These are the same programs as far as quantitation processes. As Josef said TargetLynx has more parameters to work with. You will be able to provide more information when running reports if you use TargetLynx. Basically TargetLynx opens more columns to populate in your reporting tool, which provides more information. You can use this additional information to perform calculations not available in QuanLynx. If you don't need that additional info, don't use TargetLynx, or just start off with TargetLynx and don't use QuanLynx. Here is a link to manual from Waters that has section on Quan-Optimise http://www.waters.com/webassets/cms/support/docs/quanlynx_40.pdf