Dear developers of mzmine,
I have recentlyasked the same question in you support site:
https://sourceforge.net/p/mzmine/support-requests/5/
but since you seem to prefer the mailing list, I will write it here, too.
first of all thanks for all the work you are putting into this software.
I have some questions regarding different ways of identifications.
1. I have tried using the pubchem database to indentify all the
compounds in the sample (it is the test sample given in on your website,
so approx. 2000 different substances). The connection is terminated
after a short time (sometimes less than a minute) with this error:
Task Error: Could not search PubChem Compound Database:
java.io.IOException:java.io.IOException: Invalid Http response
(PubChemGateway.java.151).
It does however work when I just search one substance seperately. I've
searched a bit in your mailing lists and found a discussion with an HMDB
developer: https://sourceforge.net/mailarchive/message.php?msg_id=30163058
It seems this might be the same problem and I was wondering if the
changes that were discussed would work for pubchem, too or if you have
any other ideas how I might work around that problem.
(I had the same problem with chemspider too, although the connection did last
longer than it did with pubchem)
2. This brings me to my second question. I have used the single
substance search and the molecular formula prediction tool. I find them
both very usefull but I have the problem, that I can only keep one
formula from the results. Is it intended this way or did I miss
something? Also is there a way to perform mutiple formula searches
either at the same time or one after another with one command? Somthing
like the identification via peak list methods. I didn't find it listed
in the batch mode options so that doesn't seem to work.
If there should be any information I need to provide please let me know.
Thank you in advance.
Alexander Hahn
Student from the TU-Freiberg
Germany
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