Ion Peak Seperation

These chromatographic peaks have merged.

Either the column is old or the method is not very robust.  Have these chromatographic peaks always been merged or have they been baseline separated until now?  When was the last time that full injection port maintenance was done including replacing the liner?  If it is a Split/Splitless injection port when was the last time that the gold seal was replaced?  When was the last time that the column was replaced?  Column life depends on the sample preparation, sample type, injection volume, method parameters, and number of injections. 

What are your chromatographic conditions and sample type?  Please upload the acqmeth.txt file that is underneath your run method's Windows subdirectory.