I can only speak generally on the subject: Specific software varies according to the name brand of your EDS software, regarding how to input a known standard into your software. Quality ZAF quantification requires a well qualified standard. That standard needs to be well quantified itself, and then that data needs to be input into the EDS software as a known standard. I do this by doing 5-6 separate analyses of the chosen standard and then average those results. I then input that “average” into the software as the known standard. The standard should be as close as possible to the elemental content of your unknown sample. One then quantifies the unknown using this standard as the “known” comparator.
Having said this, I have also found that “some” alternate methods to ZAF can be more accurate than ZAF, even more accurate than ZAF with a well qualified known standard. In example, I have been able to reproduce the chemical formula for various amino acids using a Least Squares quantification method with a well qualified standard.
Dear Muhammad Aleem Zahid , your question is a bit fuzzy. I believe you made standardless "quantitative" TEM/EDS analysis of Si-O compound and you are not happy with results. You cannot "convert" data you already have. By the way quantification of specimens like yours with TEM/EDS is nearly impossible. Of course if you have suitable (certified?) SiO2 foil to serve as a standard, you may want to try.