I have updated the tags for visibility . The alignment procedure aligns the ALS so that the turret and needle carriage move properly. The alignment is most often performed when changing turrets. Reproducibility should not be effected by this alignment. Reproducibility on the auto sampler , if there are issues, could be syringe or plunger motor. Syringe is an easy thing to try. There are other areas that can effect performance that are not related to autosampler such as inlet maintenance and leaks,aged column etc.
Thank you James; I was at first under the understanding that this procedure was more related to turret/syringe alignment and just that. I was performing a USP method verification and the %RSD of the system suitability were close to borderline 2.0%. New column, new insert, new syringe, RRTs spot on, clean chromatographic profile, etc. I ran multiple injections of standard on another instrument with the other new column, same conditions, new insert, syringe, etc. with same response as the fist GC, but very reproducible (0.6% RSD). After, performing the alignment and not changing any thing else, the result was now a 0.2% RSD with the same std solution. Possibly this alignment also optimizes needle depth into the injection port? Thanks again.