unusual shaped chromatograms in SIM mode recorded by LC/MS

[shohreh]

Hi everybody,

I am working with a LC/MS instrument(Agilent,6400 series,triple quadrupole).The main problem i have are the chromatograms in SIM mode.When my sample concentrations are between 1 ng/mL and 200 ng/mL,the obtained chromatograms are weird.They are stair-like and crinky and the height of the graph(abundance) are 5-6*10.It seems the ionization is not sufficient since when the height changes to 5*100 or more,the chromatogram has normal shape.On the other hand,I don't have any problem with ng concentrations when i am working with the scan mode.I have changed the fragmentor voltage,Dwell,gas flow,... but nothing helped.Any comment in this regard would be highly appreciated.
Tnx
Shohreh

[Widebore]

Hi
If your chromatogram looks fine with scan mode then SIM must work. This is an interesting problem because SIM just usually yields smoother chromatograms than scan mode.The counts you've quoted make no sense to me and appear abnormally low - but maybe its the instrument brand. I'm not sure if you can monitor all of the read-back voltages for the instrument but make sure that when you monitor a single m/z channel that there is not too much fluctuation. On the instruments that I work with you can view the quad voltages and so forth and the mass allowed through the quad. I have used those read-backs to diagnose collision cell problems in the past. Double check that there is not too much fluctuation.

[shohreh]

Thank you for your reply.
Yeah,it's interesting but driving me crazy.
As for the numbers,yes they are too low(40-80).that's why i cannot see the smooth
chromatogram.In the past,when i worked with SIM mode,the height of the abundance plot was 400-800
with the same concentration(1 ng/ml) and 4000-8000 for the higher concentrations while the chromatograms were very smooth and in a normal shape.But now,the height has decreased to 40-80 and
the chromatogram is stair-like(most of the time in the tail part of it).I have changed the capillary voltage,Gas flow,dwell time and also replaced all tubes and the needle,but didn't work.I am thinking about the horn and EMV now.Could they possibly be related to this issue?
BTW,How can i upload an image of my chromatogram on this page?
Tnx