Re 1) Ok, so that's interesting to know! At least if we can extract the MSMS m/z/intensity pairs as text we can use that file to input the queries one by one, or if concatenated, using the 'batch' function into the web databases. I can't see how to extract that info in MZmine 2.2, even if the program is actually doing it internally. So in 2.3 will it be actually possible to access the text version of that data? Re 2) I don't have any experience with Java programming! I just have many demands without being able to solve them myself :-) Sound familiar? Like any biologists you know? Anyway, I am making enquiries as to who might be able to help us with this in our department. Thanks for the clue! I also found out that Massbank already has a SOAP based API on the web, guess that will be useful!
Chiarina On 27/05/2011 08:56, Tomas Pluskal wrote: > Hi Chiarina, > > The step 1) is already implemented. Currently it is the part of Chromatogram > builder, but from MZmine 2.3 it will be a separate module, because there is a > need for providing this kind of "mass detection" for MS2 data in several > places in MZmine. > > I believe nobody is working on step 2) at this moment. If you want to start > working on that, I can help you. But first please let me know whether you > have any experience with Java programming :) > > Best regards, > > Tomas > > > On May 25, 2011, at 8:11 PM, Chiarina Darrah wrote: > >> Hi everyone, we are interested in creating a plugin that can search >> Massbank MSMS libraries to facilitate compound identification in our >> plant extracts - the current online databases which are linked to are >> all just using mass which of course returns huge numbers of spurious >> results, and often plant secondary metabolites are not well represented >> in these databases. >> To do this, we need, 1) a way of converting MSMS spectra to text files >> comprising a simple list of m/z and intensity pairs >> http://www.massbank.jp/sample/sample.txt, and 2) a way of interacting >> with the Massbank databases http://www.massbank.jp/SearchPage.html or a >> similar, personal massbank format database. >> So, two questions: is anybody doing this already? Or, can we have some >> clues about, the strategy and software you guys would use to write this >> stuff? Where would you guys start? >> Thanks for your input, >> Chiarina Darrah >> >> -- >> ================================================================== >> Chiarina Darrah >> >> Tel:+32 (0)9 331 38 85 fax:+32 (0)9 3313809 >> VIB Department of Plant Systems Biology, Ghent University >> Technologiepark 927, 9052 Gent, BELGIUM >> ch...@psb.vib-ugent.be http://www.psb.vib-ugent.be >> ================================================================== >> >> >> ------------------------------------------------------------------------------ >> vRanger cuts backup time in half-while increasing security. >> With the market-leading solution for virtual backup and recovery, >> you get blazing-fast, flexible, and affordable data protection. >> Download your free trial now. >> http://p.sf.net/sfu/quest-d2dcopy1 >> _______________________________________________ >> Mzmine-devel mailing list >> Mzmine-devel@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/mzmine-devel >> > =============================================== > Tomas Pluskal > G0 Cell Unit, Okinawa Institute of Science and Technology > 1919-1 Tancha, Onna-son, Okinawa 904-0412, Japan > TEL: +81-98-966-8684 > > > > -- ================================================================== Chiarina Darrah Tel:+32 (0)9 331 38 85 fax:+32 (0)9 3313809 VIB Department of Plant Systems Biology, Ghent University Technologiepark 927, 9052 Gent, BELGIUM ch...@psb.vib-ugent.be http://www.psb.vib-ugent.be ================================================================== ------------------------------------------------------------------------------ vRanger cuts backup time in half-while increasing security. With the market-leading solution for virtual backup and recovery, you get blazing-fast, flexible, and affordable data protection. Download your free trial now. http://p.sf.net/sfu/quest-d2dcopy1 _______________________________________________ Mzmine-devel mailing list Mzmine-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/mzmine-devel
