Online database search

Description

This module allows identification of peaks or whole peak lists using an on-line compound database. Databases are queried for the calculated neutral mass of the peak and matching compounds are returned.

Selection of peak for identification:

Results of database query:

Displaying the structure of the database compound:

Method parameters

Database
On-line database to search (see below)
Peak m/z
Detected m/z value of the peak. This is set automatically according to the peak subjected to identification.
Charge
Charge of the peak being identified. This value is used to calculate the neutral mass.
Ionization method
Type of ionization that produced the peak subjected to identification. This is used to calculate the neutral mass.
Neutral mass
This value is automatically calculated from the parameters above. The neutral mass represents the final search term for querying the on-line database.
Number of results
Limit for the number of results to be retrieved from the on-line database.
Mass tolerance
Tolerance of the neutral mass for searching the database.
Isotope pattern filter
If selected, only results which fit the required isotope pattern similarity score will be returned.
Isotope pattern score threshold
The score required for the isotope pattern filter.

On-line databases

Currently supported databases are listed below. Support for other databases may be implemented as additional plugins.

PubChem

PubChem database (http://pubchem.ncbi.nlm.nih.gov/) contains millions of chemical compound structures.

KEGG

KEGG database (http://www.genome.jp/kegg/) contains metabolites and other biomolecules present in natural metabolic pathways.

HMDB

The Human Metabolome Database (HMDB) (http://www.hmdb.ca/) contains over 7,000 known metabolites found in human body.

YMDB

The Yeast Metabolome Database (YMDB) (http://www.ymdb.ca) is a manually curated database of small molecule metabolites found in or produced by Saccharomyces cerevisiae (also known as Baker’s yeast and Brewer’s yeast).

ChemSpider

The ChemSpider database (http://www.chemspider.com/) contains over 67 million compounds. To search ChemSpider you must provide a "Security key" from your ChemSpider API account. If you don't have an account, please register at https://developer.rsc.org.

PlantCyc

The Plant metabolic pathway database (http://plantcyc.org) provides access to manually curated or reviewed information about shared and unique metabolic pathways present in over 350 plant species.