Pathway analysis tool does not recognize the IDs

Hello, I’m trying to run pathway analysis on my dataset (run on Waters Xevo QTOF, analyzed and identifications made by Progenesis QI, by different libraries). I have a list of all the compounds with PubChem IDs, InChIKeys, SMILES and common names. The problem is that none of these is recognized by the pathways tool. When I use common names, it works the best, but still writes that “Over half of the compound IDs could not be matched to our database. Please make sure that correct compound IDs or common compound names are used”.
Is there any possibility to use something like SMILES or InChiKey for IDs? Many molecules are neither in KEGG nor in HMDB.