In GC-MS/MS pesticide analysis the base line is neither starting from zero nor it is straight even it is fluctuating from peak to peak. Baseline also vary when changing selected ions in SIM scan. For one ions baseline is different and for others it is different (i.e. by changing method base line also changed). I gave blank run(vail without solvent) its give same base line as in solvent and sample (except extra peaks apears when analyzing sample). I checked air water test, autotune MS/MS, every thing is ok, i also changed septa, washed column by running aceton at higher temperature but still noise remained. Company recently (2 month ago) installed new GC every thing is new, sample run is clean but still these problems are out of understanding. If anyone have knowledge about this please suggest me some tips to overcome this issue. For assistance picture is also attached. Thanks
It looks like you are examining the Total Ion Chromatogram (TIC) only but you need to be looking at the SIM or MRM data using the Extracted Ion Chromatogram (XIC).
Probably the difference in baselines is due to the different number of scans within each area. With many scans up until 6.5 minutes the baselines add up but with only a few scans from 6.5 to 7.5 minutes there will be little total background and therefore the lower total signal.
Hi Noel W Davies and Richard Evers, i attached 3 images having mass spectra at different retention times(at lower and higher base line), the method i am using SIM mode and the ions i selected also displayed on left hand side of picture, i think this is extracted ion chromatogram, if i wrong please correct me. Thanks
Your top chart shows the Total Ion Chromatogram (TIC).
There should be an option to show an extracted ion chromatogram (XIC)
Select XIC and when it asks what ion select 189 the ion that (if I understand correctly) corresponds to tricyclazole. You should then get a smooth baseline with a peak for tricyclazole Do the same for all fragments that you wish to examine.
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