Dear Forum

Could I please ask for some peak finding and integration parameter settings advice for MassLynx 4.1.

I am new to chromatographic analysis and I have read the MassLynx Help files.
I have developed a Method file, but am finding that the method that I worked out for the samples at the front of the run is not doing such a good job of catching the peaks at the end of the run. If I open up the Retention time window it changes [degrades] the quality of the integrated peaks and I get square corners instead integrating the peak into the tail. Am I missing something in the method file parameters?

Predicted Retention Time: peak finder parameter is clear to me.

Retention Time Window (min+/-): parameter is less clear to me
Is this RT Window set to catch the drift of the peak apex over the run or is this parameter set to catch the width of the peak (+/- half peak width)

There is another parameter which I am not sure if it would influence this the :
Integration Extent Window. My current method has this set at 2. I have tried changing this [to 0.2] and it really scrambles my integration.

Any pointers in the right direction would be so appreciated as I am getting lost in all the possibilities.

Thank you in advance