Analysis of paired smaples for metabolomic pathway analysis

First of all I am new to both this program and the forum. Thanks to all for their contribution to this great resource!
My question involves metabolome pathway analysis using paired samples for example form animals before and after a treatment. I have tried entering the data using the “index” variables 1 , -1. 2. -2 etc but the program does not seem to recognize this as paired data. Please let me know if there is a way to the pathway analysis performed on paired samples.
Thanks for your help.

Paired analysis is designed for statistical analysis module. You can certainly use the significant compounds (or ranked peaks) generated from paired analysis for pathway analysis.