73
4.6 Other Approaches to Metabolomics
Pathway analysis introduces a unique view of identified metabolites and their biological relevance. Metabolomics offers a plethora of biological significance through
the metabolites identified, but many times metabolomics through routine LC-MS
lack dimensions of information. There are highly complementary approaches that
can be used in the study of metabolism. Three specific examples are described below: multiomic sample preparation methodologies, imaging MS for the addition of
spatial information, and NMR for high reproducibility [88–90].
Table 4.1 A variety of spectral libraries and databases are available for metabolite identification.
From left to right the database or spectral library, the number of total compounds, target data types,
organism base/ Focus and a brief description are shown [71, 81–86]
Spectral Library/
database
Total
Compounds
Targets
Organism Base/
focus
Description
MoNA
>200,000
EI, MS/MS,
MSn
Multiple species,
Curated
Curated Spectra
Metlin
>500,000
CID-MS/MS
Multiple species
Commonly used,
Original use QTOF
NIST
>574,000
EI-MS,
CID-MS/MS
Multiple species
Curated database
m/z cloud
8904
MSn
Multiple species
Multiple stage MSn
KEGG
18,612
Metabolites
Multiple species
Pathway database
HMDB
114,100
Metabolites
Human
Spectra, physical and
biological properties
ChemSpider
67,000,000
All small
molecules
Curated data,
compounds
Curated data
Mass Bank
>38,000
EI, MS/MS,
MSn
Multiple species
Long standing
community database
MINE
>571,000
Metabolites
In silico predicted
metabolites
Predicted database
Table 4.2 Pathway analysis databases provide the biological context for individual metabolite
measurements within a system. From left to right the database, number of reference pathways, and
organisms included are shown
Database
Reference Pathways
Organisms
KEGG
88
372
>700
MetaCyc
89
1100
1500
WikiPathways
90
100
20
4 Fundamentals of Mass Spectrometry-Based Metabolomics