plot.
last august, i was able to participate in the 3rd INQR Symposium. See http://irri.org/news-events/irri-news/thailand-international-network-for-quality-rice-meets-in-bangkok. meeting and interacting with other scientists and getting to know what cool stuff they are doing is simply amazing! every member of the network was generous enough to share their knowledge and humble enough to listen to comments and other ideas on how they could improve their experiments.
well, so far, i had been learning more stuff from my colleagues on gas chromatography, laboratory management, rice chemistry and more more on rice.
Wednesday, October 5, 2011
Thursday, June 23, 2011
Baseline problem with FID on Agilent 6890GC
It has been more than a month since I started with this new instrument -
Agilent 6890 Gas chromatograph.
Parts were cleaned and at the same time familiarized. Extraction procedures were repeatedly done for the analyses of the fragrant chemical in rice and yet, I still couldn’t find the peak on my samples.
The precious peaks were only seen on the reference material which was from 2ppm 2-AP Japan in ethanol and in-house standard 2-AP pandan (Yes, 2-acetyl-1-pyroline can be extracted from pandan leaves with dichloromethane).
Why couldn’t I find them in the obviously fragrant samples that I have??
Since the GC was started to be used again last May, the baseline was already observed to be at ~ 90. For an optimum setting, baseline should not be more than 20pa. I only have 2 suspicions as sources of this problem:
1. Since I couldn’t detect 2-AP from my samples, it could be possible that I may have committed an error on the extraction itself.
2. It could also be possible that the problem lies within the GC system.
Over all, a high baseline is a result of the following factors:
1. Gas supply problems and inefficient oxygen trap (for helium) and moisture trap (for compressed air)
2. Poor or bleeding column
3. Electrical current leakage
4. Poor flame stability and contaminated FID jet assembly
One by one, these factors were evaluated.
1. Checking on the gas traps, those were indeed old and needed replacements. They have been used since 2006. :)) Furthermore, one is really not sure.
2. The old column (HP-5MS) was baked; the baseline was still the same. A new column (HP-5) was installed and conditioned. Baseline was still at ~70-90pa. It could be possible that the column is really not the problem. [Changing the column meant that the GC also has to have some changes on its settings but these changes are automatic, so no worries on that part.]
3. leakages on the fid set up was evaluated using the procedures described by Agilent. Flame was first extinguished and the level of current observed at the baseline is evaluated. As expected, the signal (for baseline) gradually went down to nil. This is a good sign that the fid doesn’t have any "stray" electric current which may have caused the high baseline. During this evaluation, the fid was still at its operating temperature at 300deg C where as the column and injector temperatures were not at their usual set points.
4. At this point, the column and the carrier gases are eliminated as the culprits. The column was detached to the detector where as the latter was fitted with a no-hole ferrule. The FID was then again ignited, allowed to stabilize and then the baseline was again checked for any significantly unusual change. Still, we are all in vain.
The guy from the technical support had already given us the go signal, if we are that brave, we could bypass the moisture and oxygen traps and let the gases flow directly from the tanks to the instrument. Hmm, at this stage, we won’t do anything that may cause more damage to the GC.
The only safest thing left to do is dismantle the FID assembly and check for any contamination.
And so we did. The fid jet was indeed charry. So the finest sandpaper was used to scratch-off all the char from the jet.
The result made us all happy. The baseline had decreased to 60 and now we are trying to condition it so that we could have a more stable baseline.
As of yesterday, we are now getting peaks from the standards as well as from my samples. This only goes to show that there was no error in preparing the samples just that the fid needs a lot of care and maintenance these days.
Agilent 6890 Gas chromatograph.
Parts were cleaned and at the same time familiarized. Extraction procedures were repeatedly done for the analyses of the fragrant chemical in rice and yet, I still couldn’t find the peak on my samples.
The precious peaks were only seen on the reference material which was from 2ppm 2-AP Japan in ethanol and in-house standard 2-AP pandan (Yes, 2-acetyl-1-pyroline can be extracted from pandan leaves with dichloromethane).
Why couldn’t I find them in the obviously fragrant samples that I have??
Since the GC was started to be used again last May, the baseline was already observed to be at ~ 90. For an optimum setting, baseline should not be more than 20pa. I only have 2 suspicions as sources of this problem:
1. Since I couldn’t detect 2-AP from my samples, it could be possible that I may have committed an error on the extraction itself.
2. It could also be possible that the problem lies within the GC system.
Over all, a high baseline is a result of the following factors:
1. Gas supply problems and inefficient oxygen trap (for helium) and moisture trap (for compressed air)
2. Poor or bleeding column
3. Electrical current leakage
4. Poor flame stability and contaminated FID jet assembly
One by one, these factors were evaluated.
1. Checking on the gas traps, those were indeed old and needed replacements. They have been used since 2006. :)) Furthermore, one is really not sure.
2. The old column (HP-5MS) was baked; the baseline was still the same. A new column (HP-5) was installed and conditioned. Baseline was still at ~70-90pa. It could be possible that the column is really not the problem. [Changing the column meant that the GC also has to have some changes on its settings but these changes are automatic, so no worries on that part.]
3. leakages on the fid set up was evaluated using the procedures described by Agilent. Flame was first extinguished and the level of current observed at the baseline is evaluated. As expected, the signal (for baseline) gradually went down to nil. This is a good sign that the fid doesn’t have any "stray" electric current which may have caused the high baseline. During this evaluation, the fid was still at its operating temperature at 300deg C where as the column and injector temperatures were not at their usual set points.
4. At this point, the column and the carrier gases are eliminated as the culprits. The column was detached to the detector where as the latter was fitted with a no-hole ferrule. The FID was then again ignited, allowed to stabilize and then the baseline was again checked for any significantly unusual change. Still, we are all in vain.
The guy from the technical support had already given us the go signal, if we are that brave, we could bypass the moisture and oxygen traps and let the gases flow directly from the tanks to the instrument. Hmm, at this stage, we won’t do anything that may cause more damage to the GC.
The only safest thing left to do is dismantle the FID assembly and check for any contamination.
And so we did. The fid jet was indeed charry. So the finest sandpaper was used to scratch-off all the char from the jet.
The result made us all happy. The baseline had decreased to 60 and now we are trying to condition it so that we could have a more stable baseline.
As of yesterday, we are now getting peaks from the standards as well as from my samples. This only goes to show that there was no error in preparing the samples just that the fid needs a lot of care and maintenance these days.
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