Hi Luigi,

Have a peek at the Plant Metabolic Network at:

http://www.plantcyc.org/

I think you will find a lot of information at that site.

Cheers,

Frank

Dear Frank, thanks for reply; days ago I tried to export a database, however I was not able to do that.. what I would like to do, is to export an excel or csv file (or something to be copy-pasted in this format) to be interfaced to vendor software (agilent qual)

Do you know if I can from plantcyc?

thanks again. Luigi

Hi Luigi,

I am not sure about the export capacity and possibility foreseen by the site owners. I would first browse through the site. If you don't get what you like, try to contact the website owners and cut some deal if possible to export the datasets you need.

Cheers,

Frank

Hi,

you can easily download a tab-deiimited plain text file

at ftp://ftp.plantcyc.org/Pathways/Data_dumps/PMN8_July2013/ there are the plain texts of the compound records of the respective "cyc" e. g. aracyc_compounds.20130709. They provide e. g. smiles, the chemical formula and the molecular weight, but not the monoisotopic mass. However, once imported into Excel you should be able to calculate this from the elemtal composition using a simple Excel-add in (e. g. http://www.sciencechatforum.com/viewtopic.php?f=15&t=26204&p=253151#p253151). A good resource for LC_MS based plant metabolomics: http://prime.psc.riken.jp/

Hope this helps. Let us know how it went.

Cheers,

Holger

I understand you need a database for accurate mass and name lookup in CSV or EXCEL format to paste into QUAL. You can use that one with 65,000 metabolites, including many plant metabolites: Ideom-Metabolome-Adduct-Table

https://www.researchgate.net/publication/261871741_Ideom-Metabolome-Adduct-Table

In order to create such a DB you would need the structures and referenced names, then create formulas, then create accurate masses, then add all possible adducts. Be aware that plant databases are not complete, actually very incomplete. Also a simple adduct mass lookup can be futile. Example: 99 different isomers for 595.1657 Da or 100 Million isomers for C6H6N4O2. If you want to make a smaller version, you can crossreference via InchiKey or Compound name, but again, you will miss thousands of candidates.

Metabolomic database annotations via query of elemental compositions: Mass accuracy is insufficient even at less than 1 ppm

http://www.biomedcentral.com/1471-2105/7/234

How Large Is the Metabolome? A Critical Analysis of Data Exchange Practices in Chemistry.

http://dx.doi.org/10.1371/journal.pone.0005440

Sources for Ideom-Metabolome-Adduct-Table are:

Ideom v19 (D. Creek)

http://sourceforge.net/projects/mzmatch/files/Ideom/

ESI-Adduct Calculator (T. Kind)

http://fiehnlab.ucdavis.edu/staff/kind/Metabolomics/MS-Adduct-Calculator/

A better solution would be

1) exact mass matching with retention time matching

2) exact mass based MS/MS search and retention time matching

use RIKEN Respect, MassBank, Metlin, LipidBlast, NIST12/Wiley databases.

Hope this helps.

Data Ideom-Metabolome-Adduct-Table