hi John,

Thanks for your answer.

I agree that ion count might decrease, if I decrease cone or capillary voltages.

I did direct infusion of TLC resolved samples.The solvent was chloroform: methanol (2:1) with 0.1 % formic acid and did it in positive mode.Sorry wanted to correct here, the repeat unit is ~28m/z apart and not 78m/z apart. I have attached file to show the result.

Instrument was clean, I am sure that it was not coming from the cone.....or any other instrument part but good point next time, I will clean them.

Deepti

Are you perhaps using parafilm in your sample prep? Parafilm is a paraffin film, which consists of a series of alkanes which are interspaced by 28u. These compounds are easily extracted by chloroform : methanol, even when there's no direct contact!

I've shut the rough pump off on a GC-MS before and had alkane contamination from oil "backing up" into the instrument. Maybe something is the solvents or plates are contaminated and you can narrow it down. Are you using a nano-chip system where you cover a 96-well plate with a plastic film for direct infusion?  That's all I could think of, best of luck getting it resolved!

Re-extraction of TLC bands gives rise to many sources of impurities. For this kind of analyses it is important to use highest purity solvents since you need plenty of it for quantitative re-extraction. Thereby all possible solvent stabilizers will be enriched by the final evaporation step and become clearly detectable with MS. Which solvents are u using?? (e.g. CHCl3 is often stabilized with amylene/pentene/C5H10).  

Second question :). Do u use plastic or metal TLC plates??

Hi Thomas,

Yes...I am  using CHCl3 for lipid extraction throughout my experiment and even while acquiring MS data through direct infusion ...seems these contamination might be coming from CHCl3 as you suggested.

I am using TLC silica gel 60 which is essentially a glass plate having  silica layer on top.

Thanks you!!

The direct infusion of CHCl3 is usually not the problem since the solvent additives are low concentrated. However during extraction you concentrate a high volume of CHCl3 which increases the noise. The glass plates shouldn´t be a problem. Depending on the "polarity" of your "lipid of interest" just try different solvents e.g. MeOH or 2-propanol. 

Is your lipid "confidential" or can you upload a TLC pic. If u are lucky somebody faced the same identification problem and can help u....which would be faster than MS identification :).

Otherwise....good luck!!!

Try using more polar solvents such as dichloromethane or a mixture of dichloromethane/methanol in ratio 1:1 as your extraction solvent. This may help reduce interference MS is dictating.