In the MSMS mode you will be using a collision gas to look at the MS/MS  peaks. If the collision gas is not pure enough you will see such extraneous mass peaks at relatively high level

Hi Chris,

Thanks for your response. In this case I know that the high abundance analytes are from the sample, I also wondered whether they could affect the retention of compounds in the GC column?

Hello Thomas,

Yes, such high concentration of interferences will affect the ionization efficiency of the compound of interest. If possible slow down the temperature ramp on the GC  as will as lowering the initial temp and staying a little longer at the initial temp before starting to ramp up the column temp. If this doesn't work change the column. If you are using a non-polar column change to a moderate polar column. 

Hi Koli,

Great, thanks. Can this occur even if the target analyte and interfering analyte have different retention times?

Is your chromatography working properly? Did you validate the instrument? If the target analytes have different retention time than interfering analytes, I doubt that there would be a problem. Did you calculate the method detection limit for your target analyte? You can always turn the detector off when interfering analytes are reaching the detector.

Ion traps in general use a mechanism called AGC (Automatic Gain Control) to prevent the trap from overloading. The ion injection time is set to maintain the optimum quantity of ions for every scan. AGC consists of a prescan and the following analytical scan. During the prescan the intesity of incoming ions is measured and used to determine the ion sampling time for the analytical scan. This leeds to an influence of coeluting analytes especially for in context with the LOD.

If the target analyte and interfering analyte have different retention times there should be no influence at all.