Biology Reference
In-Depth Information
mobile phases. It would also require high-
resolution MS for accurate mass analysis,
statistical analysis software for data mining,
metabolite databases, and access to a broad
array of hundreds of pure compounds for
con
first step in metabolite characterization is
the identi
The
cation of the MS molecular ion using
both positive and negative electrospray ioniza-
tion (ESI) modes that produce protonated
(M
H) þ and deprotonated (M-H) - ions. In
some cases, positive mode molecular adducts
(Na þ ,K þ ,NH 4 þ , etc.) and aggregate ions
(2M
þ
rmation.
A number of accessible and useful databases to
aid in the identi
H) þ ,(3M
H) þ ,etc.)areobservedthat
cation of unknown metabolites
have been created and are listed in Table 3 .
Some databases can be single or batch searched
with a
þ
þ
allow the con
rmation of the observed molec-
ular weight. The presence of a particular mass
defect d for example, a chlorine or bromine;
ahighpercentageofC,H,N,O,S,orP;the
incorporation of deuterium or
file of m/z values; others can be searched
with only one m/z range at a time. These database
searches will result in a range, from zero to many,
of metabolite hits. The metabolite structures
require individual inspection against the respec-
tive experimental mass spectrum. Metabolite
identi
13 Cintothe
molecule d can aid in the identi
cation. Each
of these incorporations results in a detectable
signaturethatcangiveionpatternsthatare
not commonly present in the background.
Molecular ions and fragments with zero or
even numbers of nitrogen will have an even
mass (nitrogen rule). Utilizing the known abun-
dances of naturally occurring isotopes gives
additional information. If MS/MS techniques
cations should allow for the proper
nomenclature to be assigned. Generally, many
database hits result
cations,
because the compounds in the databases repre-
sent a small fraction of the total number of endog-
enous metabolites in an organism.
in a few identi
TABLE 3 Databases That Aid in Metabolite Identi
cation
Name
URL
Data Type
Human Metabolome Database
http://www.hmdb.ca
MS & NMR
Madison Metabolomic Consortium Database
http://mmcd.nmrfam.wisc.edu
MS & NMR
Spectral Database for Organic Compounds
http://riodb01.ibase.aist.go.jp/sdbs/cgi-bin/
cre_index.cgi
MS & NMR
HRMAS Database
http://www.massbank.jp
MS
Lipid Maps
http://www.lipidmaps.org
MS
METLIN
http://metlin.scripps.edu
MS
NIST Chemistry Web Book
http://webbook.nist.gov/chemistry
MS
Biological Magnetic Resonance Data Bank
http://www.bmrb.wisc.edu
NMR
Birmingham Metabolite Library
http://www.bml-nmr.org
NMR
Metabolomics Database of Linkoping
http://www.liu.se/hu/mdl/main
NMR
NMRShiftDB
http://nmrshiftdb.nmr.uni-koeln.de
NMR
The Magnetic Resonance Metabolomics
Database
http://www.liu.se/hu/mdl/main
NMR
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