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…

You may (or may not!) be interested in some of the functions I’ve played around with here: https://github.com/schymane/ReSOLUTION https://github.com/schymane/ReSOLUTION/blob/master/R/MetFragConfigR.R In my latest scripts (not yet online) I ended up hard coding a limit based on file size, but I ran all the MetFrag results in advance, it was rather the function I used post processing couldn’t deal with the file size of the excels generated. Someone has pointed me to a better one, but I have not yet had a chance to try it. I basically run my dataset on a small database first before trying PubChem, and just leave the long stuff running as long as it needs … I have more than enough to keep me busy while waiting for results so have not really optimized it time wise ;-) If you are using command line and PubChem and will be doing it a lot, it may be worth investigating using PubChem as a local database to increase speed (it’s what the web interface does); just this will not work if you need patent and reference information (this has to be retrieved via the web services and is not in the downloaded mirror). I am not the right person to ask about having PubChem as a local database, I have not done this ;-) as I need the refs and patents, but the experts in Halle can help you there!