There is no explicit max candidates parameter at this stage as far as I am aware, this is also somewhat problematic as candidates are retrieved effectively randomly, so if you only retrieve a portion, you may be missing “the one”. My gut feeling is that generally above 1000 candidates is difficult to pick the right answer, and above 10,000 candidates the chances of a good result is minimal, but a lot of this depends on your metadata and context, as well as, of course, on the quality and distinctiveness of the fragmentation spectrum. If you search with massive mass windows, you will retrieve far too many candidates and need to restrict the search window further, if possible. Through the web interface, you retrieve candidates first, can see the numbers, then decide whether to proceed. If you use command line, I would recommend to run your queries on a small database (KEGG, HMDB etc) before jumping for PubChem, so you can grasp the possible candidate numbers first (candidate numbers are orders of magnitude greater on PubChem and ChemSpider than the smaller databases). Note that since the scoring is normalized, and MetFrag now has very many scoring options, providing a generalised score cut-off is challenging as this depends on your settings every time … if you have only fragmentation, you can still get score 1 with a very poor match, if all other candidates are even worse … Some reading: https://jcheminf.biomedcentral.com/articles/10.1186/s13321-016-0115-9 http://www.chemconnector.com/2017/12/08/guest-post-by-emma-schymanski-suspect-screening-with-metfrag-and-the-comptox-chemistry-dashboard/ Hope that helps for now…