I have example functions, data and documentation here:
https://github.com/schymane/ReSOLUTION/
https://github.com/schymane/ReSOLUTION/blob/master/R/MetFragConfigR.R

We are looking at improving this our side and streamlining documentation etc, if you can install this package from github this should get you started in the interim. The IPB team also have other workflows that may be useful for you.

Thanks, Emma,
I tried the examples in ReSOLUTION package as following

peaklist_path <- system.file("extdata","EA026206_Simazine_peaks.txt",package="ReSOLUTION")
test_dir <- "I:/software/MetFrag/test_190520"
config_file <- MetFragConfig(201.0776, 
                             "[M+H]+", 
                             "Simazine_neutralMass_PubChem", 
                             peaklist_path, 
                             test_dir, 
                             DB="PubChem", 
                             neutralPrecursorMass=TRUE)
MetFragAdductTypes <- read.csv(system.file("extdata","MetFrag_AdductTypes.csv",package="ReSOLUTION"))
metfrag_dir <- "I:/software/MetFrag/"

MetFragCL_name <- "MetFrag2.4.3-CL.jar"
runMetFrag(config_file, metfrag_dir, MetFragCL_name)

It founds 1022 candidates, and return a final result with 682 candidates. However, which function should I use to export the all 1022 candidates? Or how do I modify the parameter to download all 1022 candidates?

This is the log:

INFO de.ipbhalle.metfraglib.database.OnlineExtendedPubChemDatabase - Fetching candidates from PubChem
INFO de.ipbhalle.metfraglib.database.OnlineExtendedPubChemDatabase - Fetching PubMed references
INFO de.ipbhalle.metfraglib.database.OnlineExtendedPubChemDatabase - Fetching patents
INFO de.ipbhalle.metfraglib.process.CombinedMetFragProcess - Got 1022 candidate(s)
INFO de.ipbhalle.metfraglib.process.ProcessingStatus - 10 %
INFO de.ipbhalle.metfraglib.process.ProcessingStatus - 20 %
INFO de.ipbhalle.metfraglib.process.ProcessingStatus - 30 %
INFO de.ipbhalle.metfraglib.process.ProcessingStatus - 40 %
INFO de.ipbhalle.metfraglib.process.ProcessingStatus - 50 %
INFO de.ipbhalle.metfraglib.process.ProcessingStatus - 60 %
INFO de.ipbhalle.metfraglib.process.ProcessingStatus - 70 %
INFO de.ipbhalle.metfraglib.process.ProcessingStatus - 80 %
INFO de.ipbhalle.metfraglib.process.ProcessingStatus - 90 %
INFO de.ipbhalle.metfraglib.process.ProcessingStatus - 100 %
INFO de.ipbhalle.metfraglib.process.CombinedMetFragProcess - Processed 951 candidate(s)
INFO de.ipbhalle.metfraglib.process.CombinedMetFragProcess - 71 candidate(s) were discarded before processing due to pre-filtering
INFO de.ipbhalle.metfraglib.process.CombinedMetFragProcess - 0 candidate(s) discarded during processing due to errors
INFO de.ipbhalle.metfraglib.process.CombinedMetFragProcess - 269 candidate(s) discarded after processing due to post-filtering
INFO de.ipbhalle.metfraglib.process.CombinedMetFragProcess - Stored 682 candidate(s)

The log indicates that your post processing settings are reducing the candidates:
de.ipbhalle.metfraglib.process.CombinedMetFragProcess - 269 candidate(s) discarded after processing due to post-filtering

I highly recommend you choose some examples and try them on the web interface, see what settings result in the parameter files (which you can download) and use this to choose the options that suit what you want to do.

Thanks, I can set "filter_by_InChIKey" and "filter_isotopes" as FALSE to turn off the post-filtering.

However, it still indicates 70 cancidates were discarded before processing due to pre-filter. How do I turn off this function?

Besides, I try the same netural mass in the web server with same setting, but it only retrieve 700 candidates. So I wonder to know why the difference? In the local computer, I use the MetFrag2.4.3-CL.

I attach the config, log and config in webserver.
MetFragWeb_Parameters.txt

Simazine_neutralMass_PubChem_new_2_log.txt

Simazine_neutralMass_PubChem_new_2_config.txt

These candidates are salts / mixtures / disconnected and cannot possibly be observed at the mass of interest and are thus excluded entirely. It is a factor of the way the data is retrieved from PubChem. Since they will not be observed at the mass you have given, it makes no sense to include them, so we have not added an "on/off" option for this case.

To check compatibility between web and CL version in detail, you have to compare the parameter files. Some discrepancy can arise if the web uses the local PubChem mirror versus the live online PubChem query.

Thanks a lot for the patient explanation.

I agree your point that the difference may be casued by the pubchem mirror and online query. But how can I know which it used in webserver and CL verison? I compared both parameter files, and do not find the corresponding parameter to clarify.

In addition, if the CL verison use the online query, how to make the result reproducible?

Thanks again.

You have to check the database parameters to see. On the web, if you tick the references box, it automatically uses the online version. I can't seem to download your parameter file from here. I just gave and posted a talk on this today, maybe the slides help a little? https://zenodo.org/record/3046373