The sensitivity of a GC analysis is judged by the signal to noise ratio. GC septa is an important source of GC background noise. Low bleed septa reduces background noise .In most of the GC-MS soft-wares are provided by the equipment manufacturer capable of removing background noise by subtraction method. The average mass spectrum from the baseline region adjacent to the targeted peak is subtracted from the mass spectrum of the targeted peak.

Thanks alot

These ups and downs are probably related to how you are acquiring data. I would guess from this that you are running fewer SIM scans from 6.2 - 7.2 minutes than from 5.2 - 6.2 and many more after 7.2 minutes. Examination of a single SIM trace should show no shift like this. If there is a shift then it may be due to the data collection time for each SIM cycle.

If you are getting interference between your apple matrix and your pesticides then you may need to either clean up your extraction, change your chromatographic conditions or monitor different ion in your SIM experiments.

Thanks Richard Evers, can i use MRM to overcome these interferences? I seen in picture attached

You say you are running GC-MS/MS so MRM data should be possible, although if you have many analytes then MRM data may not be right for you.

Probably plotting the extracted ion chromatogram (XIC) should give you a sufficiently clean background that the background effects in your first trace will be eliminated.

Unless your method is at the very early stages of development I would examine your XIC data first before considering a method change.

Thanks alot @Richard Evers for such a nice explanation