I am attempting to perform identity confirmation of an alcohol on a Varian GC/Ion Trap MS system. The GC is a CP-3800 and the MS is a Saturn 2000.

This requires derivatization with BSTFA/1%TMCS in order to obtain a stable M-15 fragment. Eliminating the derivatization step is not an option since alcohols typically will not yield a molecular ion.

The problem is that when I inject the derivatized alcohol (MW 155) I get an enormous background that prevents adequated detection. This is evidenced by an extremely low ionization time through out the run. This problem only happens when I attempt to inject derivatized samples.

I prepare the derivatized alcohol by combining a solution of ~1000 ng/uL of alcohol in acetone with the BSTFA/1% TMCS at a ratio of 1:1.

My GC conditions are as follows: injection temp 270°C; split ratio 1:40; He flow 1.0 mL/min; oven temp program 100°C for 2 minutes then ramp to 250°C @ 10°C/minute; injection volume 1 uL; injection speed 5 uL/second; column DB-5MS.

I would greatly appreciate any insight you could provide.

Thanks,
Dave

Have you tried injecting a blank of your derivatising reagent solution without the alcohol?

Yes. When the blank is injected, I get the high background. The ionization time is less than a hundred microseconds when it typically runs several thousand when injecting non-derivatized samples. I wonder if my chromatographic conditions could be changed to rid eliminate the huge excess of derivatizing agent right after injections and thus eliminate the high background. Unfortunately, I know more about MS than GC.

Thanks,
Dave

You could try reducing the large excess of derivatising agent solution you are using. The problem is that if there is water in your sample, this reacts with silylating reagents and uses them up. Thus, some people use large excesses. In this regard, I'm not sure that acetone is the best solvent to use, since it probably is contaminated with water.

I don't know the volatility of your alcohol, but it may be possible to blow your derivative solution to dryness with dry nitrogen and reconstitute in a different solvent. This will solve your problem as long as the alcohol derivative didn't go up the chimney too.

Why do you need the molecular ion to confirm identity? The fragmentation pattern should indicate what alcohol is present. If you need the molecular ion, I would try using CI instead of derivitization on an ion trap. As you have noticed, the ion trap is very sensitive to the high background in BSTFA reacted samples. If you try to blow down the sample as suggested above, you will probably evaporate the alcohol and leave he reagent. A different column may help, but there is not enough information given above to tell.

Assuming you are making the TMS ether derivative a MW of 155 leaves the alcohol 'tail' to have a wt of 94 (TMS=61) or about 6.5 carbons. This is fairly volatile, and stable? to run as an alcohol.

I would consider making the acetate or trifluoroacetate ester of the alcohol if it is stable to this derivitization. This can be done at 37°C.

Otherwise I would try drying the alcohol sample and running it underivatized. You might dehydrate the alcohol to the olefin but you could always sum the ions.